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Tungsten in PDB 5erv: Ternary Complex of Gephe - Adp - Tungsten Cluster

Enzymatic activity of Ternary Complex of Gephe - Adp - Tungsten Cluster

All present enzymatic activity of Ternary Complex of Gephe - Adp - Tungsten Cluster:
2.10.1.1; 2.7.7.75;

Protein crystallography data

The structure of Ternary Complex of Gephe - Adp - Tungsten Cluster, PDB code: 5erv was solved by V.B.Kasaragod, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.83 / 1.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 87.661, 99.675, 113.237, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 20.3

Other elements in 5erv:

The structure of Ternary Complex of Gephe - Adp - Tungsten Cluster also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Calcium (Ca) 1 atom

Tungsten Binding Sites:

The binding sites of Tungsten atom in the Ternary Complex of Gephe - Adp - Tungsten Cluster (pdb code 5erv). This binding sites where shown within 5.0 Angstroms radius around Tungsten atom.
In total 10 binding sites of Tungsten where determined in the Ternary Complex of Gephe - Adp - Tungsten Cluster, PDB code: 5erv:
Jump to Tungsten binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Tungsten binding site 1 out of 10 in 5erv

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Tungsten binding site 1 out of 10 in the Ternary Complex of Gephe - Adp - Tungsten Cluster


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 1 of Ternary Complex of Gephe - Adp - Tungsten Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W803

b:0.4
occ:1.00
 W A:W811 3.5 0.1 1.0
W A:W810 3.8 0.9 1.0
HH22 A:ARG670 4.5 40.4 1.0
HH21 A:ARG670 4.9 40.4 1.0
NH2 A:ARG670 4.9 33.6 1.0

Tungsten binding site 2 out of 10 in 5erv

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Tungsten binding site 2 out of 10 in the Ternary Complex of Gephe - Adp - Tungsten Cluster


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 2 of Ternary Complex of Gephe - Adp - Tungsten Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W804

b:89.2
occ:1.00
 O3 A:WO4816 1.9 0.9 1.0
W A:W810 2.9 0.9 1.0
W A:WO4816 2.9 0.4 1.0
HH12 A:ARG670 3.0 40.0 1.0
W A:W811 3.1 0.1 1.0
W A:W809 3.1 0.9 1.0
W A:W807 3.3 99.4 1.0
O1 A:WO4816 3.3 0.0 1.0
HB2 A:LEU605 3.5 23.8 1.0
H A:GLY604 3.5 26.9 1.0
H A:LEU605 3.6 23.4 1.0
O2 A:WO4816 3.7 0.6 1.0
HA A:PRO603 3.8 23.7 1.0
NH1 A:ARG670 3.9 33.4 1.0
HB3 A:LEU605 4.0 23.8 1.0
HH22 A:ARG670 4.0 40.4 1.0
CB A:LEU605 4.2 19.8 1.0
HD22 A:LEU605 4.2 67.4 1.0
HH11 A:ARG670 4.3 40.0 1.0
N A:GLY604 4.3 22.4 1.0
N A:LEU605 4.4 19.5 1.0
HD3 A:PRO606 4.4 24.0 1.0
O4 A:WO4816 4.5 95.9 1.0
W A:W808 4.5 0.5 1.0
HG3 A:LYS602 4.5 34.6 1.0
CA A:PRO603 4.6 19.8 1.0
NH2 A:ARG670 4.7 33.6 1.0
HA A:LYS602 4.7 22.6 1.0
HB3 A:PRO603 4.8 30.5 1.0
HD23 A:LEU605 4.8 67.4 1.0
CZ A:ARG670 4.8 34.2 1.0
HB2 A:PRO603 4.8 30.5 1.0
CD2 A:LEU605 4.9 56.2 1.0
C A:PRO603 4.9 24.7 1.0
HG A:SER630 4.9 28.5 1.0
CB A:PRO603 5.0 25.4 1.0
HD2 A:PRO606 5.0 24.0 1.0
CA A:LEU605 5.0 18.1 1.0

Tungsten binding site 3 out of 10 in 5erv

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Tungsten binding site 3 out of 10 in the Ternary Complex of Gephe - Adp - Tungsten Cluster


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 3 of Ternary Complex of Gephe - Adp - Tungsten Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W805

b:0.7
occ:1.00
 W A:W807 2.9 99.4 1.0
W A:W811 3.0 0.1 1.0
O A:HOH1262 3.6 45.0 1.0
W A:W806 3.6 0.1 1.0
W A:W809 4.2 0.9 1.0
W A:W808 4.6 0.5 1.0

Tungsten binding site 4 out of 10 in 5erv

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Tungsten binding site 4 out of 10 in the Ternary Complex of Gephe - Adp - Tungsten Cluster


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 4 of Ternary Complex of Gephe - Adp - Tungsten Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W806

b:0.1
occ:1.00
 HE2 A:LYS602 3.3 55.3 1.0
W A:W805 3.6 0.7 1.0
HZ3 A:LYS602 3.6 72.4 1.0
W A:W811 3.7 0.1 1.0
W A:W809 3.7 0.9 1.0
CE A:LYS602 4.0 46.0 1.0
HE3 A:LYS602 4.0 55.3 1.0
O A:HOH1262 4.1 45.0 1.0
NZ A:LYS602 4.2 60.3 1.0
HZ2 A:LYS602 4.5 72.4 1.0
HH22 A:ARG670 4.9 40.4 1.0
HZ1 A:LYS602 4.9 72.4 1.0

Tungsten binding site 5 out of 10 in 5erv

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Tungsten binding site 5 out of 10 in the Ternary Complex of Gephe - Adp - Tungsten Cluster


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 5 of Ternary Complex of Gephe - Adp - Tungsten Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W807

b:99.4
occ:1.00
 O2 A:WO4816 2.5 0.6 1.0
W A:W808 2.8 0.5 1.0
W A:W805 2.9 0.7 1.0
W A:W811 3.1 0.1 1.0
W A:W809 3.3 0.9 1.0
W A:W804 3.3 89.2 1.0
W A:WO4816 3.4 0.4 1.0
O A:HOH1262 3.4 45.0 1.0
O1 A:WO4816 3.6 0.0 1.0
O3 A:WO4816 3.9 0.9 1.0
O A:HOH1226 4.0 35.5 1.0
HG A:SER630 4.8 28.5 1.0
W A:W810 4.8 0.9 1.0
HB2 A:ASN627 4.9 23.1 1.0
O4 A:WO4816 5.0 95.9 1.0

Tungsten binding site 6 out of 10 in 5erv

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Tungsten binding site 6 out of 10 in the Ternary Complex of Gephe - Adp - Tungsten Cluster


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 6 of Ternary Complex of Gephe - Adp - Tungsten Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W808

b:0.5
occ:1.00
 O A:HOH1226 2.4 35.5 1.0
W A:W807 2.8 99.4 1.0
O1 A:WO4816 2.8 0.0 1.0
O A:HOH940 3.3 58.9 1.0
O2 A:WO4816 3.6 0.6 1.0
W A:WO4816 3.9 0.4 1.0
O A:HOH1005 4.2 27.4 1.0
W A:W804 4.5 89.2 1.0
W A:W805 4.6 0.7 1.0
W A:W811 4.6 0.1 1.0
O3 A:WO4816 4.9 0.9 1.0
O A:HOH1155 5.0 34.8 1.0
O2B A:ADP801 5.0 34.3 1.0
HB2 A:ASN627 5.0 23.1 1.0

Tungsten binding site 7 out of 10 in 5erv

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Tungsten binding site 7 out of 10 in the Ternary Complex of Gephe - Adp - Tungsten Cluster


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 7 of Ternary Complex of Gephe - Adp - Tungsten Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W809

b:0.9
occ:1.00
 O A:HOH1262 2.9 45.0 1.0
W A:W811 3.1 0.1 1.0
W A:W804 3.1 89.2 1.0
W A:W807 3.3 99.4 1.0
HE2 A:LYS602 3.4 55.3 1.0
HG3 A:LYS602 3.5 34.6 1.0
HB3 A:PRO603 3.5 30.5 1.0
HA A:PRO603 3.6 23.7 1.0
W A:W806 3.7 0.1 1.0
O3 A:WO4816 3.8 0.9 1.0
HZ2 A:LYS602 3.9 72.4 1.0
HG2 A:LYS602 4.1 34.6 1.0
W A:W805 4.2 0.7 1.0
HH22 A:ARG670 4.2 40.4 1.0
O2 A:WO4816 4.2 0.6 1.0
CG A:LYS602 4.2 28.8 1.0
CB A:PRO603 4.2 25.4 1.0
CE A:LYS602 4.2 46.0 1.0
CA A:PRO603 4.3 19.8 1.0
HZ3 A:LYS602 4.3 72.4 1.0
NZ A:LYS602 4.4 60.3 1.0
HH12 A:ARG670 4.4 40.0 1.0
HB2 A:PRO603 4.5 30.5 1.0
W A:WO4816 4.6 0.4 1.0
CD A:LYS602 4.8 37.8 1.0
HA A:LYS602 4.9 22.6 1.0
NH2 A:ARG670 4.9 33.6 1.0
HE3 A:LYS602 5.0 55.3 1.0

Tungsten binding site 8 out of 10 in 5erv

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Tungsten binding site 8 out of 10 in the Ternary Complex of Gephe - Adp - Tungsten Cluster


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 8 of Ternary Complex of Gephe - Adp - Tungsten Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W810

b:0.9
occ:1.00
 HD22 A:LEU605 2.6 67.4 1.0
W A:W804 2.9 89.2 1.0
W A:W811 2.9 0.1 1.0
HD23 A:LEU605 3.3 67.4 1.0
CD2 A:LEU605 3.4 56.2 1.0
HH12 A:ARG670 3.5 40.0 1.0
HH22 A:ARG670 3.7 40.4 1.0
HB2 A:LEU605 3.7 23.8 1.0
W A:W803 3.8 0.4 1.0
HD21 A:LEU605 3.9 67.4 1.0
NH1 A:ARG670 4.0 33.4 1.0
HB3 A:LEU605 4.1 23.8 1.0
NH2 A:ARG670 4.2 33.6 1.0
CB A:LEU605 4.3 19.8 1.0
CZ A:ARG670 4.4 34.2 1.0
CG A:LEU605 4.4 41.8 1.0
HH11 A:ARG670 4.5 40.0 1.0
O3 A:WO4816 4.6 0.9 1.0
HD13 A:LEU605 4.6 48.2 1.0
HH21 A:ARG670 4.7 40.4 1.0
W A:W807 4.8 99.4 1.0
O1 A:WO4816 4.9 0.0 1.0
O A:HOH1155 4.9 34.8 1.0

Tungsten binding site 9 out of 10 in 5erv

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Tungsten binding site 9 out of 10 in the Ternary Complex of Gephe - Adp - Tungsten Cluster


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 9 of Ternary Complex of Gephe - Adp - Tungsten Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W811

b:0.1
occ:1.00
 W A:W810 2.9 0.9 1.0
W A:W805 3.0 0.7 1.0
W A:W807 3.1 99.4 1.0
W A:W804 3.1 89.2 1.0
W A:W809 3.1 0.9 1.0
W A:W803 3.5 0.4 1.0
HH22 A:ARG670 3.7 40.4 1.0
W A:W806 3.7 0.1 1.0
HH12 A:ARG670 4.4 40.0 1.0
NH2 A:ARG670 4.5 33.6 1.0
W A:W808 4.6 0.5 1.0
HE2 A:LYS602 4.6 55.3 1.0
O A:HOH1262 4.7 45.0 1.0
O3 A:WO4816 4.7 0.9 1.0
HH21 A:ARG670 4.9 40.4 1.0

Tungsten binding site 10 out of 10 in 5erv

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Tungsten binding site 10 out of 10 in the Ternary Complex of Gephe - Adp - Tungsten Cluster


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 10 of Ternary Complex of Gephe - Adp - Tungsten Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W816

b:0.4
occ:1.00
 W A:WO4816 0.0 0.4 1.0
O3 A:WO4816 1.7 0.9 1.0
O4 A:WO4816 1.7 95.9 1.0
O1 A:WO4816 1.7 0.0 1.0
O2 A:WO4816 1.7 0.6 1.0
HG A:SER630 2.6 28.5 1.0
W A:W804 2.9 89.2 1.0
H A:GLY604 3.1 26.9 1.0
OG A:SER630 3.4 23.8 1.0
W A:W807 3.4 99.4 1.0
O A:HOH1005 3.6 27.4 1.0
HD2 A:PRO606 3.6 24.0 1.0
HD3 A:PRO606 3.7 24.0 1.0
N A:GLY604 3.9 22.4 1.0
HB2 A:PRO603 3.9 30.5 1.0
H A:LEU605 3.9 23.4 1.0
HB3 A:PRO625 3.9 24.3 1.0
W A:W808 3.9 0.5 1.0
HB3 A:SER630 4.0 21.5 1.0
HB3 A:ASN627 4.1 23.1 1.0
CD A:PRO606 4.1 20.0 1.0
CB A:SER630 4.1 17.9 1.0
HA2 A:GLY604 4.2 27.0 1.0
HB2 A:SER630 4.3 21.5 1.0
HB2 A:PRO625 4.3 24.3 1.0
HG3 A:PRO606 4.4 27.6 1.0
CB A:PRO625 4.5 20.2 1.0
N A:LEU605 4.5 19.5 1.0
HG2 A:PRO625 4.5 30.1 1.0
CA A:GLY604 4.5 22.5 1.0
HB2 A:ASN627 4.5 23.1 1.0
O A:HOH1226 4.6 35.5 1.0
HA A:PRO603 4.6 23.7 1.0
CB A:PRO603 4.6 25.4 1.0
W A:W809 4.6 0.9 1.0
HB3 A:PRO603 4.6 30.5 1.0
HB3 A:LEU605 4.7 23.8 1.0
CG A:PRO606 4.7 23.0 1.0
CB A:ASN627 4.7 19.2 1.0
C A:PRO603 4.8 24.7 1.0
CA A:PRO603 4.9 19.8 1.0
CG A:PRO625 4.9 25.1 1.0
C A:GLY604 4.9 23.3 1.0
HB2 A:LEU605 4.9 23.8 1.0
HG2 A:PRO606 4.9 27.6 1.0
HG3 A:PRO625 4.9 30.1 1.0

Reference:

V.B.Kasaragod, H.Schindelin. Structural Framework For Metal Incorporation During Molybdenum Cofactor Biosynthesis. Structure V. 24 782 2016.
ISSN: ISSN 0969-2126
PubMed: 27112598
DOI: 10.1016/J.STR.2016.02.023
Page generated: Sat Oct 12 04:49:11 2024

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