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Zinc in PDB 2xx0: Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans

Enzymatic activity of Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans

All present enzymatic activity of Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans:
1.7.2.1;

Protein crystallography data

The structure of Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2xx0 was solved by S.V.Antonyuk, N.G.H.Leferink, C.Han, D.J.Heyes, S.E.J.Rigby, M.A.Hough, R.R.Eady, N.S.Scrutton, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.00 / 1.46
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 89.246, 89.246, 288.271, 90.00, 90.00, 120.00
R / Rfree (%) 12.509 / 15.054

Other elements in 2xx0:

The structure of Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes 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 N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans (pdb code 2xx0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2xx0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2xx0

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Zinc binding site 1 out of 6 in the Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes 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 N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1338

b:13.3
occ:0.80
 CU A:CU1339 0.2 14.6 0.2
O A:HOH2358 1.9 18.6 1.0
NE2 A:HIS129 2.0 13.4 1.0
NE2 A:HIS94 2.0 12.8 1.0
CD2 A:HIS129 2.9 11.8 1.0
CE1 A:HIS94 3.0 12.1 1.0
CE1 A:HIS129 3.0 14.2 1.0
CD2 A:HIS94 3.1 15.2 1.0
OD2 A:ASP92 3.6 17.6 0.8
O A:HOH2181 4.0 34.7 0.5
ND1 A:HIS94 4.1 12.8 1.0
CG A:HIS129 4.1 11.7 1.0
ND1 A:HIS129 4.1 13.0 1.0
CG A:HIS94 4.2 12.3 1.0
CG A:ASP92 4.3 16.5 0.8
OD1 A:ASP92 4.6 18.6 0.8

Zinc binding site 2 out of 6 in 2xx0

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Zinc binding site 2 out of 6 in the Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes 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 N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1340

b:20.0
occ:0.80
 O A:HOH2359 1.9 27.1 1.0
NE2 A:HIS165 2.0 22.6 1.0
OD2 A:ASP167 2.0 21.9 1.0
OD1 A:ASP167 2.6 21.0 1.0
CG A:ASP167 2.6 21.6 1.0
CE1 A:HIS165 2.9 23.6 1.0
CD2 A:HIS165 3.0 20.9 1.0
OG1 A:THR234 3.9 17.8 1.0
ND1 A:HIS165 4.1 22.5 1.0
CB A:ASP167 4.1 18.9 1.0
CG A:HIS165 4.1 18.2 1.0
O A:HOH2361 4.2 45.5 1.0
CB A:THR234 4.3 17.4 1.0
N A:THR234 4.4 17.0 1.0
O A:GLY232 4.6 22.8 1.0
N A:ASP167 4.7 16.9 1.0
CA A:ASP167 4.9 18.9 1.0
CA A:THR234 5.0 17.4 1.0

Zinc binding site 3 out of 6 in 2xx0

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Zinc binding site 3 out of 6 in the Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes 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 N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1343

b:30.3
occ:0.50
 O A:HOH2367 1.8 32.3 0.5
O A:HOH2364 2.0 47.4 0.8
NE2 A:HIS8 2.1 35.6 1.0
O A:HOH2366 2.1 40.3 0.8
O A:HOH2365 2.1 36.7 0.8
CE1 A:HIS8 3.0 34.8 1.0
CD2 A:HIS8 3.1 33.8 1.0
O A:ASP4 3.9 42.8 0.8
O A:LEU6 4.1 31.4 1.0
ND1 A:HIS8 4.1 34.5 1.0
O A:ALA3 4.2 38.1 0.8
CG A:HIS8 4.2 31.2 1.0
CA A:ASP4 4.3 43.6 0.8
C A:ASP4 4.3 43.0 0.8
O A:HOH2122 4.4 31.4 1.0

Zinc binding site 4 out of 6 in 2xx0

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Zinc binding site 4 out of 6 in the Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes 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 N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1339

b:14.7
occ:0.80
 CU B:CU1338 0.2 17.2 0.2
O B:HOH2317 1.8 20.3 1.0
NE2 B:HIS94 2.0 14.8 1.0
NE2 B:HIS129 2.0 14.2 1.0
CE1 B:HIS94 3.0 14.5 1.0
CD2 B:HIS129 3.0 15.0 1.0
CE1 B:HIS129 3.1 16.5 1.0
CD2 B:HIS94 3.1 16.1 1.0
OD2 B:ASP92 3.6 24.9 1.0
ND1 B:HIS94 4.1 15.5 1.0
CG B:HIS129 4.1 15.4 1.0
ND1 B:HIS129 4.1 14.8 1.0
CG B:HIS94 4.2 15.1 1.0
CG B:ASP92 4.2 22.9 1.0
OD1 B:ASP92 4.5 23.4 1.0

Zinc binding site 5 out of 6 in 2xx0

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Zinc binding site 5 out of 6 in the Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes 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 N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1340

b:24.3
occ:1.00
 OE2 A:GLU195 1.9 25.2 1.0
NE2 B:HIS165 2.0 20.6 1.0
OD2 B:ASP167 2.0 22.5 1.0
O B:HOH2318 2.1 26.4 1.0
OD1 B:ASP167 2.6 24.0 1.0
CG B:ASP167 2.6 23.3 1.0
CD A:GLU195 2.8 25.4 1.0
CE1 B:HIS165 2.9 22.6 1.0
OE1 A:GLU195 3.0 27.9 1.0
CD2 B:HIS165 3.1 20.1 1.0
O A:HOH2242 3.7 33.5 1.0
OG1 B:THR234 3.9 20.0 1.0
ND1 B:HIS165 4.1 20.2 1.0
CG A:GLU195 4.1 20.9 1.0
CB B:ASP167 4.1 21.6 1.0
O B:HOH2319 4.2 48.8 1.0
CG B:HIS165 4.2 19.2 1.0
O A:HOH2235 4.2 26.6 1.0
CB B:THR234 4.3 19.8 1.0
N B:THR234 4.4 20.1 1.0
CB A:ALA191 4.6 20.8 1.0
N B:ASP167 4.7 20.3 1.0
O B:GLY232 4.7 25.2 1.0
CA B:ASP167 4.9 21.7 1.0
CA B:THR234 5.0 19.5 1.0

Zinc binding site 6 out of 6 in 2xx0

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Zinc binding site 6 out of 6 in the Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes 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 N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1343

b:36.0
occ:0.50
 O B:HOH2324 1.9 36.7 0.5
O B:HOH2326 2.0 40.1 0.5
O B:HOH2327 2.0 36.1 0.5
O B:HOH2323 2.1 36.1 0.5
O B:HOH2325 2.1 38.9 0.5
NE2 B:HIS8 2.1 38.2 1.0
CE1 B:HIS8 3.0 38.1 1.0
CD2 B:HIS8 3.1 36.2 1.0
OD1 B:ASP4 3.8 50.1 0.5
O B:LEU6 4.1 35.1 1.0
ND1 B:HIS8 4.1 35.8 1.0
CA B:ASP4 4.1 47.0 0.5
O B:ASP4 4.1 46.9 0.8
CG B:HIS8 4.2 34.2 1.0
O B:ALA3 4.2 42.9 0.8
CA B:ASP4 4.2 46.9 0.5
C B:ASP4 4.4 46.5 0.8
O B:HOH2105 4.4 38.0 1.0
CG B:ASP4 4.7 48.9 0.5
CB B:ASP4 4.8 47.7 0.5
C B:ALA3 5.0 44.6 0.8

Reference:

N.G.H.Leferink, C.Han, S.V.Antonyuk, D.J.Heyes, S.E.J.Rigby, M.A.Hough, R.R.Eady, N.S.Scrutton, S.S.Hasnain. Proton-Coupled Electron Transfer in the Catalytic Cycle of Alcaligenes Xylosoxidans Copper-Dependent Nitrite Reductase. Biochemistry V. 50 4121 2011.
ISSN: ISSN 0006-2960
PubMed: 21469743
DOI: 10.1021/BI200246F
Page generated: Thu Oct 17 05:32:56 2024

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