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Lanthanum in PDB 6hvq: The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La

Protein crystallography data

The structure of The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La, PDB code: 6hvq was solved by K.Zeth, M.Okuda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.46 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.020, 88.020, 274.780, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.4

Lanthanum Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50;

Binding sites:

The binding sites of Lanthanum atom in the The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La (pdb code 6hvq). This binding sites where shown within 5.0 Angstroms radius around Lanthanum atom.
In total 50 binding sites of Lanthanum where determined in the The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La, PDB code: 6hvq:
Jump to Lanthanum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Lanthanum binding site 1 out of 50 in 6hvq

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Lanthanum binding site 1 out of 50 in the The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 1 of The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La201

b:28.2
occ:0.85
O C:HOH359 2.3 34.4 1.0
O A:HOH375 2.4 31.3 1.0
O E:HOH398 2.4 31.4 1.0
OD1 C:ASP130 2.5 36.8 1.0
OD1 A:ASP130 2.5 35.3 1.0
OD1 E:ASP130 2.5 32.8 1.0
OD2 A:ASP130 2.7 32.2 1.0
OD2 C:ASP130 2.7 38.3 1.0
OD2 E:ASP130 2.8 35.5 1.0
CG C:ASP130 2.9 39.7 1.0
CG A:ASP130 2.9 31.1 1.0
CG E:ASP130 3.0 32.7 1.0
HD12 E:ILE133 4.2 38.5 1.0
HD12 C:ILE133 4.3 44.2 1.0
HD12 A:ILE133 4.4 36.1 1.0
HD22 E:ASN129 4.4 39.9 1.0
CB C:ASP130 4.4 37.5 1.0
O C:HOH341 4.4 49.4 1.0
HD13 E:ILE133 4.4 38.5 1.0
CB A:ASP130 4.4 31.6 1.0
O E:HOH330 4.5 42.5 1.0
O A:HOH373 4.5 45.8 1.0
CB E:ASP130 4.5 31.3 1.0
HD13 C:ILE133 4.6 44.2 1.0
HA C:ASP130 4.6 41.8 1.0
HA E:ASP130 4.6 35.7 1.0
HA A:ASP130 4.6 34.8 1.0
HD13 A:ILE133 4.6 36.1 1.0
HD21 E:ASN129 4.7 39.9 1.0
CD1 E:ILE133 4.8 32.0 1.0
HB3 C:ASP130 4.8 45.0 1.0
HB3 A:ASP130 4.8 38.0 1.0
HB3 E:ASP130 4.8 37.6 1.0
CD1 C:ILE133 4.9 36.9 1.0
ND2 E:ASN129 4.9 33.2 1.0
O C:HOH318 4.9 33.1 1.0
O E:HOH318 4.9 31.2 1.0
HB2 A:ASP130 5.0 38.0 1.0
CD1 A:ILE133 5.0 30.1 1.0
OD1 C:ASN129 5.0 35.3 1.0
HB2 C:ASP130 5.0 45.0 1.0

Lanthanum binding site 2 out of 50 in 6hvq

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Lanthanum binding site 2 out of 50 in the The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 2 of The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La202

b:29.6
occ:0.99
O B:HOH353 2.4 28.1 1.0
OE2 A:GLU62 2.4 35.1 1.0
O B:HOH326 2.5 35.3 1.0
O C:HOH392 2.5 26.7 0.8
OD2 A:ASP58 2.6 32.5 1.0
O B:HOH312 2.6 24.4 1.0
OE1 A:GLU62 2.7 34.7 1.0
NE2 B:HIS31 2.8 28.1 1.0
OD1 A:ASP58 2.8 39.5 1.0
CD A:GLU62 2.9 34.6 1.0
CG A:ASP58 3.1 36.6 1.0
CD2 B:HIS31 3.7 31.6 1.0
CE1 B:HIS31 3.7 28.7 1.0
HD2 B:HIS31 3.8 37.9 1.0
HE1 B:HIS31 3.8 34.4 1.0
HZ1 C:LYS141 4.0 60.1 1.0
LA A:LA208 4.1 0.6 0.8
NE2 B:HIS43 4.3 33.8 1.0
HE1 B:TRP32 4.4 36.7 1.0
CG A:GLU62 4.4 32.2 1.0
O A:HOH301 4.5 41.4 1.0
HE1 B:HIS43 4.6 40.0 1.0
CB A:ASP58 4.6 31.8 1.0
OD2 B:ASP47 4.6 36.7 1.0
OD1 B:ASP47 4.6 34.7 1.0
HG3 A:GLU62 4.6 38.7 1.0
HH2 C:TRP144 4.7 40.6 1.0
O C:HOH444 4.7 47.7 0.8
CE1 B:HIS43 4.8 33.3 1.0
NZ C:LYS141 4.8 50.1 1.0
HD1 B:TRP32 4.8 33.4 1.0
HG2 A:GLU62 4.8 38.7 1.0
ND1 B:HIS31 4.9 28.4 1.0
O C:HOH436 4.9 44.5 1.0
CG B:HIS31 4.9 30.1 1.0
HB3 A:ASP58 4.9 38.2 1.0
HB2 A:ASP58 4.9 38.2 1.0
HE3 C:LYS141 4.9 53.3 1.0
O A:HOH401 4.9 0.4 1.0
HZ2 C:LYS141 5.0 60.1 1.0

Lanthanum binding site 3 out of 50 in 6hvq

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Lanthanum binding site 3 out of 50 in the The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 3 of The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La203

b:47.2
occ:0.56
O A:HOH358 2.2 49.8 1.0
O A:SER6 2.3 54.1 1.0
O A:HOH306 2.3 55.8 1.0
O A:HOH351 2.4 49.9 0.9
O A:HOH374 2.5 0.6 1.0
OE2 A:GLU11 2.6 49.1 1.0
OE1 A:GLU11 2.7 62.2 1.0
OD1 A:ASN5 2.8 84.3 1.0
O A:HOH339 2.8 91.5 1.0
CD A:GLU11 3.0 52.6 1.0
C A:SER6 3.5 65.0 1.0
HA A:VAL7 3.6 73.9 1.0
CG A:ASN5 3.9 84.9 1.0
HD21 A:ASN5 4.1 0.7 1.0
H A:ASP8 4.1 58.1 1.0
H A:SER6 4.2 0.8 1.0
N A:SER6 4.3 94.9 1.0
CA A:VAL7 4.4 61.6 1.0
N A:VAL7 4.4 68.8 1.0
ND2 A:ASN5 4.5 84.7 1.0
CG A:GLU11 4.5 44.6 1.0
CA A:SER6 4.5 78.8 1.0
C A:ASN5 4.7 72.8 1.0
N A:ASP8 4.7 48.4 1.0
HG3 A:GLU11 4.8 53.6 1.0
OD2 A:ASP8 4.8 59.8 1.0
HA A:ASN5 4.8 96.6 1.0
HG2 A:GLU11 4.9 53.6 1.0
HG22 A:VAL7 5.0 77.7 1.0
HB2 A:SER6 5.0 95.2 1.0

Lanthanum binding site 4 out of 50 in 6hvq

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Lanthanum binding site 4 out of 50 in the The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 4 of The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La204

b:47.5
occ:0.37
O A:HOH367 2.4 76.2 1.0
O E:HOH326 2.5 69.0 1.0
LA A:LA205 2.5 0.2 1.0
OE1 A:GLU118 2.6 68.7 1.0
O A:HOH412 2.7 66.2 0.9
OE2 A:GLU118 2.7 71.4 1.0
CD A:GLU118 3.0 66.7 1.0
O A:HOH435 3.5 68.1 0.6
OD2 A:ASP121 4.3 68.6 1.0
O E:HOH350 4.3 36.1 0.6
HA A:GLU118 4.4 48.3 1.0
HA2 E:GLY124 4.4 50.5 1.0
CG A:GLU118 4.5 54.9 1.0
OD2 E:ASP126 4.9 45.9 1.0
HZ1 A:LYS114 4.9 76.1 1.0
HA3 E:GLY124 4.9 50.5 1.0
HG2 A:GLU118 4.9 65.8 1.0
HG3 A:GLU118 4.9 65.8 1.0
HZ2 A:LYS114 5.0 76.1 1.0
O A:HOH386 5.0 43.4 1.0

Lanthanum binding site 5 out of 50 in 6hvq

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Lanthanum binding site 5 out of 50 in the The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 5 of The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La205

b:0.2
occ:1.00
LA A:LA204 2.5 47.5 0.4
O A:HOH435 2.6 68.1 0.6
O E:HOH350 3.0 36.1 0.6
LA E:LA204 3.0 0.5 0.5
O E:HOH326 3.0 69.0 1.0
OD2 A:ASP121 3.4 68.6 1.0
O A:HOH305 3.5 43.1 0.5
O A:HOH412 3.8 66.2 0.9
O E:HOH424 4.4 79.3 1.0
HA2 E:GLY124 4.5 50.5 1.0
OD1 E:ASP121 4.5 59.7 1.0
O A:HOH367 4.6 76.2 1.0
CG A:ASP121 4.6 61.7 1.0
O A:HOH386 4.7 43.4 1.0
OD1 E:ASP126 4.8 50.2 1.0
O E:ASP121 4.8 40.2 1.0
OE1 A:GLU118 4.9 68.7 1.0
OE2 A:GLU118 5.0 71.4 1.0
O A:HOH436 5.0 40.4 0.8

Lanthanum binding site 6 out of 50 in 6hvq

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Lanthanum binding site 6 out of 50 in the The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 6 of The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La206

b:0.0
occ:0.46
OE2 A:GLU44 2.6 91.0 1.0
O A:HOH399 2.6 45.1 0.4
LA F:LA205 2.8 0.7 0.5
O D:HOH454 2.8 49.3 0.8
O A:HOH362 2.8 81.1 1.0
LA D:LA205 2.9 86.1 0.5
OE1 A:GLU44 2.9 87.9 1.0
CD A:GLU44 3.1 84.1 1.0
O F:HOH356 3.7 41.6 0.4
O F:HOH429 4.0 31.1 0.4
O D:HOH302 4.1 86.4 1.0
CG A:GLU44 4.5 65.8 1.0
O A:HOH335 4.7 48.2 1.0
HG2 A:GLU44 4.8 79.0 1.0
O A:HOH344 4.9 49.5 1.0
HG3 A:GLU44 5.0 79.0 1.0

Lanthanum binding site 7 out of 50 in 6hvq

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Lanthanum binding site 7 out of 50 in the The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 7 of The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La207

b:0.9
occ:0.68
O A:HOH303 2.5 57.2 0.9
O E:HOH432 2.5 47.8 0.5
O A:HOH305 2.6 43.1 0.5
O A:HOH354 2.7 65.8 0.9
O A:HOH431 3.0 72.5 0.8
O A:HOH436 3.0 40.4 0.8
O C:HOH423 3.2 79.7 0.7
OD1 A:ASP121 3.2 63.9 1.0
O C:HOH406 3.3 58.6 0.9
LA C:LA206 3.6 81.0 0.5
OD2 C:ASP121 3.9 66.9 1.0
O E:HOH424 3.9 79.3 1.0
LA C:LA207 4.0 0.5 0.7
O A:HOH326 4.0 47.2 0.9
CG A:ASP121 4.2 61.7 1.0
LA E:LA204 4.2 0.5 0.5
O A:HOH410 4.3 71.0 1.0
OD2 A:ASP121 4.3 68.6 1.0
O C:HOH429 4.4 73.3 1.0
O E:HOH303 4.6 95.5 1.0
OD1 C:ASP121 4.6 59.6 1.0
CG C:ASP121 4.6 57.5 1.0
O C:HOH311 4.9 61.0 0.8

Lanthanum binding site 8 out of 50 in 6hvq

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Lanthanum binding site 8 out of 50 in the The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 8 of The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La208

b:0.6
occ:0.80
O A:HOH401 2.4 0.4 1.0
O C:HOH392 2.4 26.7 0.8
LA A:LA209 2.6 99.2 0.3
O C:HOH444 2.7 47.7 0.8
O A:HOH427 2.7 70.8 1.0
O C:HOH398 2.8 56.1 0.6
OD2 A:ASP58 3.0 32.5 1.0
LA A:LA202 4.1 29.6 1.0
HZ1 C:LYS141 4.1 60.1 1.0
CG A:ASP58 4.2 36.6 1.0
HZ2 C:LYS141 4.3 60.1 1.0
HB3 A:ASP58 4.4 38.2 1.0
O A:HOH301 4.5 41.4 1.0
O B:HOH326 4.5 35.3 1.0
NZ C:LYS141 4.6 50.1 1.0
O B:HOH312 4.6 24.4 1.0
HG2 A:GLU55 4.7 88.6 1.0
OE1 A:GLU62 4.9 34.7 1.0
O A:HOH432 4.9 86.4 1.0
HZ3 C:LYS141 4.9 60.1 1.0
CB A:ASP58 4.9 31.8 1.0

Lanthanum binding site 9 out of 50 in 6hvq

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Lanthanum binding site 9 out of 50 in the The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 9 of The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La209

b:99.2
occ:0.34
O A:HOH401 2.4 0.4 1.0
LA A:LA208 2.6 0.6 0.8
O C:HOH398 2.7 56.1 0.6
O A:HOH432 2.8 86.4 1.0
O A:HOH427 4.1 70.8 1.0
HB3 A:GLU55 4.1 64.8 1.0
HB2 A:GLU59 4.2 55.3 1.0
OE1 A:GLU59 4.4 73.1 1.0
O C:HOH444 4.4 47.7 0.8
HG2 A:GLU55 4.5 88.6 1.0
O C:HOH392 4.6 26.7 0.8
OE1 A:GLU55 4.7 91.1 1.0
OD2 A:ASP58 5.0 32.5 1.0
CB A:GLU55 5.0 54.0 1.0
HZ2 C:LYS141 5.0 60.1 1.0

Lanthanum binding site 10 out of 50 in 6hvq

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Lanthanum binding site 10 out of 50 in the The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 10 of The Structure of Dps From Listeria Innocua Soaked Before Soaking Experiments with Zn, Co and La within 5.0Å range:
probe atom residue distance (Å) B Occ
B:La201

b:30.5
occ:0.99
O B:HOH350 2.5 36.3 1.0
OE2 B:GLU62 2.5 35.3 1.0
O A:HOH342 2.6 31.3 1.0
O B:HOH390 2.6 27.4 0.9
OD2 B:ASP58 2.6 31.2 1.0
O A:HOH304 2.6 31.0 1.0
NE2 A:HIS31 2.7 31.5 1.0
OE1 B:GLU62 2.7 30.8 1.0
OD1 B:ASP58 2.8 31.6 1.0
CD B:GLU62 3.0 32.8 1.0
CG B:ASP58 3.1 32.4 1.0
CE1 A:HIS31 3.6 32.4 1.0
CD2 A:HIS31 3.7 28.1 1.0
HE1 A:HIS31 3.7 38.9 1.0
HD2 A:HIS31 3.8 33.7 1.0
HZ1 D:LYS141 4.2 65.7 1.0
NE2 A:HIS43 4.3 35.8 1.0
HE1 A:TRP32 4.4 34.4 1.0
CG B:GLU62 4.4 30.1 1.0
O B:HOH309 4.5 38.6 1.0
CB B:ASP58 4.6 36.0 1.0
OD1 A:ASP47 4.6 40.4 1.0
HE1 A:HIS43 4.6 43.3 1.0
OD2 A:ASP47 4.6 33.3 1.0
O A:HOH429 4.6 61.9 1.0
HG3 B:GLU62 4.7 36.1 1.0
HH2 D:TRP144 4.7 37.9 1.0
O A:HOH418 4.7 0.7 1.0
CE1 A:HIS43 4.8 36.1 1.0
O A:HOH422 4.8 43.0 1.0
ND1 A:HIS31 4.8 29.9 1.0
HD1 A:TRP32 4.8 33.3 1.0
O A:HOH408 4.9 45.0 1.0
CG A:HIS31 4.9 29.6 1.0
LA B:LA206 4.9 0.8 1.0
HB3 B:ASP58 4.9 43.1 1.0
HG2 B:GLU62 4.9 36.1 1.0
HB2 B:ASP58 4.9 43.1 1.0
HE3 D:LYS141 4.9 59.8 1.0

Reference:

K.Zeth, E.Sancho-Vaello, M.Okuda. Metal Positions and Translocation Pathways of the Dodecameric Ferritin-Like Protein Dps. Inorg.Chem. V. 58 11351 2019.
ISSN: ISSN 0020-1669
PubMed: 31433627
DOI: 10.1021/ACS.INORGCHEM.9B00301
Page generated: Mon Dec 14 03:14:33 2020

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