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

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: Wed Sep 23 13:36:54 2020
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy