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Copper in PDB 6qpv: Crystal Structure of As Isolated Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii

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

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

Protein crystallography data

The structure of Crystal Structure of As Isolated Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii, PDB code: 6qpv 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) 42.83 / 1.60
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 128.230, 128.230, 172.650, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 19.6

Other elements in 6qpv:

The structure of Crystal Structure of As Isolated 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 As Isolated Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii (pdb code 6qpv). 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 As Isolated Y323A Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii, PDB code: 6qpv:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 6qpv

Go back to Copper Binding Sites List in 6qpv
Copper binding site 1 out of 4 in the Crystal Structure of As Isolated 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 As Isolated 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:12.5
occ:1.00
ND1 A:HIS143 2.0 10.8 1.0
ND1 A:HIS94 2.1 12.3 1.0
SG A:CYS135 2.2 12.0 1.0
SD A:MET148 2.6 13.3 1.0
CE1 A:HIS143 2.9 13.6 1.0
CE1 A:HIS94 3.0 11.7 1.0
CG A:HIS143 3.1 11.9 1.0
CG A:HIS94 3.1 12.3 1.0
CB A:CYS135 3.2 10.3 1.0
CE A:MET148 3.4 12.3 1.0
CB A:HIS94 3.5 12.5 1.0
CB A:HIS143 3.5 10.8 1.0
CA A:HIS94 3.7 11.9 1.0
NE2 A:HIS143 4.1 12.1 1.0
O A:PRO93 4.1 12.2 1.0
CD2 A:HIS143 4.1 12.2 1.0
CG A:MET148 4.2 11.9 1.0
NE2 A:HIS94 4.2 12.4 1.0
CD2 A:HIS94 4.2 12.4 1.0
OG1 A:THR137 4.3 11.4 1.0
CB A:THR137 4.3 11.9 1.0
CA A:CYS135 4.6 10.9 1.0
CE3 A:TRP61 4.6 12.4 1.0
N A:ASN95 4.6 11.7 1.0
CA A:HIS143 4.6 10.8 1.0
CB A:MET148 4.6 12.3 1.0
C A:HIS94 4.7 12.8 1.0
N A:HIS94 4.7 12.8 1.0
C A:PRO93 4.8 12.3 1.0

Copper binding site 2 out of 4 in 6qpv

Go back to Copper Binding Sites List in 6qpv
Copper binding site 2 out of 4 in the Crystal Structure of As Isolated 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 As Isolated 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:12.7
occ:1.00
O A:HOH707 1.9 17.4 1.0
NE2 A:HIS134 2.0 10.7 1.0
NE2 A:HIS99 2.0 10.9 1.0
CD2 A:HIS134 2.9 10.4 1.0
CE1 A:HIS99 3.0 10.8 1.0
CD2 A:HIS99 3.1 10.6 1.0
CE1 A:HIS134 3.1 10.9 1.0
OD2 A:ASP97 3.8 21.8 1.0
ND1 A:HIS99 4.1 10.5 1.0
CG A:HIS134 4.1 10.8 1.0
ND1 A:HIS134 4.2 11.9 1.0
CG A:HIS99 4.2 10.7 1.0
CG A:ASP97 4.3 19.2 1.0
OD1 A:ASP97 4.5 22.2 1.0
O A:HOH781 4.6 39.3 1.0

Copper binding site 3 out of 4 in 6qpv

Go back to Copper Binding Sites List in 6qpv
Copper binding site 3 out of 4 in the Crystal Structure of As Isolated 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 As Isolated 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:12.1
occ:1.00
ND1 I:HIS143 2.0 10.3 1.0
ND1 I:HIS94 2.1 12.0 1.0
SG I:CYS135 2.2 12.2 1.0
SD I:MET148 2.6 12.9 1.0
CE1 I:HIS143 2.9 11.2 1.0
CE1 I:HIS94 3.1 12.6 1.0
CG I:HIS143 3.1 11.2 1.0
CG I:HIS94 3.1 12.5 1.0
CB I:CYS135 3.2 11.6 1.0
CE I:MET148 3.4 12.9 1.0
CB I:HIS94 3.5 11.7 1.0
CB I:HIS143 3.5 10.9 1.0
CA I:HIS94 3.7 11.7 1.0
O I:PRO93 4.0 12.5 1.0
NE2 I:HIS143 4.1 10.6 1.0
CD2 I:HIS143 4.1 11.1 1.0
CG I:MET148 4.2 12.0 1.0
NE2 I:HIS94 4.2 12.2 1.0
CD2 I:HIS94 4.2 11.7 1.0
OG1 I:THR137 4.3 12.1 1.0
CB I:THR137 4.4 12.1 1.0
CA I:HIS143 4.6 11.0 1.0
N I:ASN95 4.6 11.6 1.0
CE3 I:TRP61 4.6 11.5 1.0
CA I:CYS135 4.6 11.0 1.0
CB I:MET148 4.6 11.4 1.0
C I:HIS94 4.7 12.3 1.0
N I:HIS94 4.7 11.8 1.0
C I:PRO93 4.8 11.9 1.0

Copper binding site 4 out of 4 in 6qpv

Go back to Copper Binding Sites List in 6qpv
Copper binding site 4 out of 4 in the Crystal Structure of As Isolated 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 As Isolated 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:12.9
occ:1.00
NE2 I:HIS99 2.0 11.1 1.0
NE2 I:HIS134 2.0 10.3 1.0
O I:HOH669 2.0 18.9 1.0
CD2 I:HIS134 2.9 10.2 1.0
CE1 I:HIS99 2.9 11.3 1.0
CD2 I:HIS99 3.0 11.6 1.0
CE1 I:HIS134 3.0 10.9 1.0
OD2 I:ASP97 3.8 20.0 1.0
ND1 I:HIS99 4.1 11.1 1.0
CG I:HIS134 4.1 9.8 1.0
ND1 I:HIS134 4.1 10.7 1.0
CG I:HIS99 4.1 11.8 1.0
CG I:ASP97 4.4 18.9 1.0
OD1 I:ASP97 4.6 20.6 1.0
O I:HOH771 4.7 41.1 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: Wed Jul 31 06:47:35 2024

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