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Copper in PDB 1mzy: Crystal Structure of Nitrite Reductase

Enzymatic activity of Crystal Structure of Nitrite Reductase

All present enzymatic activity of Crystal Structure of Nitrite Reductase:
1.7.99.3;

Protein crystallography data

The structure of Crystal Structure of Nitrite Reductase, PDB code: 1mzy was solved by H.Guo, K.Olesen, Y.Xue, J.Shapliegh, L.Sjolin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.54 / 1.46
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 71.392, 71.392, 146.246, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 21

Other elements in 1mzy:

The structure of Crystal Structure of Nitrite Reductase also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Nitrite Reductase (pdb code 1mzy). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of Nitrite Reductase, PDB code: 1mzy:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 1mzy

Go back to Copper Binding Sites List in 1mzy
Copper binding site 1 out of 2 in the Crystal Structure of Nitrite Reductase


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 Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:13.2
occ:1.00
ND1 A:HIS126 2.1 7.0 1.0
ND1 A:HIS177 2.2 9.0 1.0
SG A:CYS167 2.2 10.9 1.0
SD A:MET182 2.4 1.0 0.0
CE1 A:HIS126 3.0 9.1 1.0
CE1 A:HIS177 3.1 10.3 1.0
CG A:HIS126 3.1 7.5 1.0
CB A:CYS167 3.2 6.9 1.0
CG A:HIS177 3.2 9.8 1.0
CE A:MET182 3.4 1.0 0.0
CE A:MET182 3.4 1.0 0.0
CB A:HIS126 3.5 6.7 1.0
CB A:HIS177 3.5 8.1 1.0
CG A:MET182 3.7 2.0 0.0
CA A:HIS126 3.8 7.7 1.0
CG A:MET182 3.9 2.1 0.0
O A:PRO125 4.1 8.6 1.0
NE2 A:HIS126 4.2 8.0 1.0
NE2 A:HIS177 4.2 9.3 1.0
CB A:MET182 4.3 2.9 0.0
CD2 A:HIS126 4.3 7.5 1.0
CG A:PRO169 4.3 9.5 1.0
CB A:MET182 4.3 2.9 0.0
SD A:MET182 4.3 1.0 0.0
CD2 A:HIS177 4.3 9.9 1.0
CA A:CYS167 4.6 6.3 1.0
CE A:MET93 4.6 3.7 1.0
N A:ASN127 4.7 6.4 1.0
CA A:HIS177 4.8 7.8 1.0
CD A:PRO169 4.8 9.7 1.0
C A:HIS126 4.8 7.5 1.0
N A:HIS126 4.9 7.4 1.0
C A:PRO125 4.9 8.9 1.0

Copper binding site 2 out of 2 in 1mzy

Go back to Copper Binding Sites List in 1mzy
Copper binding site 2 out of 2 in the Crystal Structure of Nitrite Reductase


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 Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:6.8
occ:1.00
NE2 A:HIS131 2.0 5.6 1.0
NE2 A:HIS166 2.0 7.4 1.0
O A:HOH689 2.1 13.0 1.0
CE1 A:HIS131 2.9 4.0 1.0
CD2 A:HIS166 3.0 7.0 1.0
CE1 A:HIS166 3.1 7.3 1.0
CD2 A:HIS131 3.1 4.1 1.0
OD2 A:ASP129 3.8 9.9 1.0
ND1 A:HIS131 4.1 5.2 1.0
O A:HOH703 4.1 22.2 1.0
CG A:HIS166 4.1 6.5 1.0
ND1 A:HIS166 4.2 6.5 1.0
CG A:HIS131 4.2 4.2 1.0
CG A:ASP129 4.4 8.3 1.0
OD1 A:ASP129 4.7 9.7 1.0

Reference:

H.Guo, K.Olesen, Y.Xue, J.Shapliegh, L.Sjolin. The High Resolution Crystal Structures of Nitrite Reductase and Its Mutant MET182THR From Rhodobacter Sphaeroides Reveal A Gating Mechanism For the Electron Transfer to the Type 1 Copper Center To Be Published.
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