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Sodium in PDB 1jrz: Crystal Structure of ARG402TYR Mutant Flavocytochrome C3 From Shewanella Frigidimarina

Enzymatic activity of Crystal Structure of ARG402TYR Mutant Flavocytochrome C3 From Shewanella Frigidimarina

All present enzymatic activity of Crystal Structure of ARG402TYR Mutant Flavocytochrome C3 From Shewanella Frigidimarina:
1.3.99.1;

Protein crystallography data

The structure of Crystal Structure of ARG402TYR Mutant Flavocytochrome C3 From Shewanella Frigidimarina, PDB code: 1jrz was solved by C.G.Mowat, R.Moysey, C.S.Miles, D.Leys, M.K.Doherty, P.Taylor, M.D.Walkinshaw, G.A.Reid, S.K.Chapman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.072, 87.906, 90.163, 90.00, 105.03, 90.00
R / Rfree (%) 17.6 / 25.5

Other elements in 1jrz:

The structure of Crystal Structure of ARG402TYR Mutant Flavocytochrome C3 From Shewanella Frigidimarina also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of ARG402TYR Mutant Flavocytochrome C3 From Shewanella Frigidimarina (pdb code 1jrz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of ARG402TYR Mutant Flavocytochrome C3 From Shewanella Frigidimarina, PDB code: 1jrz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1jrz

Go back to Sodium Binding Sites List in 1jrz
Sodium binding site 1 out of 2 in the Crystal Structure of ARG402TYR Mutant Flavocytochrome C3 From Shewanella Frigidimarina


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of ARG402TYR Mutant Flavocytochrome C3 From Shewanella Frigidimarina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1810

b:20.5
occ:1.00
O A:GLU534 2.5 11.0 1.0
O A:THR506 2.5 7.8 1.0
O A:HOH1837 2.5 11.3 1.0
O A:THR536 2.5 10.1 1.0
O A:GLY508 2.6 10.9 1.0
O A:MET507 3.0 10.9 1.0
C A:MET507 3.2 12.3 1.0
C A:GLY508 3.4 13.5 1.0
C A:GLU534 3.5 13.3 1.0
O A:HOH1812 3.5 13.7 1.0
C A:THR506 3.6 12.5 1.0
N A:GLY508 3.6 10.1 1.0
C A:THR536 3.6 12.0 1.0
CA A:MET507 3.7 12.0 1.0
CA A:GLU534 3.9 10.8 1.0
CA A:GLY508 4.0 12.1 1.0
CG A:GLU534 4.0 12.1 1.0
O A:HOH1886 4.1 13.3 1.0
N A:MET507 4.1 12.4 1.0
N A:THR536 4.2 12.8 1.0
N A:GLY509 4.3 11.7 1.0
C A:VAL535 4.3 14.9 1.0
O A:HOH1862 4.3 14.8 1.0
N A:GLY537 4.5 12.5 1.0
N A:VAL535 4.5 12.3 1.0
CA A:GLY537 4.5 13.1 1.0
CA A:THR536 4.5 11.8 1.0
CA A:GLY509 4.6 12.2 1.0
CB A:GLU534 4.6 9.9 1.0
OG1 A:THR506 4.6 10.0 1.0
O A:VAL535 4.7 14.8 1.0
CA A:VAL535 4.7 13.4 1.0
NE2 A:HIS505 4.8 9.0 1.0
CA A:THR506 4.8 9.6 1.0
O A:GLY533 4.8 11.3 1.0
CB A:THR506 5.0 12.0 1.0

Sodium binding site 2 out of 2 in 1jrz

Go back to Sodium Binding Sites List in 1jrz
Sodium binding site 2 out of 2 in the Crystal Structure of ARG402TYR Mutant Flavocytochrome C3 From Shewanella Frigidimarina


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of ARG402TYR Mutant Flavocytochrome C3 From Shewanella Frigidimarina within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2810

b:16.0
occ:1.00
O B:GLU534 2.5 10.6 1.0
O B:THR506 2.5 9.3 1.0
O B:HOH1036 2.5 9.8 1.0
O B:THR536 2.5 11.1 1.0
O B:GLY508 2.6 11.3 1.0
O B:MET507 3.0 9.7 1.0
C B:MET507 3.3 12.8 1.0
C B:GLU534 3.4 9.8 1.0
C B:GLY508 3.5 13.8 1.0
O B:HOH1016 3.6 12.8 1.0
C B:THR506 3.6 13.1 1.0
C B:THR536 3.6 12.1 1.0
CA B:MET507 3.7 13.4 1.0
N B:GLY508 3.7 12.0 1.0
CA B:GLU534 3.9 10.5 1.0
CG B:GLU534 4.0 9.0 1.0
O B:HOH1139 4.0 10.9 1.0
CA B:GLY508 4.1 12.1 1.0
N B:MET507 4.1 11.7 1.0
O B:HOH1077 4.2 13.1 1.0
N B:THR536 4.2 10.1 1.0
C B:VAL535 4.4 11.4 1.0
N B:GLY509 4.4 13.9 1.0
N B:VAL535 4.4 11.8 1.0
N B:GLY537 4.5 11.8 1.0
CA B:GLY537 4.5 13.1 1.0
CA B:THR536 4.5 12.9 1.0
CB B:GLU534 4.6 10.2 1.0
CA B:GLY509 4.6 15.6 1.0
NE2 B:HIS505 4.7 11.2 1.0
O B:GLY533 4.7 12.1 1.0
OG1 B:THR506 4.7 12.1 1.0
O B:VAL535 4.8 14.1 1.0
CA B:VAL535 4.8 10.8 1.0
CA B:THR506 4.8 9.8 1.0

Reference:

C.G.Mowat, R.Moysey, C.S.Miles, D.Leys, M.K.Doherty, P.Taylor, M.D.Walkinshaw, G.A.Reid, S.K.Chapman. Kinetic and Crystallographic Analysis of the Key Active Site Acid/Base Arginine in A Soluble Fumarate Reductase. Biochemistry V. 40 12292 2001.
ISSN: ISSN 0006-2960
PubMed: 11591148
DOI: 10.1021/BI011360H
Page generated: Tue Dec 15 05:26:23 2020

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