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Copper in PDB 1mzz: Crystal Structure of Mutant (M182T)of Nitrite Reductase

Enzymatic activity of Crystal Structure of Mutant (M182T)of Nitrite Reductase

All present enzymatic activity of Crystal Structure of Mutant (M182T)of Nitrite Reductase:
1.7.99.3;

Protein crystallography data

The structure of Crystal Structure of Mutant (M182T)of Nitrite Reductase, PDB code: 1mzz 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) 30.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.495, 123.729, 130.173, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.8

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Mutant (M182T)of Nitrite Reductase (pdb code 1mzz). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structure of Mutant (M182T)of Nitrite Reductase, PDB code: 1mzz:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1mzz

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Copper binding site 1 out of 6 in the Crystal Structure of Mutant (M182T)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 Mutant (M182T)of Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:65.3
occ:1.00
SG A:CYS167 2.4 37.0 1.0
ND1 A:HIS177 2.4 20.9 1.0
ND1 A:HIS126 2.6 20.0 1.0
CB A:CYS167 3.1 25.4 1.0
CE1 A:HIS177 3.3 21.1 1.0
CG A:HIS177 3.4 21.2 1.0
CE1 A:HIS126 3.4 20.4 1.0
OG1 A:THR182 3.5 23.7 1.0
CB A:HIS177 3.5 21.2 1.0
CG A:HIS126 3.6 20.3 1.0
CB A:HIS126 3.8 19.9 1.0
CG A:PRO169 4.0 29.6 1.0
CA A:HIS126 4.1 20.7 1.0
CG2 A:THR182 4.1 20.4 1.0
CB A:THR182 4.1 18.4 1.0
SD A:MET93 4.4 34.3 1.0
O A:PRO125 4.4 23.6 1.0
NE2 A:HIS177 4.5 23.3 1.0
CD2 A:HIS177 4.5 22.3 1.0
CA A:CYS167 4.5 22.6 1.0
NE2 A:HIS126 4.6 19.4 1.0
CA A:HIS177 4.7 18.5 1.0
CD2 A:HIS126 4.7 20.1 1.0
CD A:PRO169 4.7 28.7 1.0
N A:ASN127 4.9 19.7 1.0
CB A:MET93 4.9 24.8 1.0

Copper binding site 2 out of 6 in 1mzz

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Copper binding site 2 out of 6 in the Crystal Structure of Mutant (M182T)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 Mutant (M182T)of Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:20.6
occ:1.00
O A:HOH3541 1.8 26.1 1.0
NE2 B:HIS1338 2.0 16.0 1.0
NE2 A:HIS131 2.0 17.0 1.0
NE2 A:HIS166 2.1 16.7 1.0
CE1 A:HIS131 3.0 16.0 1.0
CE1 B:HIS1338 3.0 14.9 1.0
CE1 A:HIS166 3.0 17.6 1.0
CD2 B:HIS1338 3.0 16.1 1.0
CD2 A:HIS166 3.1 18.8 1.0
CD2 A:HIS131 3.1 14.8 1.0
OD2 A:ASP129 3.5 25.1 1.0
NE2 B:HIS1287 3.8 22.9 1.0
CD2 B:HIS1287 3.9 23.9 1.0
ND1 B:HIS1338 4.1 14.0 1.0
ND1 A:HIS131 4.1 14.0 1.0
ND1 A:HIS166 4.2 18.6 1.0
CG B:HIS1338 4.2 16.1 1.0
CG A:HIS131 4.2 14.9 1.0
CG A:HIS166 4.3 17.9 1.0
CG A:ASP129 4.3 22.8 1.0
CE1 B:HIS1287 4.5 23.2 1.0
OD1 A:ASP129 4.6 23.1 1.0
CG B:HIS1287 4.9 22.6 1.0

Copper binding site 3 out of 6 in 1mzz

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Copper binding site 3 out of 6 in the Crystal Structure of Mutant (M182T)of Nitrite Reductase


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 Mutant (M182T)of Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1401

b:71.7
occ:1.00
ND1 B:HIS1126 2.4 24.5 1.0
SG B:CYS1167 2.5 36.8 1.0
ND1 B:HIS1177 2.5 22.1 1.0
CE1 B:HIS1126 3.2 22.7 1.0
CB B:CYS1167 3.2 25.9 1.0
CE1 B:HIS1177 3.3 23.9 1.0
CG B:HIS1177 3.4 22.6 1.0
CG B:HIS1126 3.4 24.0 1.0
OG1 B:THR1182 3.6 24.5 1.0
CB B:HIS1177 3.7 21.1 1.0
CB B:HIS1126 3.8 22.8 1.0
CA B:HIS1126 3.9 23.3 1.0
CG B:PRO1169 4.0 31.5 1.0
O B:PRO1125 4.2 25.7 1.0
CB B:THR1182 4.3 20.3 1.0
CG2 B:THR1182 4.3 21.7 1.0
NE2 B:HIS1126 4.4 22.3 1.0
NE2 B:HIS1177 4.4 23.4 1.0
CD2 B:HIS1177 4.5 23.5 1.0
CD2 B:HIS1126 4.5 23.6 1.0
SD B:MET1093 4.6 36.3 1.0
CD B:PRO1169 4.6 29.8 1.0
CA B:CYS1167 4.6 25.1 1.0
CA B:HIS1177 4.7 19.8 1.0
CB B:MET1093 4.8 26.7 1.0
N B:ASN1127 5.0 21.7 1.0

Copper binding site 4 out of 6 in 1mzz

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Copper binding site 4 out of 6 in the Crystal Structure of Mutant (M182T)of Nitrite Reductase


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 Mutant (M182T)of Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1402

b:21.1
occ:1.00
O B:HOH3542 1.9 40.5 1.0
NE2 B:HIS1131 2.0 14.5 1.0
NE2 C:HIS2338 2.0 15.8 1.0
NE2 B:HIS1166 2.0 16.0 1.0
CE1 C:HIS2338 2.9 16.1 1.0
CE1 B:HIS1131 2.9 14.9 1.0
CD2 B:HIS1166 3.0 16.2 1.0
CD2 C:HIS2338 3.0 17.2 1.0
CD2 B:HIS1131 3.1 14.3 1.0
CE1 B:HIS1166 3.1 16.1 1.0
OD2 B:ASP1129 3.7 25.8 1.0
NE2 C:HIS2287 3.8 22.9 1.0
CD2 C:HIS2287 4.1 23.0 1.0
ND1 B:HIS1131 4.1 13.8 1.0
ND1 C:HIS2338 4.1 15.8 1.0
CG B:HIS1131 4.2 15.1 1.0
CG C:HIS2338 4.2 15.4 1.0
CG B:HIS1166 4.2 17.9 1.0
ND1 B:HIS1166 4.2 17.2 1.0
CG B:ASP1129 4.4 23.8 1.0
CE1 C:HIS2287 4.5 22.5 1.0
OD1 B:ASP1129 4.7 22.5 1.0
O B:HOH3130 5.0 20.3 1.0
CG C:HIS2287 5.0 21.9 1.0

Copper binding site 5 out of 6 in 1mzz

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Copper binding site 5 out of 6 in the Crystal Structure of Mutant (M182T)of Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Mutant (M182T)of Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu2401

b:63.9
occ:1.00
SG C:CYS2167 2.4 38.6 1.0
ND1 C:HIS2177 2.4 22.1 1.0
ND1 C:HIS2126 2.6 20.3 1.0
CB C:CYS2167 3.2 25.8 1.0
CE1 C:HIS2177 3.3 23.1 1.0
CG C:HIS2177 3.3 21.6 1.0
CE1 C:HIS2126 3.3 20.4 1.0
OG1 C:THR2182 3.4 20.8 1.0
CB C:HIS2177 3.6 19.3 1.0
CG C:HIS2126 3.6 20.4 1.0
CB C:HIS2126 3.9 20.5 1.0
CG C:PRO2169 4.0 30.4 1.0
CA C:HIS2126 4.1 21.2 1.0
SD C:MET2093 4.2 24.7 1.0
CG2 C:THR2182 4.2 20.5 1.0
CB C:THR2182 4.2 16.6 1.0
NE2 C:HIS2177 4.4 24.0 1.0
CD2 C:HIS2177 4.4 23.3 1.0
CA C:CYS2167 4.5 25.4 1.0
O C:PRO2125 4.5 24.6 1.0
NE2 C:HIS2126 4.5 19.7 1.0
CB C:MET2093 4.6 23.5 1.0
CA C:HIS2177 4.7 17.8 1.0
CD2 C:HIS2126 4.7 20.0 1.0
CD C:PRO2169 4.7 29.2 1.0
N C:ASN2127 4.9 20.9 1.0

Copper binding site 6 out of 6 in 1mzz

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Copper binding site 6 out of 6 in the Crystal Structure of Mutant (M182T)of Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Mutant (M182T)of Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu2402

b:20.8
occ:1.00
O C:HOH3543 1.8 34.9 1.0
NE2 C:HIS2166 2.0 14.8 1.0
NE2 A:HIS338 2.1 12.9 1.0
NE2 C:HIS2131 2.1 13.5 1.0
CE1 A:HIS338 3.0 14.9 1.0
CE1 C:HIS2131 3.0 15.3 1.0
CD2 C:HIS2166 3.0 15.9 1.0
CD2 A:HIS338 3.1 13.6 1.0
CE1 C:HIS2166 3.1 16.8 1.0
CD2 C:HIS2131 3.2 14.6 1.0
OD2 C:ASP2129 3.6 25.5 1.0
NE2 A:HIS287 3.9 25.2 1.0
ND1 C:HIS2131 4.1 14.3 1.0
CD2 A:HIS287 4.2 24.9 1.0
ND1 A:HIS338 4.2 12.9 1.0
CG C:HIS2166 4.2 16.6 1.0
CG A:HIS338 4.2 14.4 1.0
ND1 C:HIS2166 4.3 16.2 1.0
CG C:HIS2131 4.3 14.4 1.0
CG C:ASP2129 4.3 23.9 1.0
CE1 A:HIS287 4.5 23.7 1.0
OD1 C:ASP2129 4.7 25.6 1.0
CG A:HIS287 4.9 23.5 1.0
O C:HOH3173 5.0 21.3 1.0
CD1 A:ILE289 5.0 20.6 1.0
ND1 A:HIS287 5.0 24.4 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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