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Copper in PDB 6qpx: Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii

Enzymatic activity of Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii

All present enzymatic activity of Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii, PDB code: 6qpx was solved by S.V.Antonyuk, R.T.Shenoy, T.M.Hedison, R.R.Eady, S.S.Hasnain, N.S.Scrutton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.33 / 1.70
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 128.500, 128.500, 172.470, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 20.3

Other elements in 6qpx:

The structure of Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii (pdb code 6qpx). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii, PDB code: 6qpx:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 6qpx

Go back to Copper Binding Sites List in 6qpx
Copper binding site 1 out of 4 in the Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:14.5
occ:1.00
ND1 A:HIS143 2.0 14.1 1.0
ND1 A:HIS94 2.1 12.9 1.0
SG A:CYS135 2.2 15.3 1.0
SD A:MET148 2.6 15.8 1.0
CE1 A:HIS143 2.9 15.0 1.0
CE1 A:HIS94 3.0 13.0 1.0
CG A:HIS143 3.1 14.3 1.0
CG A:HIS94 3.1 13.3 1.0
CB A:CYS135 3.2 14.3 1.0
CE A:MET148 3.4 16.2 1.0
CB A:HIS94 3.5 13.7 1.0
CB A:HIS143 3.5 13.8 1.0
CA A:HIS94 3.7 14.0 1.0
O A:PRO93 4.1 14.8 1.0
NE2 A:HIS143 4.1 15.2 1.0
CD2 A:HIS143 4.1 14.9 1.0
NE2 A:HIS94 4.1 13.5 1.0
CG A:MET148 4.2 14.8 1.0
CD2 A:HIS94 4.2 13.7 1.0
OG1 A:THR137 4.2 16.0 1.0
CB A:THR137 4.3 16.4 1.0
N A:ASN95 4.6 14.6 1.0
CA A:HIS143 4.6 13.8 1.0
CA A:CYS135 4.6 14.3 1.0
CE3 A:TRP61 4.6 14.1 1.0
CB A:MET148 4.7 13.8 1.0
N A:HIS94 4.7 14.8 1.0
C A:HIS94 4.7 14.7 1.0
C A:PRO93 4.8 15.4 1.0

Copper binding site 2 out of 4 in 6qpx

Go back to Copper Binding Sites List in 6qpx
Copper binding site 2 out of 4 in the Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:18.4
occ:0.80
N A:NO2504 1.7 32.7 0.8
NE2 A:HIS134 2.0 13.7 1.0
NE2 A:HIS99 2.0 13.7 1.0
O1 A:NO2504 2.1 29.7 0.8
O2 A:NO2504 2.7 34.2 0.8
CD2 A:HIS134 2.9 13.9 1.0
CE1 A:HIS99 2.9 13.9 1.0
CD2 A:HIS99 3.1 14.0 1.0
CE1 A:HIS134 3.1 14.4 1.0
OD2 A:ASP97 4.0 28.7 1.0
CG A:HIS134 4.1 13.4 1.0
ND1 A:HIS99 4.1 13.8 1.0
ND1 A:HIS134 4.2 14.2 1.0
CG A:HIS99 4.2 13.9 1.0
CG A:ASP97 4.4 24.2 1.0
OD1 A:ASP97 4.6 27.5 1.0

Copper binding site 3 out of 4 in 6qpx

Go back to Copper Binding Sites List in 6qpx
Copper binding site 3 out of 4 in the Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu501

b:13.7
occ:1.00
ND1 I:HIS94 2.0 12.0 1.0
ND1 I:HIS143 2.1 13.2 1.0
SG I:CYS135 2.2 13.5 1.0
SD I:MET148 2.6 15.1 1.0
CE1 I:HIS143 3.0 13.5 1.0
CE1 I:HIS94 3.0 12.2 1.0
CG I:HIS94 3.1 12.5 1.0
CG I:HIS143 3.1 12.8 1.0
CB I:CYS135 3.2 12.9 1.0
CB I:HIS94 3.4 12.7 1.0
CE I:MET148 3.4 15.6 1.0
CB I:HIS143 3.5 12.8 1.0
CA I:HIS94 3.7 13.1 1.0
O I:PRO93 4.1 13.7 1.0
NE2 I:HIS143 4.1 13.7 1.0
NE2 I:HIS94 4.1 12.7 1.0
CD2 I:HIS143 4.2 13.7 1.0
CD2 I:HIS94 4.2 12.7 1.0
CG I:MET148 4.2 14.0 1.0
CB I:THR137 4.3 15.5 1.0
OG1 I:THR137 4.4 15.6 1.0
CE3 I:TRP61 4.5 14.7 1.0
CA I:HIS143 4.6 12.8 1.0
N I:ASN95 4.6 13.8 1.0
CA I:CYS135 4.6 12.7 1.0
CB I:MET148 4.7 12.9 1.0
N I:HIS94 4.7 13.7 1.0
C I:HIS94 4.7 13.6 1.0
C I:PRO93 4.8 14.4 1.0

Copper binding site 4 out of 4 in 6qpx

Go back to Copper Binding Sites List in 6qpx
Copper binding site 4 out of 4 in the Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Nitrite Bound Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu502

b:16.2
occ:0.75
N I:NO2504 1.9 28.4 0.8
O1 I:NO2504 1.9 25.1 0.8
NE2 I:HIS134 1.9 13.1 1.0
NE2 I:HIS99 2.0 14.8 1.0
CD2 I:HIS134 2.8 12.9 1.0
O2 I:NO2504 2.9 28.1 0.5
CE1 I:HIS99 3.0 15.3 1.0
CE1 I:HIS134 3.0 13.5 1.0
CD2 I:HIS99 3.1 14.8 1.0
OD2 I:ASP97 3.9 25.9 1.0
CG I:HIS134 4.0 12.2 1.0
ND1 I:HIS134 4.1 12.9 1.0
ND1 I:HIS99 4.1 14.6 1.0
CG I:HIS99 4.2 14.5 1.0
CG I:ASP97 4.5 22.5 1.0
OD1 I:ASP97 4.8 24.9 1.0

Reference:

T.M.Hedison, R.T.Shenoy, A.I.Iorgu, D.J.Heyes, K.Fisher, G.Wright, S.Hay, R.R.Eady, S.S.Hasnain, N.S.Scrutton. Unexpected Roles of A Tether Harboring A Tyrosine Gatekeeper Residue in Modular Nitrite Reductase Catalysis Acs Catalysis 2019.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.9B01266
Page generated: Sun Dec 13 11:24:59 2020

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