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Molybdenum in PDB 2nya: Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli

Enzymatic activity of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli

All present enzymatic activity of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli:
1.7.99.4;

Protein crystallography data

The structure of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli, PDB code: 2nya was solved by B.J.N.Jepson, D.J.Richardson, A.M.Hemmings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.449, 94.596, 131.211, 90.00, 96.34, 90.00
R / Rfree (%) 18.1 / 24.3

Other elements in 2nya:

The structure of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli (pdb code 2nya). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 2 binding sites of Molybdenum where determined in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli, PDB code: 2nya:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in 2nya

Go back to Molybdenum Binding Sites List in 2nya
Molybdenum binding site 1 out of 2 in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo2002

b:20.3
occ:1.00
S12 A:MGD3001 2.3 20.2 1.0
S12 A:MGD4001 2.4 21.1 1.0
S13 A:MGD3001 2.4 19.2 1.0
SG A:CYS143 2.5 20.2 1.0
S13 A:MGD4001 2.5 13.2 1.0
O A:HOH4003 2.5 5.9 1.0
CB A:CYS143 3.2 21.7 1.0
C12 A:MGD3001 3.3 16.5 1.0
C13 A:MGD3001 3.4 16.2 1.0
C12 A:MGD4001 3.4 18.5 1.0
C13 A:MGD4001 3.4 16.1 1.0
CG A:GLN374 4.2 14.5 1.0
NH2 A:ARG684 4.2 28.5 1.0
CA A:GLY373 4.2 14.4 1.0
N A:GLN374 4.2 14.6 1.0
NE2 A:GLN374 4.3 9.2 1.0
NH1 A:ARG684 4.5 30.6 1.0
CA A:CYS143 4.5 21.1 1.0
C A:GLY373 4.5 14.2 1.0
CE1 A:HIS690 4.5 23.1 1.0
N A:GLY373 4.7 15.4 1.0
CZ A:ARG684 4.7 27.6 1.0
NE2 A:HIS690 4.7 22.7 1.0
CD A:GLN374 4.7 13.5 1.0
SD A:MET336 4.8 21.2 1.0
C11 A:MGD3001 4.8 17.5 1.0
C14 A:MGD3001 4.8 16.3 1.0
C14 A:MGD4001 4.8 15.5 1.0
C11 A:MGD4001 4.8 20.7 1.0
CB A:GLN374 4.9 14.6 1.0

Molybdenum binding site 2 out of 2 in 2nya

Go back to Molybdenum Binding Sites List in 2nya
Molybdenum binding site 2 out of 2 in the Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Crystal Structure of the Periplasmic Nitrate Reductase (Nap) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mo5002

b:24.4
occ:1.00
S12 F:MGD6001 2.3 21.4 1.0
S13 F:MGD6001 2.3 22.3 1.0
SG F:CYS143 2.3 25.7 1.0
O F:HOH7035 2.4 5.5 1.0
S13 F:MGD7001 2.5 21.4 1.0
S12 F:MGD7001 2.6 24.4 1.0
CB F:CYS143 3.3 24.1 1.0
C12 F:MGD6001 3.4 20.3 1.0
C13 F:MGD6001 3.4 21.9 1.0
C13 F:MGD7001 3.5 21.6 1.0
C12 F:MGD7001 3.5 22.6 1.0
N F:GLN374 4.1 22.1 1.0
CA F:GLY373 4.2 24.0 1.0
CG F:GLN374 4.3 24.0 1.0
NH1 F:ARG684 4.3 33.0 1.0
NH2 F:ARG684 4.3 32.5 1.0
NE2 F:GLN374 4.4 24.1 1.0
C F:GLY373 4.5 23.5 1.0
CE1 F:HIS690 4.5 23.8 1.0
CA F:CYS143 4.6 23.4 1.0
CZ F:ARG684 4.6 31.6 1.0
N F:GLY373 4.6 25.4 1.0
NE2 F:HIS690 4.6 25.3 1.0
SD F:MET336 4.8 21.0 1.0
C11 F:MGD6001 4.8 20.7 1.0
CB F:GLN374 4.8 21.1 1.0
C14 F:MGD6001 4.8 20.2 1.0
CD F:GLN374 4.8 24.9 1.0
C14 F:MGD7001 4.9 20.4 1.0
C11 F:MGD7001 5.0 23.5 1.0

Reference:

B.J.Jepson, S.Mohan, T.A.Clarke, A.J.Gates, J.A.Cole, C.S.Butler, J.N.Butt, A.M.Hemmings, D.J.Richardson. Spectropotentiometric and Structural Analysis of the Periplasmic Nitrate Reductase From Escherichia Coli J.Biol.Chem. V. 282 6425 2007.
ISSN: ISSN 0021-9258
PubMed: 17130127
DOI: 10.1074/JBC.M607353200
Page generated: Mon Jan 25 15:37:31 2021

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