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Zinc in PDB 4csz: Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound

Enzymatic activity of Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound

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

Protein crystallography data

The structure of Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound, PDB code: 4csz 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) 68.29 / 1.75
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 89.570, 89.570, 144.011, 90.00, 90.00, 120.00
R / Rfree (%) 17.821 / 20.993

Other elements in 4csz:

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

Copper (Cu) 2 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 7 in 4csz

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Zinc binding site 1 out of 7 in the Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound within 5.0Å range:

Zinc binding site 2 out of 7 in 4csz

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Zinc binding site 2 out of 7 in the Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1339

b:22.3
occ:0.50
 NE2 A:HIS165 1.9 26.9 1.0
OD2 A:ASP167 1.9 33.5 1.0
OD1 A:ASP167 2.4 36.3 1.0
CG A:ASP167 2.5 31.9 1.0
CE1 A:HIS165 2.9 26.1 1.0
CD2 A:HIS165 2.9 27.5 1.0
OG1 A:THR234 3.9 28.3 1.0
ND1 A:HIS165 4.0 25.7 1.0
CB A:ASP167 4.0 31.8 1.0
CG A:HIS165 4.0 25.2 1.0
O A:HOH2244 4.2 52.1 1.0
CB A:THR234 4.3 29.1 1.0
N A:THR234 4.4 29.3 1.0
N A:ASP167 4.6 27.4 1.0
CA A:ASP167 4.7 31.3 1.0
O A:GLY232 4.8 34.1 1.0
CA A:THR234 5.0 27.1 1.0

Zinc binding site 3 out of 7 in 4csz

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Zinc binding site 3 out of 7 in the Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1341

b:36.2
occ:0.70
 O A:HOH2148 2.1 37.8 1.0
O A:HOH2149 3.0 18.6 0.5
O A:HOH2149 3.4 23.1 0.5
OH A:TYR197 3.9 30.2 1.0
O A:GLY134 3.9 25.1 1.0
O A:HOH2215 4.3 44.2 1.0
CG A:PRO137 4.7 21.4 1.0
CG2 A:VAL201 4.8 25.3 1.0
CZ A:TYR197 4.9 29.5 1.0
CA A:MET135 4.9 24.8 0.5
C A:GLY134 4.9 24.5 1.0
CE1 A:TYR197 5.0 25.9 1.0
CD A:PRO137 5.0 19.0 1.0
CG1 A:VAL201 5.0 26.2 1.0

Zinc binding site 4 out of 7 in 4csz

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Zinc binding site 4 out of 7 in the Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1342

b:46.0
occ:0.80
 O A:HOH2091 1.5 33.8 1.0
OD2 A:ASP73 2.2 32.0 1.0
O A:HOH2041 2.3 17.7 0.5
O A:HOH2043 2.3 24.0 0.5
ND1 A:HIS70 2.4 32.6 1.0
CG A:ASP73 3.1 32.3 1.0
CG A:HIS70 3.2 27.9 1.0
OD1 A:ASP73 3.2 34.5 1.0
CB A:HIS70 3.3 29.3 1.0
CE1 A:HIS70 3.5 32.5 1.0
NH2 A:ARG153 3.5 36.6 0.5
N A:HIS70 3.6 26.8 1.0
CA A:HIS70 4.1 26.4 1.0
NH1 A:ARG153 4.1 36.1 0.5
CZ A:ARG153 4.2 37.2 0.5
CD2 A:HIS70 4.3 30.2 1.0
NH1 A:ARG153 4.4 31.9 0.5
NE2 A:HIS70 4.4 31.6 1.0
C A:VAL69 4.5 28.1 1.0
CB A:ASP73 4.5 30.8 1.0
NH2 A:ARG153 4.7 29.5 0.5
CA A:VAL69 4.8 27.5 1.0
O A:HIS70 4.9 27.8 1.0
C A:HIS70 4.9 25.2 1.0
CZ A:ARG153 4.9 31.6 0.5
CG2 A:VAL33 5.0 34.2 1.0
CG A:LYS31 5.0 50.4 1.0
CG2 A:THR26 5.0 47.6 1.0

Zinc binding site 5 out of 7 in 4csz

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Zinc binding site 5 out of 7 in the Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1343

b:40.7
occ:0.50
 O A:HOH2293 2.0 42.8 1.0
O A:HOH2294 2.1 20.1 0.3
NE2 A:HIS313 2.2 34.8 1.0
O A:HOH2294 2.4 37.5 0.3
O A:HOH2315 2.4 53.5 1.0
CE1 A:HIS313 2.7 35.6 1.0
CD2 A:HIS313 3.3 35.0 1.0
O A:HOH2294 3.9 36.3 0.3
ND1 A:HIS313 3.9 35.6 1.0
CG A:HIS313 4.2 33.0 1.0
O A:HOH2108 4.2 29.2 0.5
CG2 A:THR222 4.7 34.0 1.0

Zinc binding site 6 out of 7 in 4csz

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Zinc binding site 6 out of 7 in the Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1344

b:32.1
occ:0.50
 SG A:CYS306 2.0 23.2 1.0
O A:HOH2287 2.5 52.4 1.0
CB A:CYS306 3.1 23.2 1.0
CA A:CYS306 3.4 20.4 1.0
O A:HOH2315 3.9 53.5 1.0
N A:CYS306 3.9 18.1 1.0
O A:HOH2293 4.0 42.8 1.0
CD2 A:LEU298 4.1 21.7 1.0
C A:ALA305 4.3 17.1 1.0
CB A:ALA311 4.5 19.3 1.0
CB A:ALA305 4.5 13.8 1.0
O A:ALA305 4.5 18.6 1.0
C A:CYS306 4.8 21.5 1.0

Zinc binding site 7 out of 7 in 4csz

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of F306C Mutant of Nitrite Reductase From Achromobacter Xylosoxidans with Nitrite Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1345

b:51.0
occ:0.50
 O A:HOH2004 1.7 36.3 0.5
O A:HOH2009 1.8 37.7 0.5
NE2 A:HIS8 2.3 46.3 1.0
CE1 A:HIS8 3.1 45.7 1.0
O A:ASP4 3.2 69.7 1.0
CD2 A:HIS8 3.4 45.9 1.0
CA A:ASP4 3.5 68.3 1.0
C A:ASP4 3.7 66.7 1.0
O A:ALA3 4.0 56.3 1.0
O A:LEU6 4.1 42.6 1.0
ND1 A:HIS8 4.3 45.3 1.0
O A:HOH2106 4.3 44.5 1.0
CB A:ASP4 4.3 68.1 1.0
OD1 A:ASP4 4.4 65.2 1.0
CG A:HIS8 4.4 44.3 1.0
N A:ASP4 4.5 64.8 1.0
O A:HOH2042 4.7 53.6 1.0
C A:ALA3 4.7 62.1 1.0
N A:LYS5 4.8 68.2 1.0
CG A:ASP4 4.9 67.0 1.0
N A:LEU6 4.9 53.4 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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