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Lanthanum in PDB 1djg: Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum

Enzymatic activity of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum

All present enzymatic activity of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum:
3.1.4.11;

Protein crystallography data

The structure of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum, PDB code: 1djg was solved by L.-O.Essen, O.Perisic, R.L.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.60
Space group F 41 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 397.920, 397.920, 397.920, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 27

Lanthanum Binding Sites:

The binding sites of Lanthanum atom in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum (pdb code 1djg). This binding sites where shown within 5.0 Angstroms radius around Lanthanum atom.
In total 8 binding sites of Lanthanum where determined in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum, PDB code: 1djg:
Jump to Lanthanum binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Lanthanum binding site 1 out of 8 in 1djg

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Lanthanum binding site 1 out of 8 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 1 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La1

b:71.1
occ:0.75
 O A:HOH1018 2.5 47.5 1.0
OE1 A:GLU390 2.5 70.9 1.0
OD2 A:ASP343 2.6 32.5 1.0
OD1 A:ASN312 2.6 23.5 1.0
OD1 A:ASP343 2.7 33.9 1.0
CG A:ASP343 3.0 33.1 1.0
CD A:GLU390 3.4 65.8 1.0
O A:HOH970 3.5 58.0 1.0
OE2 A:GLU390 3.7 63.6 1.0
CG A:ASN312 3.7 27.9 1.0
OE1 A:GLU341 3.7 38.8 1.0
O A:HOH855 3.8 35.9 1.0
O A:HOH1069 4.1 42.4 1.0
ND2 A:ASN312 4.1 16.9 1.0
CB A:ASP343 4.5 22.0 1.0
O A:HOH859 4.6 26.5 1.0
O A:HOH923 4.6 41.4 1.0
CG A:GLU390 4.6 40.4 1.0
OH A:TYR314 4.6 25.1 1.0
CB A:GLU390 4.7 27.6 1.0
CD A:GLU341 4.9 60.9 1.0
CB A:ASN312 5.0 22.7 1.0
CD2 A:HIS356 5.0 20.1 1.0

Lanthanum binding site 2 out of 8 in 1djg

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Lanthanum binding site 2 out of 8 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 2 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La2

b:71.1
occ:0.75
 O A:HOH932 1.8 0.1 1.0
O A:HOH1032 2.4 62.9 1.0
OD2 A:ASP653 2.4 42.1 1.0
OD1 A:ASN677 2.5 63.4 1.0
O A:ILE651 2.5 49.5 1.0
OD1 A:ASP653 2.6 41.2 1.0
CG A:ASP653 2.8 38.7 1.0
OG A:SER650 3.1 94.9 1.0
O A:HOH1053 3.2 46.7 1.0
CG A:ASN677 3.6 72.2 1.0
C A:ILE651 3.7 48.9 1.0
LA A:LA3 4.0 76.2 0.5
N A:ILE651 4.1 53.2 1.0
CB A:ASP653 4.3 24.9 1.0
ND2 A:ASN677 4.3 73.4 1.0
C A:VAL652 4.5 39.0 1.0
CA A:ILE651 4.5 49.1 1.0
CB A:SER650 4.5 79.5 1.0
N A:ASN677 4.5 33.8 1.0
O A:VAL652 4.5 40.1 1.0
CA A:ASN677 4.6 35.1 1.0
N A:ASP653 4.6 26.9 1.0
N A:VAL652 4.7 42.6 1.0
CB A:ASN677 4.7 44.6 1.0
O A:HOH1075 4.8 70.4 1.0
CB A:ILE651 4.8 52.1 1.0
CA A:VAL652 4.9 41.5 1.0
CA A:ASP653 5.0 23.8 1.0

Lanthanum binding site 3 out of 8 in 1djg

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Lanthanum binding site 3 out of 8 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 3 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La3

b:76.2
occ:0.50
 O A:TYR707 2.4 34.5 1.0
OD2 A:ASP653 2.5 42.1 1.0
OD1 A:ASP708 2.5 87.7 1.0
O A:HOH1053 2.7 46.7 1.0
OD1 A:ASP706 2.7 45.2 1.0
CG A:ASP706 3.3 42.8 1.0
OD2 A:ASP706 3.4 49.7 1.0
CG A:ASP653 3.4 38.7 1.0
O A:HOH1075 3.5 70.4 1.0
C A:TYR707 3.6 39.2 1.0
CG A:ASP708 3.8 81.5 1.0
CB A:ASP653 3.8 24.9 1.0
LA A:LA2 4.0 71.1 0.8
LA A:LA4 4.2 86.9 0.5
N A:ASP653 4.3 26.9 1.0
CA A:ASP708 4.3 48.1 1.0
N A:ASP708 4.4 44.6 1.0
OD1 A:ASP653 4.5 41.2 1.0
N A:TYR707 4.5 31.4 1.0
O A:HOH1032 4.5 62.9 1.0
C A:ASP706 4.6 32.8 1.0
OD2 A:ASP708 4.6 85.3 1.0
CB A:ASP708 4.6 50.8 1.0
CA A:TYR707 4.6 33.1 1.0
CB A:ASP706 4.7 30.8 1.0
CA A:ASP653 4.7 23.8 1.0
O A:ILE651 4.7 49.5 1.0
O A:ASP706 4.7 33.6 1.0
C A:VAL652 5.0 39.0 1.0

Lanthanum binding site 4 out of 8 in 1djg

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Lanthanum binding site 4 out of 8 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 4 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La4

b:86.9
occ:0.50
 OD2 A:ASP708 2.8 85.3 1.0
OD1 A:ASP708 2.9 87.7 1.0
OD2 A:ASP714 3.1 59.1 1.0
CG A:ASP708 3.1 81.5 1.0
OD2 A:ASP706 3.3 49.7 1.0
O A:HOH1073 3.5 68.3 1.0
CG A:ASP714 3.7 61.3 1.0
CG A:ASP706 4.1 42.8 1.0
OD1 A:ASP714 4.1 69.0 1.0
O A:HOH1053 4.1 46.7 1.0
LA A:LA3 4.2 76.2 0.5
CB A:ASP714 4.4 39.7 1.0
CB A:ASP708 4.6 50.8 1.0
CB A:ASP706 4.8 30.8 1.0
OD1 A:ASP706 4.8 45.2 1.0

Lanthanum binding site 5 out of 8 in 1djg

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Lanthanum binding site 5 out of 8 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 5 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:La1

b:77.2
occ:1.00
 OD2 B:ASP343 2.6 31.6 1.0
OE1 B:GLU390 2.7 70.6 1.0
OD1 B:ASN312 2.8 25.2 1.0
OD1 B:ASP343 2.8 31.8 1.0
CG B:ASP343 3.1 31.6 1.0
O B:HOH1094 3.3 45.3 1.0
O B:HOH946 3.4 39.1 1.0
CD B:GLU390 3.5 65.6 1.0
OE1 B:GLU341 3.7 38.6 1.0
OE2 B:GLU390 3.7 63.5 1.0
CG B:ASN312 3.8 28.6 1.0
ND2 B:ASN312 4.2 17.4 1.0
O B:HOH890 4.5 30.0 1.0
OH B:TYR314 4.5 24.5 1.0
O B:HOH1045 4.5 65.1 1.0
CB B:ASP343 4.5 21.9 1.0
CG B:GLU390 4.7 40.8 1.0
CB B:GLU390 4.8 28.1 1.0
O B:HOH1118 4.9 52.5 1.0
O B:HOH864 4.9 52.7 1.0
CD B:GLU341 4.9 61.1 1.0
NE2 B:HIS311 4.9 21.8 1.0

Lanthanum binding site 6 out of 8 in 1djg

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Lanthanum binding site 6 out of 8 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 6 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:La2

b:81.5
occ:1.00
 O B:ILE651 2.3 42.5 1.0
O B:HOH920 2.5 43.3 1.0
OD1 B:ASP653 2.5 54.4 1.0
OD1 B:ASN677 2.5 63.3 1.0
O B:HOH918 2.9 38.8 1.0
OD2 B:ASP653 2.9 70.5 1.0
CG B:ASP653 3.0 54.1 1.0
O B:HOH1048 3.5 32.7 1.0
C B:ILE651 3.6 43.6 1.0
CG B:ASN677 3.7 72.1 1.0
O B:HOH965 3.9 68.2 1.0
LA B:LA3 4.0 74.0 0.6
O B:HOH1049 4.1 50.2 1.0
N B:ILE651 4.2 52.1 1.0
CA B:ILE651 4.4 47.2 1.0
ND2 B:ASN677 4.4 74.2 1.0
CB B:ASP653 4.4 27.5 1.0
OG B:SER650 4.5 84.1 1.0
C B:VAL652 4.5 30.0 1.0
N B:VAL652 4.5 35.7 1.0
O B:VAL652 4.6 30.0 1.0
N B:ASP653 4.6 23.8 1.0
N B:ASN677 4.7 33.9 1.0
CA B:ASN677 4.7 35.3 1.0
CA B:VAL652 4.8 34.1 1.0
CB B:ASN677 4.8 44.3 1.0
CB B:ILE651 4.8 49.2 1.0

Lanthanum binding site 7 out of 8 in 1djg

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Lanthanum binding site 7 out of 8 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 7 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:La3

b:74.0
occ:0.60
 OD1 B:ASP708 2.5 63.8 1.0
O B:HOH1048 2.5 32.7 1.0
O B:TYR707 2.6 30.4 1.0
OD1 B:ASP706 2.6 45.6 1.0
O B:HOH1049 3.1 50.2 1.0
CG B:ASP706 3.3 43.0 1.0
OD2 B:ASP706 3.3 49.5 1.0
OD2 B:ASP653 3.5 70.5 1.0
CG B:ASP653 3.6 54.1 1.0
C B:TYR707 3.6 35.9 1.0
LA B:LA4 3.7 77.2 0.6
CG B:ASP708 3.7 56.6 1.0
LA B:LA2 4.0 81.5 1.0
CB B:ASP653 4.0 27.5 1.0
O B:HOH965 4.1 68.2 1.0
OD1 B:ASP653 4.2 54.4 1.0
N B:ASP653 4.3 23.8 1.0
CA B:ASP708 4.4 34.6 1.0
N B:ASP708 4.4 35.6 1.0
OD2 B:ASP708 4.4 59.6 1.0
N B:TYR707 4.5 28.6 1.0
CB B:ASP708 4.6 37.0 1.0
CB B:ASP706 4.6 30.6 1.0
O B:ILE651 4.7 42.5 1.0
CA B:TYR707 4.7 29.5 1.0
C B:ASP706 4.7 32.0 1.0
O B:HOH920 4.8 43.3 1.0
CA B:ASP653 4.8 24.2 1.0
O B:ASP706 4.9 33.5 1.0

Lanthanum binding site 8 out of 8 in 1djg

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Lanthanum binding site 8 out of 8 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 8 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Lanthanum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:La4

b:77.2
occ:0.60
 OD2 B:ASP708 2.7 59.6 1.0
OD2 B:ASP714 2.8 85.5 1.0
OD1 B:ASP708 2.9 63.8 1.0
OD2 B:ASP706 3.0 49.5 1.0
CG B:ASP708 3.1 56.6 1.0
O B:HOH1111 3.4 93.3 1.0
O B:HOH1048 3.5 32.7 1.0
LA B:LA3 3.7 74.0 0.6
CG B:ASP706 3.7 43.0 1.0
CG B:ASP714 3.8 71.3 1.0
OD1 B:ASP706 4.3 45.6 1.0
O B:HOH1124 4.4 47.8 1.0
CB B:ASP714 4.4 40.1 1.0
CB B:ASP708 4.5 37.0 1.0
CB B:ASP706 4.5 30.6 1.0
OD1 B:ASP714 4.6 75.6 1.0
O B:HOH965 4.6 68.2 1.0

Reference:

L.O.Essen, O.Perisic, D.E.Lynch, M.Katan, R.L.Williams. A Ternary Metal Binding Site in the C2 Domain of Phosphoinositide-Specific Phospholipase C-DELTA1. Biochemistry V. 36 2753 1997.
ISSN: ISSN 0006-2960
PubMed: 9062102
DOI: 10.1021/BI962466T
Page generated: Tue Aug 13 01:47:48 2024

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