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Sodium in PDB 3wi9: Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus

Enzymatic activity of Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus

All present enzymatic activity of Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus, PDB code: 3wi9 was solved by Y.Fukuda, M.Nojiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.90 / 1.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 115.069, 115.069, 87.505, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 19.7

Other elements in 3wi9:

The structure of Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus also contains other interesting chemical elements:

Copper (Cu) 2 atoms
Zinc (Zn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus (pdb code 3wi9). 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 Copper Nitrite Reductase From Geobacillus Kaustophilus, PDB code: 3wi9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3wi9

Go back to Sodium Binding Sites List in 3wi9
Sodium binding site 1 out of 2 in the Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus


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 Copper Nitrite Reductase From Geobacillus Kaustophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:16.9
occ:0.50
O A:HOH834 2.0 21.2 1.0
O A:HOH740 2.1 27.9 1.0
O A:HOH790 2.2 15.0 1.0
O A:HOH726 2.7 28.1 1.0
O A:HOH749 3.8 29.6 1.0
O A:HOH660 4.0 28.4 1.0
OE2 A:GLU217 4.1 27.6 1.0
O A:HOH763 4.3 32.7 1.0
NZ A:LYS56 4.3 22.1 1.0
O A:HOH732 4.8 28.4 1.0

Sodium binding site 2 out of 2 in 3wi9

Go back to Sodium Binding Sites List in 3wi9
Sodium binding site 2 out of 2 in the Crystal Structure of Copper Nitrite Reductase From Geobacillus Kaustophilus


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 Copper Nitrite Reductase From Geobacillus Kaustophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:22.4
occ:1.00
O A:HOH741 1.8 23.0 1.0
O A:HOH727 2.0 21.0 1.0
O A:HOH742 2.2 34.1 1.0
OE1 A:GLU239 2.4 19.6 1.0
OE2 A:GLU239 2.8 18.2 1.0
CD A:GLU239 3.0 16.7 1.0
O A:HOH647 3.7 27.7 1.0
NE2 A:HIS298 4.0 8.8 1.0
O A:HOH607 4.1 23.0 1.0
O A:HOH661 4.3 32.2 1.0
CD A:PRO191 4.3 11.8 1.0
CG A:GLU239 4.4 10.9 1.0
O A:HOH551 4.5 21.5 1.0
CE1 A:HIS298 4.5 8.1 1.0
O A:HOH540 4.8 20.6 1.0
CG1 A:VAL190 4.8 13.3 1.0
O A:HOH511 5.0 13.1 1.0

Reference:

Y.Fukuda, H.Koteishi, R.Yoneda, T.Tamada, H.Takami, T.Inoue, M.Nojiri. Structural and Functional Characterization of the Geobacillus Copper Nitrite Reductase: Involvement of the Unique N-Terminal Region in the Interprotein Electron Transfer with Its Redox Partner Biochim.Biophys.Acta V.1837 396 2014.
ISSN: ISSN 0006-3002
PubMed: 24440558
DOI: 10.1016/J.BBABIO.2014.01.004
Page generated: Tue Dec 15 06:29:59 2020

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