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Zinc in PDB 4csp: Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans

Enzymatic activity of Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans

All present enzymatic activity of Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans:
1.7.2.1;

Protein crystallography data

The structure of Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans, PDB code: 4csp was solved by N.G.H.Leferink, S.V.Antonyuk, J.A.Houwman, N.S.Scrutton, R.Ready, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.47 / 1.70
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 89.990, 89.990, 289.450, 90.00, 90.00, 120.00
R / Rfree (%) 18.112 / 21.482

Other elements in 4csp:

The structure of Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans (pdb code 4csp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans, PDB code: 4csp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4csp

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Zinc binding site 1 out of 8 in the Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:26.9
occ:1.00
 O A:HOH2200 1.6 23.2 1.0
OD2 A:ASP167 2.1 22.2 1.0
NE2 A:HIS165 2.1 23.9 1.0
OE2 F:GLU195 2.2 21.6 0.5
OD1 A:ASP167 2.6 28.1 1.0
CG A:ASP167 2.7 22.6 1.0
CD F:GLU195 2.7 26.4 1.0
OE1 F:GLU195 2.9 24.0 0.5
CE1 A:HIS165 2.9 21.1 1.0
CD2 A:HIS165 3.2 23.0 1.0
O A:HOH2203 3.7 35.8 1.0
O A:HOH2263 3.9 46.2 1.0
OG1 A:THR234 3.9 20.6 1.0
CG F:GLU195 4.0 28.2 1.0
O A:HOH2202 4.0 32.7 1.0
ND1 A:HIS165 4.1 23.2 1.0
CB A:ASP167 4.2 22.0 1.0
CG A:HIS165 4.2 22.1 1.0
CB A:THR234 4.3 19.8 1.0
N A:THR234 4.4 20.1 1.0
CB F:ALA191 4.4 28.9 1.0
O A:GLY232 4.7 25.4 1.0
N A:ASP167 4.7 21.4 1.0
CA A:ASP167 4.9 22.8 1.0
CA A:THR234 5.0 21.3 1.0
O F:HOH2187 5.0 36.4 1.0

Zinc binding site 2 out of 8 in 4csp

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Zinc binding site 2 out of 8 in the Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:28.1
occ:0.20
 SG A:CYS306 2.6 25.2 1.0
O A:HOH2304 3.4 36.9 1.0
CB A:CYS306 3.6 21.0 1.0
CA A:CYS306 3.6 18.8 1.0
N A:CYS306 3.8 16.1 1.0
CB A:ALA311 3.9 17.4 1.0
CD2 A:LEU298 4.0 20.4 1.0
C A:ALA305 4.0 16.6 1.0
O A:ALA305 4.1 18.3 1.0
CB A:ALA305 4.2 14.1 1.0
O A:HOH2295 4.7 26.1 1.0
CA A:ALA305 4.7 14.8 1.0
C A:CYS306 5.0 18.5 1.0

Zinc binding site 3 out of 8 in 4csp

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Zinc binding site 3 out of 8 in the Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn511

b:38.1
occ:0.50
 O A:HOH2305 1.8 16.3 0.2
NE2 A:HIS313 2.0 28.9 1.0
O A:HOH2303 2.3 31.4 0.5
O A:HOH2304 2.5 36.9 1.0
CE1 A:HIS313 2.7 28.6 1.0
O A:HOH2305 3.2 34.6 0.5
CD2 A:HIS313 3.2 26.6 1.0
ND1 A:HIS313 3.9 28.8 1.0
CG A:HIS313 4.2 24.7 1.0

Zinc binding site 4 out of 8 in 4csp

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Zinc binding site 4 out of 8 in the Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn503

b:37.3
occ:0.50
 NE2 F:HIS313 1.9 35.4 1.0
O F:HOH2260 2.3 17.2 0.5
CE1 F:HIS313 2.6 33.8 1.0
O A:HOH2383 2.8 28.9 0.5
CD2 F:HIS313 3.1 32.4 1.0
ND1 F:HIS313 3.8 32.9 1.0
CG F:HIS313 4.0 28.4 1.0
O F:HOH2211 4.9 52.4 1.0

Zinc binding site 5 out of 8 in 4csp

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Zinc binding site 5 out of 8 in the Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn504

b:47.0
occ:0.50
 O F:HOH2007 1.5 62.9 1.0
O F:HOH2005 2.0 44.7 1.0
NE2 F:HIS8 2.3 44.1 1.0
CE1 F:HIS8 3.0 44.6 1.0
CD2 F:HIS8 3.5 42.2 1.0
O F:ASP4 3.6 63.8 1.0
CA F:ASP4 4.1 65.1 1.0
O F:HOH2096 4.1 32.7 1.0
C F:ASP4 4.1 63.6 1.0
ND1 F:HIS8 4.2 40.4 1.0
O F:LEU6 4.3 44.5 1.0
O F:ALA3 4.4 60.1 1.0
CG F:HIS8 4.5 40.5 1.0
OD1 F:ASP4 4.8 63.3 1.0
CB F:ASP4 4.9 65.0 1.0

Zinc binding site 6 out of 8 in 4csp

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Zinc binding site 6 out of 8 in the Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn506

b:28.3
occ:0.20
 SG F:CYS306 2.2 28.0 1.0
CB F:CYS306 3.4 23.2 1.0
CA F:CYS306 3.5 22.2 1.0
O F:HOH2260 3.8 17.2 0.5
N F:CYS306 3.9 19.5 1.0
CD2 F:LEU298 4.0 21.8 1.0
C F:ALA305 4.1 18.5 1.0
CB F:ALA305 4.2 15.8 1.0
CB F:ALA311 4.3 16.7 1.0
O F:ALA305 4.3 20.7 1.0
O A:HOH2383 4.4 28.9 0.5
O F:HOH2254 4.8 29.7 1.0
CA F:ALA305 4.9 16.7 1.0
C F:CYS306 4.9 22.3 1.0

Zinc binding site 7 out of 8 in 4csp

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Zinc binding site 7 out of 8 in the Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn507

b:22.2
occ:0.50
 ZN F:ZN507 0.0 22.2 0.5
ZN F:ZN507 1.0 20.0 0.5
NE2 F:HIS165 1.8 28.0 1.0
OD1 F:ASP167 2.0 29.6 1.0
OD2 F:ASP167 2.3 28.0 1.0
CG F:ASP167 2.5 28.9 1.0
O F:HOH2382 2.6 23.7 1.0
CE1 F:HIS165 2.8 29.4 1.0
CD2 F:HIS165 2.8 26.5 1.0
ND1 F:HIS165 3.9 26.2 1.0
CG F:HIS165 3.9 23.8 1.0
CB F:ASP167 4.0 28.9 1.0
OG1 F:THR234 4.4 26.6 1.0
N F:ASP167 4.5 26.1 1.0
CB F:THR234 4.5 26.4 1.0
CA F:ASP167 4.6 27.5 1.0
O F:HOH2166 4.7 43.1 1.0
N F:THR234 4.8 25.6 1.0
C F:TYR166 4.9 22.9 1.0

Zinc binding site 8 out of 8 in 4csp

Go back to Zinc Binding Sites List in 4csp
Zinc binding site 8 out of 8 in the Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn507

b:20.0
occ:0.50
 ZN F:ZN507 0.0 20.0 0.5
ZN F:ZN507 1.0 22.2 0.5
O F:HOH2382 1.7 23.7 1.0
OD2 F:ASP167 2.1 28.0 1.0
NE2 F:HIS165 2.5 28.0 1.0
OD1 F:ASP167 2.7 29.6 1.0
CG F:ASP167 2.8 28.9 1.0
CE1 F:HIS165 3.2 29.4 1.0
CD2 F:HIS165 3.6 26.5 1.0
OG1 F:THR234 3.7 26.6 1.0
CB F:THR234 4.2 26.4 1.0
N F:THR234 4.2 25.6 1.0
O F:GLY232 4.2 28.9 1.0
CB F:ASP167 4.3 28.9 1.0
ND1 F:HIS165 4.4 26.2 1.0
CG F:HIS165 4.6 23.8 1.0
CA F:THR234 4.8 26.6 1.0
N F:ASP167 4.9 26.1 1.0

Reference:

N.G.H.Leferink, S.V.Antonyuk, J.A.Houwman, N.S.Scrutton, R.R.Eady, S.S.Hasnain. Impact of Residues Remote From the Catalytic Centre on Enzyme Catalysis of Copper Nitrite Reductase. Nat.Commun. V. 5 4395 2014.
ISSN: ISSN 2041-1723
PubMed: 25022223
DOI: 10.1038/NCOMMS5395
Page generated: Sat Oct 26 21:04:01 2024

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