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Copper in PDB 6qpz: Crystal Structure of As Isolated Y323E Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii

Enzymatic activity of Crystal Structure of As Isolated Y323E Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii

All present enzymatic activity of Crystal Structure of As Isolated Y323E 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 Y323E Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii, PDB code: 6qpz 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) 42.73 / 1.65
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 127.550, 127.550, 172.680, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 17.8

Other elements in 6qpz:

The structure of Crystal Structure of As Isolated Y323E 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 Y323E Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii (pdb code 6qpz). 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 Y323E Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii, PDB code: 6qpz:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 6qpz

Go back to Copper Binding Sites List in 6qpz
Copper binding site 1 out of 4 in the Crystal Structure of As Isolated Y323E 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 Y323E Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:18.9
occ:1.00
ND1 A:HIS143 2.0 19.5 1.0
ND1 A:HIS94 2.1 18.3 1.0
SG A:CYS135 2.2 19.0 1.0
SD A:MET148 2.6 18.5 1.0
CE1 A:HIS143 3.0 19.5 1.0
CE1 A:HIS94 3.0 18.4 1.0
CG A:HIS143 3.1 19.2 1.0
CB A:CYS135 3.1 18.3 1.0
CG A:HIS94 3.1 19.1 1.0
CE A:MET148 3.4 18.4 1.0
CB A:HIS143 3.5 18.8 1.0
CB A:HIS94 3.5 19.0 1.0
CA A:HIS94 3.7 19.1 1.0
O A:PRO93 4.1 17.8 1.0
NE2 A:HIS143 4.1 19.7 1.0
CD2 A:HIS143 4.1 19.5 1.0
CG A:MET148 4.2 18.0 1.0
NE2 A:HIS94 4.2 19.2 1.0
CD2 A:HIS94 4.2 19.1 1.0
CB A:THR137 4.3 20.3 1.0
OG1 A:THR137 4.3 19.9 1.0
CE3 A:TRP61 4.5 19.7 1.0
CA A:CYS135 4.5 18.2 1.0
N A:ASN95 4.6 19.1 1.0
CA A:HIS143 4.6 18.5 1.0
CB A:MET148 4.7 17.7 1.0
C A:HIS94 4.7 19.5 1.0
N A:HIS94 4.7 19.2 1.0
C A:PRO93 4.8 19.1 1.0
CZ3 A:TRP61 5.0 19.4 1.0

Copper binding site 2 out of 4 in 6qpz

Go back to Copper Binding Sites List in 6qpz
Copper binding site 2 out of 4 in the Crystal Structure of As Isolated Y323E 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 Y323E Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:20.4
occ:1.00
O A:HOH626 2.0 18.1 0.8
NE2 A:HIS134 2.0 18.5 1.0
NE2 A:HIS99 2.0 18.8 1.0
O A:HOH626 2.2 17.5 0.2
CD2 A:HIS134 2.9 18.6 1.0
CE1 A:HIS99 3.0 18.5 1.0
CD2 A:HIS99 3.1 18.5 1.0
CE1 A:HIS134 3.1 18.1 1.0
OD2 A:ASP97 3.8 25.5 1.0
CG A:HIS134 4.1 18.0 1.0
ND1 A:HIS99 4.1 18.6 1.0
ND1 A:HIS134 4.2 18.6 1.0
CG A:HIS99 4.2 18.2 1.0
CG A:ASP97 4.3 24.0 1.0
OD1 A:ASP97 4.6 26.6 1.0
O A:HOH773 4.7 51.2 1.0
O A:HOH807 5.0 19.9 0.5

Copper binding site 3 out of 4 in 6qpz

Go back to Copper Binding Sites List in 6qpz
Copper binding site 3 out of 4 in the Crystal Structure of As Isolated Y323E 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 Y323E Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu501

b:12.9
occ:1.00
ND1 I:HIS94 2.0 12.0 1.0
ND1 I:HIS143 2.1 11.5 1.0
SG I:CYS135 2.2 13.4 1.0
SD I:MET148 2.6 12.4 1.0
CE1 I:HIS94 2.9 12.1 1.0
CE1 I:HIS143 3.0 11.2 1.0
CG I:HIS143 3.1 11.2 1.0
CG I:HIS94 3.1 12.4 1.0
CB I:CYS135 3.2 12.2 1.0
CE I:MET148 3.5 12.5 1.0
CB I:HIS143 3.5 11.4 1.0
CB I:HIS94 3.5 12.3 1.0
CA I:HIS94 3.7 12.1 1.0
O I:PRO93 4.0 12.2 1.0
NE2 I:HIS94 4.1 12.5 1.0
NE2 I:HIS143 4.1 11.4 1.0
CD2 I:HIS143 4.1 11.3 1.0
CG I:MET148 4.2 11.6 1.0
CD2 I:HIS94 4.2 12.4 1.0
CB I:THR137 4.3 13.6 1.0
OG1 I:THR137 4.3 14.0 1.0
CE3 I:TRP61 4.5 12.7 1.0
CA I:HIS143 4.6 11.4 1.0
N I:ASN95 4.6 11.7 1.0
CA I:CYS135 4.6 12.0 1.0
CB I:MET148 4.7 11.3 1.0
C I:HIS94 4.7 12.2 1.0
N I:HIS94 4.8 12.5 1.0
C I:PRO93 4.8 12.6 1.0

Copper binding site 4 out of 4 in 6qpz

Go back to Copper Binding Sites List in 6qpz
Copper binding site 4 out of 4 in the Crystal Structure of As Isolated Y323E 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 Y323E Mutant of Haem-Cu Containing Nitrite Reductase From Ralstonia Pickettii within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu502

b:13.7
occ:1.00
O I:HOH675 1.7 8.6 0.5
NE2 I:HIS99 2.0 12.6 1.0
NE2 I:HIS134 2.0 12.0 1.0
O I:HOH675 2.2 14.5 0.5
CD2 I:HIS134 2.9 11.8 1.0
CE1 I:HIS99 3.0 12.4 1.0
CD2 I:HIS99 3.1 12.4 1.0
CE1 I:HIS134 3.1 12.0 1.0
OD2 I:ASP97 3.8 20.0 1.0
CG I:HIS134 4.1 11.6 1.0
ND1 I:HIS99 4.1 12.3 1.0
ND1 I:HIS134 4.2 11.9 1.0
CG I:HIS99 4.2 12.3 1.0
CG I:ASP97 4.4 17.5 1.0
OD1 I:ASP97 4.6 20.2 1.0
O I:HOH718 4.6 37.9 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: Wed Jul 31 06:48:32 2024

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