Atomistry » Molybdenum » PDB 4c80-5koj » 5eru
Atomistry »
  Molybdenum »
    PDB 4c80-5koj »
      5eru »

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

Go back to Molybdenum Binding Sites List in 5eru
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

Go back to Molybdenum Binding Sites List in 5eru
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

Go back to Molybdenum Binding Sites List in 5eru
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

Go back to Molybdenum Binding Sites List in 5eru
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

Go back to Molybdenum Binding Sites List in 5eru
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

Go back to Molybdenum Binding Sites List in 5eru
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

Go back to Molybdenum Binding Sites List in 5eru
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

Go back to Molybdenum Binding Sites List in 5eru
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

Go back to Molybdenum Binding Sites List in 5eru
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: Sun Oct 6 16:22:31 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy