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Molybdenum in PDB 5eru: Ternary Complex of Gephe - Adp - Molybdenum Cluster

Protein crystallography data

The structure of Ternary Complex of Gephe - Adp - Molybdenum Cluster, PDB code: 5eru 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) 43.84 / 1.60
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 87.680, 99.100, 113.060, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 17.6

Other elements in 5eru:

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

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

Molybdenum Binding Sites:

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

Molybdenum binding site 1 out of 9 in 5eru

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Molybdenum binding site 1 out of 9 in the Ternary Complex of Gephe - Adp - Molybdenum Cluster


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Ternary Complex of Gephe - Adp - Molybdenum Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo812

b:63.1
occ:0.92
O1 A:MOO820 1.8 72.5 0.5
HH12 A:ARG670 2.7 41.2 1.0
O A:HOH1123 2.9 52.1 1.0
MO A:MOO820 3.1 64.0 1.0
MO A:MO817 3.3 0.9 1.0
H A:LEU605 3.3 25.9 1.0
HB2 A:LEU605 3.3 28.5 1.0
O2 A:MOO820 3.4 91.2 0.5
H A:GLY604 3.4 24.8 1.0
MO A:MO816 3.5 0.8 1.0
NH1 A:ARG670 3.5 34.3 1.0
HA A:PRO603 3.5 26.1 1.0
MO A:MO813 3.6 94.9 0.8
MO A:MO814 3.6 0.2 1.0
MO A:MO819 3.7 94.7 1.0
HB3 A:LEU605 3.8 28.5 1.0
HH22 A:ARG670 3.8 40.5 1.0
HH11 A:ARG670 3.9 41.2 1.0
CB A:LEU605 4.0 23.8 1.0
N A:GLY604 4.2 20.6 1.0
O3 A:MOO820 4.2 27.2 0.4
N A:LEU605 4.2 21.6 1.0
MO A:MO815 4.3 0.8 1.0
O4 A:MOO820 4.3 82.1 0.5
CA A:PRO603 4.4 21.8 1.0
HD22 A:LEU605 4.4 62.2 1.0
HA A:LYS602 4.4 22.7 0.7
HA A:LYS602 4.4 40.1 0.3
HG3 A:LYS602 4.4 40.6 0.7
NH2 A:ARG670 4.4 33.7 1.0
HD3 A:PRO606 4.4 23.1 1.0
CZ A:ARG670 4.5 40.9 1.0
HG3 A:LYS602 4.5 47.7 0.3
C A:PRO603 4.7 25.3 1.0
HB3 A:PRO603 4.7 28.7 1.0
HB2 A:PRO603 4.8 28.7 1.0
CA A:LEU605 4.8 19.5 1.0
HZ1 A:LYS602 4.8 59.6 0.3
CB A:PRO603 4.9 23.9 1.0
HD23 A:LEU605 4.9 62.2 1.0
HD2 A:PRO606 4.9 23.1 1.0
O A:MET601 4.9 22.3 1.0
HG A:SER630 4.9 30.8 1.0
CD2 A:LEU605 5.0 51.9 1.0

Molybdenum binding site 2 out of 9 in 5eru

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Molybdenum binding site 2 out of 9 in the Ternary Complex of Gephe - Adp - Molybdenum Cluster


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Ternary Complex of Gephe - Adp - Molybdenum Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo813

b:94.9
occ:0.83
HD22 A:LEU605 2.9 62.2 1.0
MO A:MO816 2.9 0.8 1.0
MO A:MO812 3.6 63.1 0.9
HD23 A:LEU605 3.6 62.2 1.0
MO A:MO814 3.6 0.2 1.0
CD2 A:LEU605 3.7 51.9 1.0
HH12 A:ARG670 3.8 41.2 1.0
HH22 A:ARG670 3.9 40.5 1.0
O A:HOH1123 4.1 52.1 1.0
HD21 A:LEU605 4.2 62.2 1.0
MO A:MO819 4.2 94.7 1.0
HB2 A:LEU605 4.3 28.5 1.0
NH1 A:ARG670 4.3 34.3 1.0
NH2 A:ARG670 4.3 33.7 1.0
HB3 A:LEU605 4.5 28.5 1.0
CZ A:ARG670 4.6 40.9 1.0
CB A:LEU605 4.7 23.8 1.0
CG A:LEU605 4.8 40.8 1.0
HH11 A:ARG670 4.8 41.2 1.0
HH21 A:ARG670 4.9 40.5 1.0
HD13 A:LEU605 4.9 41.4 1.0

Molybdenum binding site 3 out of 9 in 5eru

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Molybdenum binding site 3 out of 9 in the Ternary Complex of Gephe - Adp - Molybdenum Cluster


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 3 of Ternary Complex of Gephe - Adp - Molybdenum Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo814

b:0.2
occ:0.98
O2 A:MOO820 2.2 91.2 0.5
O A:HOH1219 2.8 44.2 1.0
MO A:MO819 3.0 94.7 1.0
MO A:MOO820 3.5 64.0 1.0
MO A:MO812 3.6 63.1 0.9
MO A:MO813 3.6 94.9 0.8
O1 A:MOO820 3.8 72.5 0.5
HD3 A:PRO606 3.9 23.1 1.0
O A:HOH1111 4.0 51.7 1.0
HB3 A:LEU605 4.0 28.5 1.0
O4 A:MOO820 4.1 82.1 0.5
HD23 A:LEU605 4.1 62.2 1.0
O A:HOH1243 4.2 34.6 1.0
HG A:SER575 4.3 56.0 1.0
HG3 A:PRO606 4.5 29.0 1.0
MO A:MO815 4.6 0.8 1.0
HD22 A:LEU605 4.7 62.2 1.0
MO A:MO816 4.7 0.8 1.0
CD A:PRO606 4.7 19.2 1.0
OG A:SER575 4.8 46.7 1.0
CD2 A:LEU605 4.8 51.9 1.0
O3 A:MOO820 4.8 27.2 0.4
HB2 A:LEU605 4.8 28.5 1.0
CB A:LEU605 4.9 23.8 1.0

Molybdenum binding site 4 out of 9 in 5eru

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Molybdenum binding site 4 out of 9 in the Ternary Complex of Gephe - Adp - Molybdenum Cluster


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 4 of Ternary Complex of Gephe - Adp - Molybdenum Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo815

b:0.8
occ:1.00
O4 A:MOO820 2.5 82.1 0.5
MO A:MO819 2.7 94.7 1.0
O1 A:MOO820 3.2 72.5 0.5
MO A:MOO820 3.5 64.0 1.0
MO A:MO817 3.5 0.9 1.0
HG A:SER630 3.6 30.8 1.0
O A:HOH1244 3.7 51.0 1.0
MO A:MO818 3.7 0.6 1.0
HB2 A:ASN627 3.8 22.1 1.0
O A:HOH1156 3.8 40.0 1.0
O A:HOH1243 4.0 34.6 1.0
HB3 A:ASN627 4.0 22.1 1.0
CG A:ASN627 4.1 25.5 1.0
OG A:SER630 4.1 25.6 1.0
CB A:ASN627 4.2 18.4 1.0
MO A:MO812 4.3 63.1 0.9
ND2 A:ASN627 4.3 34.2 1.0
O2 A:MOO820 4.4 91.2 0.5
HD22 A:ASN627 4.4 41.1 1.0
OD1 A:ASN627 4.5 35.3 1.0
MO A:MO814 4.6 0.2 1.0
HD21 A:ASN627 4.6 41.1 1.0
O A:HOH1123 4.7 52.1 1.0
HB3 A:PRO603 4.7 28.7 1.0
O A:HOH972 4.8 27.3 1.0
MO A:MO816 4.9 0.8 1.0
O3 A:MOO820 4.9 27.2 0.4

Molybdenum binding site 5 out of 9 in 5eru

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Molybdenum binding site 5 out of 9 in the Ternary Complex of Gephe - Adp - Molybdenum Cluster


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 5 of Ternary Complex of Gephe - Adp - Molybdenum Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo816

b:0.8
occ:0.98
O A:HOH1123 2.0 52.1 1.0
MO A:MO813 2.9 94.9 0.8
MO A:MO819 3.0 94.7 1.0
HH22 A:ARG670 3.2 40.5 1.0
MO A:MO817 3.4 0.9 1.0
MO A:MO812 3.5 63.1 0.9
HZ1 A:LYS602 3.9 59.6 0.3
HZ2 A:LYS602 4.0 59.6 0.3
NH2 A:ARG670 4.0 33.7 1.0
MO A:MO818 4.2 0.6 1.0
HZ3 A:LYS602 4.2 59.6 0.3
NZ A:LYS602 4.2 49.7 0.3
HH12 A:ARG670 4.2 41.2 1.0
HH21 A:ARG670 4.3 40.5 1.0
O1 A:MOO820 4.6 72.5 0.5
MO A:MO814 4.7 0.2 1.0
NH1 A:ARG670 4.9 34.3 1.0
MO A:MO815 4.9 0.8 1.0
CZ A:ARG670 4.9 40.9 1.0
HE3 A:LYS602 4.9 63.7 0.7

Molybdenum binding site 6 out of 9 in 5eru

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Molybdenum binding site 6 out of 9 in the Ternary Complex of Gephe - Adp - Molybdenum Cluster


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 6 of Ternary Complex of Gephe - Adp - Molybdenum Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo817

b:0.9
occ:1.00
O A:HOH1123 1.9 52.1 1.0
HZ1 A:LYS602 2.7 59.6 0.3
MO A:MO812 3.3 63.1 0.9
O1 A:MOO820 3.3 72.5 0.5
HG3 A:LYS602 3.4 40.6 0.7
MO A:MO816 3.4 0.8 1.0
HG3 A:LYS602 3.5 47.7 0.3
MO A:MO815 3.5 0.8 1.0
HB3 A:PRO603 3.5 28.7 1.0
HA A:PRO603 3.5 26.1 1.0
NZ A:LYS602 3.5 49.7 0.3
HZ3 A:LYS602 3.6 59.6 0.3
HE3 A:LYS602 3.7 63.7 0.7
MO A:MO819 3.9 94.7 1.0
HZ2 A:LYS602 4.0 59.6 0.3
HH22 A:ARG670 4.1 40.5 1.0
HG2 A:LYS602 4.2 47.7 0.3
CG A:LYS602 4.2 33.9 0.7
CB A:PRO603 4.2 23.9 1.0
CG A:LYS602 4.3 39.7 0.3
HG2 A:LYS602 4.3 40.6 0.7
CA A:PRO603 4.3 21.8 1.0
O A:HOH1156 4.3 40.0 1.0
HE3 A:LYS602 4.4 57.6 0.3
HH12 A:ARG670 4.5 41.2 1.0
CE A:LYS602 4.5 48.0 0.3
HB2 A:PRO603 4.6 28.7 1.0
CE A:LYS602 4.6 53.1 0.7
MO A:MO818 4.7 0.6 1.0
HA A:LYS602 4.8 40.1 0.3
HA A:LYS602 4.8 22.7 0.7
MO A:MOO820 4.8 64.0 1.0
HE2 A:LYS602 4.8 63.7 0.7
CD A:LYS602 4.8 48.0 0.7
NH2 A:ARG670 4.9 33.7 1.0
HD2 A:LYS602 4.9 57.6 0.7
O A:HOH1317 4.9 31.0 1.0
N A:PRO603 5.0 22.1 1.0
O4 A:MOO820 5.0 82.1 0.5

Molybdenum binding site 7 out of 9 in 5eru

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Molybdenum binding site 7 out of 9 in the Ternary Complex of Gephe - Adp - Molybdenum Cluster


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 7 of Ternary Complex of Gephe - Adp - Molybdenum Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo818

b:0.6
occ:1.00
MO A:MO819 2.9 94.7 1.0
MO A:MO815 3.7 0.8 1.0
MO A:MO816 4.2 0.8 1.0
MO A:MO817 4.7 0.9 1.0
O A:HOH1244 4.9 51.0 1.0

Molybdenum binding site 8 out of 9 in 5eru

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Molybdenum binding site 8 out of 9 in the Ternary Complex of Gephe - Adp - Molybdenum Cluster


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 8 of Ternary Complex of Gephe - Adp - Molybdenum Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo819

b:94.7
occ:1.00
MO A:MO815 2.7 0.8 1.0
MO A:MO818 2.9 0.6 1.0
MO A:MO816 3.0 0.8 1.0
MO A:MO814 3.0 0.2 1.0
MO A:MO812 3.7 63.1 0.9
O1 A:MOO820 3.7 72.5 0.5
MO A:MO817 3.9 0.9 1.0
O A:HOH1123 4.0 52.1 1.0
O4 A:MOO820 4.0 82.1 0.5
O2 A:MOO820 4.1 91.2 0.5
MO A:MOO820 4.2 64.0 1.0
MO A:MO813 4.2 94.9 0.8
O A:HOH1243 4.2 34.6 1.0
O A:HOH1244 4.8 51.0 1.0

Molybdenum binding site 9 out of 9 in 5eru

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


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 9 of Ternary Complex of Gephe - Adp - Molybdenum Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo820

b:64.0
occ:0.98
MO A:MOO820 0.0 64.0 1.0
O3 A:MOO820 1.7 27.2 0.4
O1 A:MOO820 1.7 72.5 0.5
O4 A:MOO820 1.7 82.1 0.5
O2 A:MOO820 1.7 91.2 0.5
HG A:SER630 2.7 30.8 1.0
MO A:MO812 3.1 63.1 0.9
H A:GLY604 3.1 24.8 1.0
HD2 A:PRO606 3.4 23.1 1.0
MO A:MO815 3.5 0.8 1.0
OG A:SER630 3.5 25.6 1.0
MO A:MO814 3.5 0.2 1.0
O A:HOH972 3.6 27.3 1.0
HD3 A:PRO606 3.6 23.1 1.0
HB3 A:PRO625 3.7 23.4 1.0
H A:LEU605 3.8 25.9 1.0
HB3 A:SER630 3.9 24.9 1.0
CD A:PRO606 3.9 19.2 1.0
N A:GLY604 3.9 20.6 1.0
HB2 A:PRO603 4.0 28.7 1.0
CB A:SER630 4.1 20.7 1.0
HB2 A:PRO625 4.2 23.4 1.0
MO A:MO819 4.2 94.7 1.0
HB3 A:ASN627 4.2 22.1 1.0
HA2 A:GLY604 4.2 25.4 1.0
HG3 A:PRO606 4.2 29.0 1.0
CB A:PRO625 4.3 19.5 1.0
HB2 A:SER630 4.3 24.9 1.0
N A:LEU605 4.4 21.6 1.0
HG2 A:PRO625 4.4 28.6 1.0
HB3 A:LEU605 4.4 28.5 1.0
CA A:GLY604 4.5 21.2 1.0
CG A:PRO606 4.5 24.2 1.0
O A:HOH1243 4.5 34.6 1.0
HA A:PRO603 4.6 26.1 1.0
HG2 A:PRO606 4.7 29.0 1.0
HG3 A:PRO625 4.7 28.6 1.0
CG A:PRO625 4.7 23.8 1.0
CB A:PRO603 4.7 23.9 1.0
HB3 A:PRO603 4.8 28.7 1.0
HB2 A:ASN627 4.8 22.1 1.0
C A:GLY604 4.8 20.9 1.0
MO A:MO817 4.8 0.9 1.0
O A:HOH1219 4.9 44.2 1.0
C A:PRO603 4.9 25.3 1.0
CB A:ASN627 4.9 18.4 1.0
HB2 A:LEU605 4.9 28.5 1.0
CA A:PRO603 5.0 21.8 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: Tue Dec 15 05:19:45 2020

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