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Copper 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:

Zinc (Zn) 6 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 4 binding sites of Copper where determined in the Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2xx0:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 2xx0

Go back to Copper Binding Sites List in 2xx0
Copper binding site 1 out of 4 in the Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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:Cu1337

b:20.1
occ:1.00
 ND1 A:HIS89 2.0 17.2 1.0
ND1 A:HIS139 2.0 16.4 1.0
SG A:CYS130 2.2 18.9 1.0
SD A:MET144 2.6 19.7 1.0
CE1 A:HIS89 2.9 17.6 1.0
CE1 A:HIS139 3.0 18.6 1.0
CG A:HIS139 3.1 15.8 1.0
CG A:HIS89 3.1 17.9 1.0
CB A:CYS130 3.2 16.4 1.0
CB A:HIS139 3.5 14.9 1.0
CE A:MET144 3.5 20.7 1.0
CB A:HIS89 3.5 18.4 1.0
CA A:HIS89 3.8 18.6 1.0
O A:PRO88 4.1 21.6 1.0
NE2 A:HIS89 4.1 17.9 1.0
CG A:MET144 4.1 18.0 1.0
NE2 A:HIS139 4.1 16.9 1.0
CG A:PRO132 4.2 21.5 1.0
CD2 A:HIS139 4.2 19.1 1.0
CD2 A:HIS89 4.2 19.3 1.0
CD A:PRO132 4.4 18.6 1.0
SD A:MET56 4.5 20.6 1.0
CA A:CYS130 4.6 15.8 1.0
CB A:MET144 4.6 15.3 1.0
N A:SER90 4.7 19.8 1.0
CA A:HIS139 4.7 14.3 1.0
N A:HIS89 4.8 19.0 1.0
C A:HIS89 4.8 19.7 1.0
C A:PRO88 4.9 20.6 1.0

Copper binding site 2 out of 4 in 2xx0

Go back to Copper Binding Sites List in 2xx0
Copper binding site 2 out of 4 in the Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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:Cu1339

b:14.6
occ:0.20
 ZN A:ZN1338 0.2 13.3 0.8
O A:HOH2358 1.7 18.6 1.0
NE2 A:HIS129 2.0 13.4 1.0
NE2 A:HIS94 2.1 12.8 1.0
CE1 A:HIS129 3.0 14.2 1.0
CD2 A:HIS129 3.0 11.8 1.0
CD2 A:HIS94 3.1 15.2 1.0
CE1 A:HIS94 3.1 12.1 1.0
OD2 A:ASP92 3.4 17.6 0.8
O A:HOH2181 3.9 34.7 0.5
CG A:ASP92 4.1 16.5 0.8
ND1 A:HIS129 4.2 13.0 1.0
CG A:HIS129 4.2 11.7 1.0
ND1 A:HIS94 4.2 12.8 1.0
CG A:HIS94 4.2 12.3 1.0
OD1 A:ASP92 4.4 18.6 0.8
O A:HOH2141 5.0 18.3 0.7

Copper binding site 3 out of 4 in 2xx0

Go back to Copper Binding Sites List in 2xx0
Copper binding site 3 out of 4 in the Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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
B:Cu1337

b:23.2
occ:1.00
 ND1 B:HIS139 2.0 19.5 1.0
ND1 B:HIS89 2.1 20.5 1.0
SG B:CYS130 2.2 21.6 1.0
SD B:MET144 2.6 22.6 1.0
CE1 B:HIS139 2.9 21.1 1.0
CE1 B:HIS89 3.0 21.3 1.0
CG B:HIS139 3.1 19.4 1.0
CG B:HIS89 3.1 21.7 1.0
CB B:CYS130 3.2 19.0 1.0
CB B:HIS139 3.5 17.0 1.0
CB B:HIS89 3.5 21.3 1.0
CE B:MET144 3.5 21.7 1.0
CA B:HIS89 3.8 21.5 1.0
CG B:PRO132 4.0 23.8 1.0
NE2 B:HIS139 4.1 20.3 1.0
CG B:MET144 4.1 19.5 1.0
CD2 B:HIS139 4.1 21.0 1.0
O B:PRO88 4.1 23.5 1.0
NE2 B:HIS89 4.2 20.8 1.0
CD2 B:HIS89 4.2 21.8 1.0
CD B:PRO132 4.4 22.2 1.0
SD B:MET56 4.4 23.9 1.0
CA B:CYS130 4.6 18.5 1.0
CB B:MET144 4.6 17.3 1.0
N B:SER90 4.7 22.9 1.0
CA B:HIS139 4.7 16.6 1.0
N B:HIS89 4.8 22.0 1.0
C B:HIS89 4.8 22.2 1.0
C B:PRO88 4.9 22.8 1.0

Copper binding site 4 out of 4 in 2xx0

Go back to Copper Binding Sites List in 2xx0
Copper binding site 4 out of 4 in the Structure of the N90S-H254F Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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:Cu1338

b:17.2
occ:0.20
 ZN B:ZN1339 0.2 14.7 0.8
O B:HOH2317 2.0 20.3 1.0
NE2 B:HIS94 2.0 14.8 1.0
NE2 B:HIS129 2.1 14.2 1.0
CE1 B:HIS94 2.9 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 3.2 16.1 1.0
OD2 B:ASP92 3.8 24.9 1.0
ND1 B:HIS94 4.1 15.5 1.0
CG B:HIS129 4.2 15.4 1.0
ND1 B:HIS129 4.2 14.8 1.0
CG B:HIS94 4.2 15.1 1.0
CG B:ASP92 4.5 22.9 1.0
OD1 B:ASP92 4.7 23.4 1.0

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: Wed Jul 31 00:17:32 2024

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