Lanthanum in PDB 8dq2: X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7

The structure of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7, PDB code: 8dq2 was solved by J.J.Jung, C.-Y.Lin, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.11 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.107, 108.658, 44.697, 90, 90.02, 90
R / Rfree (%)	19 / 20.9

The structure of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Lanthanum atom in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 (pdb code 8dq2). This binding sites where shown within 5.0 Angstroms radius around Lanthanum atom.
In total 12 binding sites of Lanthanum where determined in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7, PDB code: 8dq2:
Jump to Lanthanum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Lanthanum binding site 1 out of 12 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 1 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:La201 b:19.0 occ:0.97 OD1 A:ASP36 2.5 23.5 1.0 OD1 A:ASN34 2.5 17.4 1.0 OE1 A:GLU42 2.5 21.6 1.0 OD2 A:ASP38 2.5 22.9 1.0 O A:SER40 2.6 23.5 1.0 OD1 A:ASP38 2.6 24.0 1.0 OD2 A:ASP36 2.6 24.7 1.0 OE2 A:GLU45 2.6 17.2 1.0 OE2 A:GLU42 2.7 18.7 1.0 OE1 A:GLU45 2.7 20.3 1.0 CG A:ASP36 2.9 25.0 1.0 CG A:ASP38 2.9 23.6 1.0 CD A:GLU42 2.9 20.3 1.0 CD A:GLU45 3.0 19.2 1.0 CG A:ASN34 3.5 21.3 1.0 C A:SER40 3.7 20.2 1.0 ND2 A:ASN34 3.8 23.4 1.0 CA A:LEU41 4.3 15.6 1.0 CB A:ASP36 4.4 25.8 1.0 N A:GLU42 4.4 21.3 1.0 CB A:ASP38 4.4 22.4 1.0 CG A:GLU42 4.4 21.8 1.0 N A:LEU41 4.5 16.3 1.0 CG A:GLU45 4.5 16.1 1.0 OG A:SER40 4.5 20.9 1.0 N A:SER40 4.7 20.5 1.0 CA A:SER40 4.7 18.5 1.0 C A:LEU41 4.8 19.2 1.0 CB A:ASN34 4.8 20.0 1.0 O A:HOH304 4.8 22.3 1.0 N A:ASP36 4.9 26.2 1.0

Lanthanum binding site 2 out of 12 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 2 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:La202 b:19.5 occ:1.00 OD1 A:ASN58 2.5 19.5 1.0 OD1 A:ASP62 2.5 19.3 1.0 OD2 A:ASP60 2.5 20.0 1.0 OD1 A:ASP60 2.6 23.0 1.0 OD2 A:ASP62 2.6 18.1 1.0 O A:THR64 2.6 15.2 1.0 OE1 A:GLU66 2.6 17.5 1.0 OE1 A:GLU69 2.7 19.0 1.0 OE2 A:GLU66 2.7 15.9 1.0 OE2 A:GLU69 2.7 19.4 1.0 CG A:ASP62 2.9 19.2 1.0 CG A:ASP60 2.9 19.8 1.0 CD A:GLU66 3.0 18.9 1.0 CD A:GLU69 3.1 19.3 1.0 CG A:ASN58 3.5 19.2 1.0 C A:THR64 3.7 16.5 1.0 ND2 A:ASN58 3.8 18.1 1.0 CA A:LEU65 4.4 17.2 1.0 CB A:ASP62 4.4 20.0 1.0 CB A:ASP60 4.4 19.1 1.0 OG1 A:THR64 4.4 14.5 1.0 N A:LEU65 4.5 15.0 1.0 N A:GLU66 4.5 16.3 1.0 CG A:GLU66 4.5 14.5 1.0 CG A:GLU69 4.6 22.0 1.0 N A:THR64 4.7 14.6 1.0 CA A:THR64 4.7 14.9 1.0 CB A:ASN58 4.8 16.5 1.0 C A:LEU65 4.8 19.1 1.0 O A:HOH359 4.8 27.0 1.0 N A:ASP62 5.0 19.8 1.0 N A:ASP60 5.0 21.3 1.0

Lanthanum binding site 3 out of 12 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 3 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:La203 b:18.3 occ:0.99 OD1 A:ASN83 2.5 18.3 1.0 OE2 A:GLU94 2.5 17.3 1.0 OD1 A:ASP87 2.5 18.2 1.0 OE1 A:GLU91 2.6 15.2 1.0 OD2 A:ASP85 2.6 15.6 1.0 O A:THR89 2.6 17.4 1.0 OE1 A:GLU94 2.7 13.3 1.0 OE2 A:GLU91 2.7 17.7 1.0 OD1 A:ASP85 2.7 18.1 1.0 OD2 A:ASP87 2.7 15.4 1.0 CD A:GLU94 2.9 13.5 1.0 CD A:GLU91 3.0 17.0 1.0 CG A:ASP87 3.0 17.4 1.0 CG A:ASP85 3.0 18.6 1.0 CG A:ASN83 3.6 18.2 1.0 C A:THR89 3.8 18.9 1.0 OG1 A:THR89 4.1 22.4 1.0 ND2 A:ASN83 4.3 20.2 1.0 CG A:GLU94 4.4 12.9 1.0 CG A:GLU91 4.5 12.2 1.0 CB A:ASP87 4.5 17.3 1.0 CB A:ASP85 4.5 19.6 1.0 N A:GLU91 4.5 15.9 1.0 CA A:LEU90 4.6 15.1 1.0 N A:LEU90 4.6 20.0 1.0 CA A:THR89 4.7 21.3 1.0 N A:THR89 4.7 20.4 1.0 CB A:ASN83 4.8 17.5 1.0 NH2 C:ARG100 4.9 17.6 1.0 CA A:ASN83 4.9 16.8 1.0 CB A:THR89 5.0 22.6 1.0 NH1 C:ARG100 5.0 16.5 1.0

Lanthanum binding site 4 out of 12 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 4 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:La202 b:19.7 occ:0.97 OD2 B:ASP38 2.5 17.6 1.0 OE2 B:GLU42 2.5 21.2 1.0 OD1 B:ASP36 2.5 24.1 1.0 OD1 B:ASP38 2.6 19.6 1.0 OD1 B:ASN34 2.6 19.4 1.0 O B:SER40 2.6 19.2 1.0 OD2 B:ASP36 2.6 24.5 1.0 OE1 B:GLU42 2.6 15.5 1.0 OE1 B:GLU45 2.7 15.9 1.0 OE2 B:GLU45 2.7 18.9 1.0 CG B:ASP38 2.9 18.0 1.0 CG B:ASP36 2.9 23.5 1.0 CD B:GLU42 2.9 20.5 1.0 CD B:GLU45 3.1 18.2 1.0 CG B:ASN34 3.6 16.3 1.0 C B:SER40 3.7 18.8 1.0 ND2 B:ASN34 3.9 16.9 1.0 OG B:SER40 4.4 23.0 1.0 CA B:LEU41 4.4 17.1 1.0 CB B:ASP38 4.4 18.0 1.0 CG B:GLU42 4.4 16.7 1.0 CB B:ASP36 4.4 23.8 1.0 N B:GLU42 4.4 12.9 1.0 N B:LEU41 4.5 18.2 1.0 CG B:GLU45 4.6 17.1 1.0 O B:HOH313 4.6 39.3 1.0 O B:HOH309 4.7 37.2 1.0 N B:SER40 4.7 19.2 1.0 CA B:SER40 4.7 18.5 1.0 C B:LEU41 4.9 18.1 1.0 CB B:ASN34 5.0 17.4 1.0

Lanthanum binding site 5 out of 12 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 5 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:La203 b:19.8 occ:1.00 OD1 B:ASN58 2.4 18.6 1.0 OD2 B:ASP60 2.5 24.9 1.0 OD1 B:ASP62 2.5 18.6 1.0 O B:THR64 2.5 17.4 1.0 OD1 B:ASP60 2.6 28.5 1.0 OD2 B:ASP62 2.6 18.5 1.0 OE2 B:GLU66 2.6 18.0 1.0 OE2 B:GLU69 2.7 26.0 1.0 OE1 B:GLU69 2.7 22.0 1.0 OE1 B:GLU66 2.7 18.6 1.0 CG B:ASP60 2.9 24.7 1.0 CG B:ASP62 2.9 18.6 1.0 CD B:GLU66 3.0 19.8 1.0 CD B:GLU69 3.0 23.7 1.0 CG B:ASN58 3.5 18.7 1.0 C B:THR64 3.7 16.8 1.0 ND2 B:ASN58 3.9 19.3 1.0 CA B:LEU65 4.3 16.9 1.0 CB B:ASP60 4.4 21.2 1.0 CB B:ASP62 4.4 18.9 1.0 N B:LEU65 4.4 16.8 1.0 N B:GLU66 4.4 16.5 1.0 OG1 B:THR64 4.5 16.8 1.0 CG B:GLU66 4.5 17.0 1.0 CG B:GLU69 4.5 25.1 1.0 N B:THR64 4.7 17.3 1.0 CA B:THR64 4.7 16.7 1.0 C B:LEU65 4.7 17.1 1.0 O B:HOH353 4.8 32.2 1.0 O B:HOH311 4.8 32.4 1.0 CB B:ASN58 4.8 18.9 1.0 N B:ASP60 5.0 26.0 1.0

Lanthanum binding site 6 out of 12 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 6 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:La204 b:18.1 occ:0.99 OD2 B:ASP85 2.5 23.7 1.0 OD1 B:ASP87 2.5 17.9 1.0 OD1 B:ASN83 2.5 23.6 1.0 OD1 B:ASP85 2.6 24.1 1.0 OE2 B:GLU94 2.6 20.5 1.0 OE1 B:GLU91 2.6 17.2 1.0 OE2 B:GLU91 2.6 14.2 1.0 OE1 B:GLU94 2.7 20.1 1.0 OD2 B:ASP87 2.7 18.6 1.0 O B:THR89 2.7 20.7 1.0 CG B:ASP85 2.9 25.5 1.0 CG B:ASP87 2.9 19.3 1.0 CD B:GLU94 3.0 19.2 1.0 CD B:GLU91 3.0 17.2 1.0 CG B:ASN83 3.7 21.8 1.0 C B:THR89 3.9 19.9 1.0 ND2 B:ASN83 4.3 19.7 1.0 OG1 B:THR89 4.3 19.1 1.0 CB B:ASP85 4.4 26.8 1.0 CG B:GLU94 4.5 18.3 1.0 CG B:GLU91 4.5 15.9 1.0 CB B:ASP87 4.5 19.8 1.0 N B:GLU91 4.5 17.2 1.0 CA B:LEU90 4.6 20.4 1.0 N B:LEU90 4.7 19.2 1.0 O B:HOH307 4.7 28.1 1.0 N B:THR89 4.8 23.4 1.0 CA B:THR89 4.8 20.9 1.0 NH2 D:ARG100 4.8 16.6 1.0 CB B:ASN83 4.9 19.9 1.0 CA B:ASN83 5.0 20.4 1.0

Lanthanum binding site 7 out of 12 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 7 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ C:La201 b:26.4 occ:0.96 OD1 C:ASP36 2.5 33.4 1.0 OE1 C:GLU42 2.5 28.0 1.0 OD1 C:ASP38 2.5 33.7 1.0 OD1 C:ASN34 2.5 30.9 1.0 O C:SER40 2.6 20.3 1.0 OD2 C:ASP38 2.6 32.8 1.0 OE2 C:GLU45 2.6 24.3 1.0 OD2 C:ASP36 2.7 33.1 1.0 OE1 C:GLU45 2.7 19.9 1.0 OE2 C:GLU42 2.8 24.5 1.0 CG C:ASP38 2.9 34.2 1.0 CG C:ASP36 2.9 33.5 1.0 CD C:GLU42 3.0 27.0 1.0 CD C:GLU45 3.0 23.4 1.0 CG C:ASN34 3.6 32.3 1.0 C C:SER40 3.7 19.7 1.0 ND2 C:ASN34 4.0 34.4 1.0 CA C:LEU41 4.4 18.9 1.0 CB C:ASP38 4.4 37.1 1.0 CB C:ASP36 4.4 35.5 1.0 N C:LEU41 4.5 20.2 1.0 N C:GLU42 4.5 22.5 1.0 CG C:GLU42 4.5 24.2 1.0 OG C:SER40 4.5 22.7 1.0 CG C:GLU45 4.5 22.2 1.0 O C:HOH309 4.6 45.2 1.0 N C:SER40 4.7 22.8 1.0 CA C:SER40 4.7 21.0 1.0 C C:LEU41 4.8 20.5 1.0 O C:HOH304 4.8 28.8 1.0 CB C:ASN34 4.9 32.3 1.0 N C:ASP36 4.9 35.9 1.0

Lanthanum binding site 8 out of 12 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 8 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ C:La202 b:32.8 occ:1.00 OD1 C:ASN58 2.5 41.8 1.0 OD1 C:ASP62 2.5 25.9 1.0 OD2 C:ASP60 2.5 50.6 1.0 OE1 C:GLU66 2.6 32.4 1.0 OD1 C:ASP60 2.6 52.3 1.0 O C:THR64 2.6 24.4 1.0 OE2 C:GLU69 2.7 32.1 1.0 OE2 C:GLU66 2.7 29.3 1.0 OD2 C:ASP62 2.7 25.5 1.0 OE1 C:GLU69 2.7 33.4 1.0 CG C:ASP60 2.9 49.4 1.0 CG C:ASP62 2.9 27.3 1.0 CD C:GLU66 3.0 33.0 1.0 CD C:GLU69 3.0 36.0 1.0 CG C:ASN58 3.5 41.2 1.0 C C:THR64 3.7 27.4 1.0 ND2 C:ASN58 4.0 41.4 1.0 CB C:ASP60 4.4 46.0 1.0 CA C:LEU65 4.4 30.9 1.0 CB C:ASP62 4.4 26.9 1.0 N C:LEU65 4.5 31.4 1.0 CG C:GLU66 4.5 33.1 1.0 CG C:GLU69 4.5 34.5 1.0 OG1 C:THR64 4.5 26.1 1.0 N C:GLU66 4.6 30.2 1.0 N C:THR64 4.6 25.3 1.0 CA C:THR64 4.7 26.2 1.0 CB C:ASN58 4.8 40.4 1.0 C C:LEU65 4.8 29.9 1.0 O C:HOH345 4.9 37.9 1.0 N C:ASP62 5.0 31.4 1.0

Lanthanum binding site 9 out of 12 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 9 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ C:La203 b:23.5 occ:1.00 OD1 C:ASN83 2.4 26.5 1.0 OD2 C:ASP85 2.5 28.0 1.0 OD1 C:ASP87 2.5 26.3 1.0 OE2 C:GLU94 2.6 19.6 1.0 O C:THR89 2.6 23.4 1.0 OE2 C:GLU91 2.6 19.0 1.0 OE1 C:GLU91 2.6 19.1 1.0 OE1 C:GLU94 2.6 17.4 1.0 OD2 C:ASP87 2.7 22.3 1.0 OD1 C:ASP85 2.7 28.6 1.0 CG C:ASP85 2.9 28.3 1.0 CD C:GLU94 2.9 17.9 1.0 CD C:GLU91 3.0 19.8 1.0 CG C:ASP87 3.0 24.3 1.0 CG C:ASN83 3.6 27.8 1.0 C C:THR89 3.7 24.4 1.0 OG1 C:THR89 4.0 24.8 1.0 ND2 C:ASN83 4.2 28.0 1.0 CG C:GLU94 4.4 17.3 1.0 CB C:ASP85 4.4 27.9 1.0 CG C:GLU91 4.5 16.4 1.0 N C:GLU91 4.5 17.9 1.0 CB C:ASP87 4.5 27.2 1.0 N C:LEU90 4.6 22.7 1.0 CA C:LEU90 4.6 21.9 1.0 CA C:THR89 4.7 25.7 1.0 N C:THR89 4.7 26.4 1.0 NH2 A:ARG100 4.7 20.2 1.0 CB C:ASN83 4.7 27.6 1.0 CA C:ASN83 4.9 27.5 1.0 O C:HOH330 4.9 31.0 1.0 CB C:THR89 4.9 25.8 1.0

Lanthanum binding site 10 out of 12 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 10 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Lanthanum (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ D:La202 b:24.6 occ:0.92 OE2 D:GLU42 2.5 27.1 1.0 OD2 D:ASP38 2.5 36.1 1.0 OE2 D:GLU45 2.6 21.0 1.0 OD1 D:ASP38 2.6 36.2 1.0 O D:SER40 2.6 19.1 1.0 OD1 D:ASN34 2.7 33.7 1.0 OD1 D:ASP36 2.7 36.5 1.0 OD2 D:ASP36 2.7 34.9 1.0 OE1 D:GLU45 2.8 16.2 1.0 OE1 D:GLU42 2.8 17.2 1.0 CG D:ASP38 2.9 36.8 1.0 CD D:GLU42 3.0 22.0 1.0 CD D:GLU45 3.0 17.8 1.0 CG D:ASP36 3.0 36.9 1.0 CG D:ASN34 3.7 34.7 1.0 C D:SER40 3.7 21.8 1.0 ND2 D:ASN34 4.1 36.2 1.0 CA D:LEU41 4.3 19.0 1.0 OG D:SER40 4.4 18.6 1.0 N D:GLU42 4.4 18.6 1.0 CB D:ASP38 4.4 38.9 1.0 N D:LEU41 4.4 20.9 1.0 CG D:GLU42 4.5 17.5 1.0 CG D:GLU45 4.5 16.5 1.0 CB D:ASP36 4.5 36.5 1.0 N D:SER40 4.7 20.7 1.0 CA D:SER40 4.7 20.1 1.0 C D:LEU41 4.8 18.9 1.0 O D:HOH341 4.8 29.5 1.0

J.A.Mattocks, J.J.Jung, C.Y.Lin, Z.Dong, N.H.Yennawar, E.R.Featherston, C.S.Kang-Yun, T.A.Hamilton, D.M.Park, A.K.Boal, J.A.Cotruvo. Enhanced Rare-Earth Separation with A Metal-Sensitive Lanmodulin Dimer Nature V. 618 87 2023.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-05945-5