Atomistry » Molybdenum » PDB 2ca3-3fah » 2vpz
Atomistry »
  Molybdenum »
    PDB 2ca3-3fah »
      2vpz »

Molybdenum in PDB 2vpz: Polysulfide Reductase Native Structure

Protein crystallography data

The structure of Polysulfide Reductase Native Structure, PDB code: 2vpz was solved by M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.83 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.405, 166.265, 246.428, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 25.3

Other elements in 2vpz:

The structure of Polysulfide Reductase Native Structure also contains other interesting chemical elements:

Iron (Fe) 40 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Polysulfide Reductase Native Structure (pdb code 2vpz). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 2 binding sites of Molybdenum where determined in the Polysulfide Reductase Native Structure, PDB code: 2vpz:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in 2vpz

Go back to Molybdenum Binding Sites List in 2vpz
Molybdenum binding site 1 out of 2 in the Polysulfide Reductase Native Structure


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Polysulfide Reductase Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo1767

b:35.0
occ:1.00
S12 A:MGD1766 2.3 31.7 1.0
S12 A:MGD1765 2.3 31.0 1.0
SG A:CYS173 2.3 34.0 1.0
S13 A:MGD1766 2.4 33.0 1.0
S13 A:MGD1765 2.6 32.9 1.0
C13 A:MGD1766 3.3 34.6 1.0
C12 A:MGD1766 3.4 34.6 1.0
C13 A:MGD1765 3.4 34.7 1.0
C12 A:MGD1765 3.4 34.0 1.0
CB A:CYS173 3.5 33.7 1.0
NE A:ARG332 4.3 36.1 1.0
CD A:ARG332 4.4 33.9 1.0
CZ A:PHE631 4.6 28.5 1.0
CG A:ARG332 4.6 33.3 1.0
O A:HOH2170 4.6 66.4 1.0
CE2 A:PHE631 4.6 29.4 1.0
NH2 A:ARG625 4.7 29.9 1.0
C14 A:MGD1765 4.7 36.2 1.0
C14 A:MGD1766 4.8 33.2 1.0
C11 A:MGD1765 4.8 32.3 1.0
CA A:CYS173 4.8 35.5 1.0
C11 A:MGD1766 4.9 31.6 1.0
CB A:SER169 4.9 36.6 1.0

Molybdenum binding site 2 out of 2 in 2vpz

Go back to Molybdenum Binding Sites List in 2vpz
Molybdenum binding site 2 out of 2 in the Polysulfide Reductase Native Structure


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Polysulfide Reductase Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mo1767

b:32.0
occ:1.00
SG E:CYS173 2.1 35.8 1.0
O E:HOH2217 2.2 20.2 1.0
S13 E:MGD1766 2.5 32.9 1.0
S12 E:MGD1765 2.5 36.5 1.0
S13 E:MGD1765 2.5 37.8 1.0
S12 E:MGD1766 2.5 27.7 1.0
C13 E:MGD1766 3.4 33.1 1.0
C13 E:MGD1765 3.5 37.1 1.0
C12 E:MGD1766 3.5 31.9 1.0
C12 E:MGD1765 3.5 36.9 1.0
CB E:CYS173 3.5 35.9 1.0
NE E:ARG332 4.3 27.5 1.0
CD E:ARG332 4.4 27.9 1.0
O E:HOH2218 4.4 36.0 1.0
CG E:ARG332 4.6 29.4 1.0
CE2 E:PHE631 4.7 30.1 1.0
CZ E:PHE631 4.7 30.5 1.0
NH2 E:ARG625 4.7 33.7 1.0
C14 E:MGD1765 4.8 38.1 1.0
C11 E:MGD1766 4.9 30.4 1.0
CA E:CYS173 4.9 37.4 1.0
C14 E:MGD1766 4.9 32.0 1.0
C11 E:MGD1765 5.0 34.2 1.0

Reference:

M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, S.Iwata. Molecular Mechanism of Energy Conservation in Polysulfide Respiration Nat.Struct.Mol.Biol. V. 15 730 2008.
ISSN: ISSN 1545-9993
PubMed: 18536726
DOI: 10.1038/NSMB.1434
Page generated: Tue Dec 15 05:17:28 2020

Last articles

Zn in 7RE3
Zn in 7RDX
Zn in 7RDZ
Zn in 7RWM
Zn in 7PGU
Zn in 7PGR
Zn in 7PGT
Zn in 7PGS
Zn in 7SQE
Zn in 7RWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy