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Copper in PDB 3wia: Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase

Enzymatic activity of Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase

All present enzymatic activity of Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase, PDB code: 3wia was solved by Y.Fukuda, M.Nojiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.70 / 1.77
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.317, 164.991, 126.561, 90.00, 102.27, 90.00
R / Rfree (%) 17.1 / 19.2

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase (pdb code 3wia). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 18 binding sites of Copper where determined in the Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase, PDB code: 3wia:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 18 in 3wia

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Copper binding site 1 out of 18 in the Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper 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 the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:22.2
occ:1.00
 ND1 A:HIS95 2.1 21.1 1.0
ND1 A:HIS143 2.1 21.1 1.0
SG A:CYS135 2.1 21.4 1.0
SD A:MET148 2.6 23.1 1.0
CE1 A:HIS143 2.9 22.5 1.0
CE1 A:HIS95 3.0 21.8 1.0
CG A:HIS143 3.0 20.6 1.0
CG A:HIS95 3.1 21.9 1.0
CB A:CYS135 3.1 21.4 1.0
CB A:HIS95 3.4 21.4 1.0
CB A:HIS143 3.5 20.4 1.0
CE A:MET148 3.5 22.6 1.0
CA A:HIS95 3.7 22.1 1.0
NE2 A:HIS143 4.0 21.8 1.0
O A:PRO94 4.0 20.6 1.0
CD2 A:HIS143 4.1 22.9 1.0
NE2 A:HIS95 4.1 22.0 1.0
CG A:MET148 4.1 21.5 1.0
CD2 A:HIS95 4.2 20.7 1.0
CB A:THR137 4.3 21.4 1.0
OG1 A:THR137 4.3 22.3 1.0
N A:SER96 4.4 22.5 1.0
CA A:CYS135 4.5 21.1 1.0
CB A:MET148 4.5 20.5 1.0
CA A:HIS143 4.6 20.0 1.0
C A:HIS95 4.6 22.6 1.0
CE3 A:TRP63 4.6 22.1 1.0
N A:HIS95 4.7 21.6 1.0
C A:PRO94 4.8 22.1 1.0

Copper binding site 2 out of 18 in 3wia

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Copper binding site 2 out of 18 in the Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper 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 the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:23.7
occ:1.00
 NE2 A:HIS100 2.0 21.2 1.0
NE2 A:HIS134 2.0 20.5 1.0
NE2 B:HIS294 2.1 18.3 1.0
O B:HOH671 2.2 29.8 0.5
O2 B:FMT401 2.5 23.8 0.5
CE1 A:HIS100 3.0 20.9 1.0
CD2 B:HIS294 3.0 18.0 1.0
CD2 A:HIS134 3.0 20.2 1.0
CE1 A:HIS134 3.0 20.6 1.0
CD2 A:HIS100 3.1 20.3 1.0
CE1 B:HIS294 3.1 20.3 1.0
C B:FMT401 3.5 23.9 0.5
CD2 B:HIS244 3.9 21.6 1.0
NE2 B:HIS244 3.9 20.7 1.0
O1 B:FMT401 3.9 24.1 0.5
OD1 A:ASP98 4.0 26.7 1.0
ND1 A:HIS100 4.1 19.8 1.0
ND1 A:HIS134 4.1 20.6 1.0
CG A:HIS134 4.1 19.2 1.0
CG B:HIS294 4.1 17.2 1.0
ND1 B:HIS294 4.2 17.9 1.0
CG A:HIS100 4.2 20.2 1.0
CG A:ASP98 4.4 23.1 1.0
OD2 A:ASP98 4.4 23.4 1.0
O A:HOH512 4.8 24.0 1.0
CE1 B:HIS244 4.8 23.8 1.0
CE2 B:PHE296 4.8 21.8 1.0
CG B:HIS244 4.8 20.6 1.0

Copper binding site 3 out of 18 in 3wia

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Copper binding site 3 out of 18 in the Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper 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 the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:23.3
occ:1.00
 ND1 B:HIS143 2.0 18.4 1.0
ND1 B:HIS95 2.1 22.2 1.0
SG B:CYS135 2.2 21.4 1.0
SD B:MET148 2.6 23.8 1.0
CE1 B:HIS143 2.9 22.5 1.0
CE1 B:HIS95 3.0 24.5 1.0
CG B:HIS143 3.1 18.7 1.0
CG B:HIS95 3.1 23.8 1.0
CB B:CYS135 3.1 20.5 1.0
CE B:MET148 3.4 22.9 1.0
CB B:HIS95 3.4 22.6 1.0
CB B:HIS143 3.5 18.9 1.0
CA B:HIS95 3.7 22.9 1.0
NE2 B:HIS143 4.0 20.9 1.0
O B:PRO94 4.1 24.5 1.0
CG B:MET148 4.1 21.0 1.0
CD2 B:HIS143 4.1 20.9 1.0
NE2 B:HIS95 4.1 23.5 1.0
CD2 B:HIS95 4.2 22.0 1.0
CB B:THR137 4.3 22.6 1.0
OG1 B:THR137 4.4 21.4 1.0
N B:SER96 4.5 20.6 1.0
CB B:MET148 4.5 20.9 1.0
CA B:CYS135 4.6 21.1 1.0
CA B:HIS143 4.6 19.1 1.0
CE3 B:TRP63 4.6 24.0 1.0
C B:HIS95 4.7 22.4 1.0
N B:HIS95 4.8 23.9 1.0
C B:PRO94 4.8 24.9 1.0

Copper binding site 4 out of 18 in 3wia

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Copper binding site 4 out of 18 in the Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper 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 the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu403

b:22.7
occ:1.00
 O C:HOH675 1.9 22.8 0.5
NE2 C:HIS294 2.0 16.4 1.0
NE2 B:HIS100 2.0 18.5 1.0
NE2 B:HIS134 2.0 21.1 1.0
O2 C:FMT401 2.7 27.5 0.5
CD2 B:HIS134 2.9 21.7 1.0
CE1 B:HIS100 2.9 16.4 1.0
CE1 C:HIS294 2.9 18.0 1.0
CD2 C:HIS294 3.0 19.5 1.0
C C:FMT401 3.0 28.2 0.5
CE1 B:HIS134 3.1 21.3 1.0
CD2 B:HIS100 3.1 20.1 1.0
NE2 C:HIS244 3.9 20.6 1.0
CD2 C:HIS244 3.9 21.8 1.0
OD1 B:ASP98 3.9 26.5 1.0
ND1 C:HIS294 4.1 17.1 1.0
CG B:HIS134 4.1 21.9 1.0
ND1 B:HIS100 4.1 18.8 1.0
CG C:HIS294 4.1 17.6 1.0
ND1 B:HIS134 4.1 21.6 1.0
O1 C:FMT401 4.1 29.4 0.5
CG B:HIS100 4.2 17.8 1.0
CG B:ASP98 4.3 24.1 1.0
OD2 B:ASP98 4.4 23.4 1.0
CE1 C:HIS244 4.8 21.7 1.0
O B:HOH541 4.8 25.7 1.0
CG C:HIS244 4.8 19.8 1.0
CE2 C:PHE296 4.9 20.9 1.0

Copper binding site 5 out of 18 in 3wia

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Copper binding site 5 out of 18 in the Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper 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 the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu402

b:21.7
occ:1.00
 ND1 C:HIS143 2.0 19.0 1.0
ND1 C:HIS95 2.1 19.7 1.0
SG C:CYS135 2.2 21.3 1.0
SD C:MET148 2.5 21.5 1.0
CE1 C:HIS143 2.9 20.5 1.0
CG C:HIS95 3.0 22.6 1.0
CG C:HIS143 3.1 19.4 1.0
CE1 C:HIS95 3.1 23.1 1.0
CB C:CYS135 3.2 19.7 1.0
CE C:MET148 3.3 18.8 1.0
CB C:HIS95 3.3 20.7 1.0
CB C:HIS143 3.5 19.1 1.0
CA C:HIS95 3.7 21.8 1.0
NE2 C:HIS143 4.0 20.2 1.0
CD2 C:HIS143 4.1 19.8 1.0
CG C:MET148 4.1 19.5 1.0
O C:PRO94 4.1 22.1 1.0
NE2 C:HIS95 4.2 23.4 1.0
CD2 C:HIS95 4.2 23.1 1.0
CB C:THR137 4.3 20.4 1.0
OG1 C:THR137 4.3 21.0 1.0
N C:SER96 4.4 20.0 1.0
CB C:MET148 4.6 18.6 1.0
CA C:CYS135 4.6 19.8 1.0
CA C:HIS143 4.6 19.6 1.0
C C:HIS95 4.6 21.4 1.0
CE3 C:TRP63 4.7 19.9 1.0
N C:HIS95 4.7 20.8 1.0
C C:PRO94 4.9 22.0 1.0

Copper binding site 6 out of 18 in 3wia

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Copper binding site 6 out of 18 in the Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper 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 the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu403

b:22.4
occ:1.00
 NE2 C:HIS100 1.9 16.3 1.0
NE2 C:HIS134 2.0 19.8 1.0
O A:HOH690 2.1 16.1 0.5
NE2 A:HIS294 2.1 18.5 1.0
O2 A:FMT404 2.5 24.8 0.5
CE1 C:HIS100 2.8 18.8 1.0
C A:FMT404 2.8 25.8 0.5
CD2 C:HIS134 2.9 19.2 1.0
CE1 C:HIS134 3.0 18.5 1.0
CD2 C:HIS100 3.0 19.9 1.0
CD2 A:HIS294 3.0 16.3 1.0
CE1 A:HIS294 3.1 19.4 1.0
NE2 A:HIS244 3.8 20.1 1.0
CD2 A:HIS244 3.9 22.0 1.0
O1 A:FMT404 4.0 26.2 0.5
ND1 C:HIS100 4.0 18.0 1.0
CG C:HIS100 4.1 18.3 1.0
ND1 C:HIS134 4.1 19.1 1.0
CG C:HIS134 4.1 18.0 1.0
OD1 C:ASP98 4.1 25.7 1.0
ND1 A:HIS294 4.2 19.6 1.0
CG A:HIS294 4.2 18.2 1.0
CG C:ASP98 4.3 23.2 1.0
OD2 C:ASP98 4.3 23.9 1.0
CE1 A:HIS244 4.7 20.9 1.0
O C:HOH501 4.7 24.5 1.0
CG A:HIS244 4.8 19.8 1.0
CE2 A:PHE296 4.9 17.9 1.0

Copper binding site 7 out of 18 in 3wia

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Copper binding site 7 out of 18 in the Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu401

b:21.9
occ:1.00
 ND1 D:HIS143 1.9 17.4 1.0
ND1 D:HIS95 2.1 22.5 1.0
SG D:CYS135 2.2 21.4 1.0
SD D:MET148 2.6 21.5 1.0
CE1 D:HIS143 2.8 20.4 1.0
CG D:HIS143 3.0 19.0 1.0
CE1 D:HIS95 3.1 23.2 1.0
CG D:HIS95 3.1 21.6 1.0
CB D:CYS135 3.2 19.7 1.0
CB D:HIS95 3.4 21.9 1.0
CE D:MET148 3.5 20.0 1.0
CB D:HIS143 3.5 19.1 1.0
CA D:HIS95 3.7 21.9 1.0
NE2 D:HIS143 3.9 17.7 1.0
CD2 D:HIS143 4.0 18.5 1.0
O D:PRO94 4.1 22.0 1.0
CG D:MET148 4.1 19.3 1.0
NE2 D:HIS95 4.2 23.2 1.0
CD2 D:HIS95 4.2 21.6 1.0
CB D:THR137 4.3 19.9 1.0
OG1 D:THR137 4.4 21.5 1.0
N D:SER96 4.4 20.8 1.0
CB D:MET148 4.6 18.4 1.0
CA D:CYS135 4.6 19.9 1.0
CA D:HIS143 4.6 19.1 1.0
C D:HIS95 4.6 22.1 1.0
CE3 D:TRP63 4.7 20.5 1.0
N D:HIS95 4.7 21.9 1.0
C D:PRO94 4.8 21.9 1.0

Copper binding site 8 out of 18 in 3wia

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Copper binding site 8 out of 18 in the Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu402

b:22.7
occ:1.00
 O D:HOH663 2.0 20.3 0.5
NE2 D:HIS100 2.0 17.0 1.0
NE2 D:HIS134 2.0 19.7 1.0
NE2 E:HIS294 2.1 20.6 1.0
O2 D:FMT404 2.3 26.5 0.5
C D:FMT404 2.8 27.0 0.5
CD2 E:HIS294 3.0 18.9 1.0
CE1 D:HIS100 3.0 18.7 1.0
CD2 D:HIS134 3.0 18.7 1.0
CD2 D:HIS100 3.0 17.9 1.0
CE1 D:HIS134 3.0 20.6 1.0
CE1 E:HIS294 3.1 19.3 1.0
O1 D:FMT404 3.8 26.4 0.5
NE2 E:HIS244 3.8 20.5 1.0
CD2 E:HIS244 3.9 17.9 1.0
OD1 D:ASP98 4.0 29.4 1.0
ND1 D:HIS100 4.1 18.6 1.0
ND1 D:HIS134 4.1 17.6 1.0
CG D:HIS134 4.2 17.6 1.0
CG E:HIS294 4.2 19.0 1.0
ND1 E:HIS294 4.2 19.1 1.0
CG D:HIS100 4.2 18.8 1.0
CG D:ASP98 4.3 23.9 1.0
OD2 D:ASP98 4.4 24.2 1.0
CE1 E:HIS244 4.7 20.2 1.0
O D:HOH508 4.7 19.0 1.0
CG E:HIS244 4.8 18.9 1.0
CE2 E:PHE296 4.8 21.9 1.0

Copper binding site 9 out of 18 in 3wia

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Copper binding site 9 out of 18 in the Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu401

b:23.1
occ:1.00
 ND1 E:HIS95 2.1 22.5 1.0
ND1 E:HIS143 2.1 20.4 1.0
SG E:CYS135 2.1 21.0 1.0
SD E:MET148 2.6 23.1 1.0
CE1 E:HIS143 3.0 20.5 1.0
CE1 E:HIS95 3.0 25.2 1.0
CG E:HIS143 3.1 20.3 1.0
CG E:HIS95 3.1 22.3 1.0
CB E:CYS135 3.1 20.3 1.0
CB E:HIS95 3.4 22.3 1.0
CE E:MET148 3.4 21.8 1.0
CB E:HIS143 3.5 19.1 1.0
CA E:HIS95 3.7 22.3 1.0
NE2 E:HIS143 4.1 21.7 1.0
O E:PRO94 4.1 23.1 1.0
CG E:MET148 4.1 21.1 1.0
CD2 E:HIS143 4.1 22.2 1.0
NE2 E:HIS95 4.2 25.8 1.0
CD2 E:HIS95 4.2 23.4 1.0
CB E:THR137 4.3 20.7 1.0
OG1 E:THR137 4.4 20.9 1.0
N E:SER96 4.5 21.0 1.0
CB E:MET148 4.5 19.9 1.0
CA E:CYS135 4.6 19.9 1.0
CA E:HIS143 4.6 18.9 1.0
C E:HIS95 4.7 22.1 1.0
CE3 E:TRP63 4.7 24.1 1.0
N E:HIS95 4.8 22.5 1.0
C E:PRO94 4.8 23.4 1.0

Copper binding site 10 out of 18 in 3wia

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Copper binding site 10 out of 18 in the Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of the N-Terminal 1-37 Residues Deleted Mutant of Geobacillus Copper Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu402

b:22.7
occ:1.00
 NE2 E:HIS134 2.0 22.6 1.0
NE2 E:HIS100 2.0 20.0 1.0
NE2 F:HIS294 2.0 17.9 1.0
O E:HOH666 2.2 21.4 0.5
O1 E:FMT404 2.8 29.6 0.5
CD2 E:HIS134 2.9 21.1 1.0
CE1 E:HIS100 3.0 20.3 1.0
CD2 F:HIS294 3.0 18.7 1.0
CE1 E:HIS134 3.0 19.2 1.0
CD2 E:HIS100 3.0 17.9 1.0
CE1 F:HIS294 3.1 17.7 1.0
C E:FMT404 3.2 30.2 0.5
NE2 F:HIS244 3.9 22.4 1.0
CD2 F:HIS244 3.9 21.1 1.0
CG E:HIS134 4.0 19.0 1.0
OD1 E:ASP98 4.1 27.0 1.0
ND1 E:HIS134 4.1 20.3 1.0
ND1 E:HIS100 4.1 19.7 1.0
CG F:HIS294 4.1 15.8 1.0
ND1 F:HIS294 4.1 17.7 1.0
CG E:HIS100 4.2 18.7 1.0
O2 E:FMT404 4.3 30.1 0.5
CG E:ASP98 4.4 24.0 1.0
OD2 E:ASP98 4.4 24.0 1.0
CE1 F:HIS244 4.7 20.4 1.0
O E:HOH519 4.8 22.0 1.0
CG F:HIS244 4.8 21.0 1.0
CE2 F:PHE296 4.8 18.3 1.0

Reference:

Y.Fukuda, H.Koteishi, R.Yoneda, T.Tamada, H.Takami, T.Inoue, M.Nojiri. Structural and Functional Characterization of the Geobacillus Copper Nitrite Reductase: Involvement of the Unique N-Terminal Region in the Interprotein Electron Transfer with Its Redox Partner Biochim.Biophys.Acta V.1837 396 2014.
ISSN: ISSN 0006-3002
PubMed: 24440558
DOI: 10.1016/J.BBABIO.2014.01.004
Page generated: Wed Jul 31 02:21:33 2024

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