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Copper in PDB 6hbe: Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01

Protein crystallography data

The structure of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01, PDB code: 6hbe was solved by D.J.Opperman, F.M.Ferroni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.51 / 1.63
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.692, 110.553, 88.810, 90.00, 107.51, 90.00
R / Rfree (%) 16.1 / 19

Other elements in 6hbe:

The structure of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 (pdb code 6hbe). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01, PDB code: 6hbe:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 6hbe

Go back to Copper Binding Sites List in 6hbe
Copper binding site 1 out of 9 in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu500

b:26.7
occ:1.00
 ND1 A:HIS390 2.0 22.8 1.0
ND1 A:HIS431 2.0 24.5 1.0
SG A:CYS428 2.2 25.7 1.0
CE1 A:HIS390 2.9 23.8 1.0
CE1 A:HIS431 2.9 25.5 1.0
SD A:MET434 3.0 26.6 1.0
CG A:HIS431 3.1 25.9 1.0
CG A:HIS390 3.1 23.6 1.0
CB A:CYS428 3.2 27.6 1.0
CB A:HIS431 3.5 26.2 1.0
CB A:HIS390 3.5 23.9 1.0
O A:ARG389 3.6 24.4 1.0
CA A:HIS390 3.7 24.5 1.0
CE A:MET434 3.8 25.4 1.0
N A:HIS431 3.8 26.5 1.0
NE2 A:HIS390 4.0 24.5 1.0
NE2 A:HIS431 4.1 26.2 1.0
CD2 A:HIS390 4.2 24.5 1.0
CD2 A:HIS431 4.2 25.0 1.0
CB A:ILE430 4.2 30.7 1.0
CA A:HIS431 4.3 27.8 1.0
C A:ARG389 4.5 25.3 1.0
CG A:MET434 4.5 27.9 1.0
N A:HIS390 4.6 23.9 1.0
C A:ILE430 4.6 29.0 1.0
CA A:CYS428 4.7 27.0 1.0
N A:ASP391 4.7 26.8 1.0
O A:HIS431 4.7 26.7 1.0
CG2 A:ILE430 4.8 29.3 1.0
CA A:ILE430 4.8 29.8 1.0
C A:HIS390 4.8 26.8 1.0
N A:ILE430 4.9 26.9 1.0
C A:HIS431 5.0 26.8 1.0

Copper binding site 2 out of 9 in 6hbe

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Copper binding site 2 out of 9 in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:22.1
occ:1.00
 O A:HOH657 2.0 28.9 1.0
NE2 A:HIS80 2.0 20.6 1.0
NE2 A:HIS114 2.0 21.5 1.0
NE2 C:HIS267 2.1 19.7 1.0
CE1 A:HIS80 2.8 20.8 1.0
CD2 A:HIS114 2.9 19.5 1.0
CE1 C:HIS267 3.0 19.8 1.0
CE1 A:HIS114 3.1 21.4 1.0
CD2 C:HIS267 3.1 19.7 1.0
CD2 A:HIS80 3.2 19.8 1.0
NE2 C:HIS216 3.5 22.3 1.0
CD2 C:HIS216 3.9 21.6 1.0
OG A:SER78 3.9 24.9 1.0
ND1 A:HIS80 4.0 20.1 1.0
CG A:HIS114 4.1 19.4 1.0
ND1 C:HIS267 4.1 18.3 1.0
ND1 A:HIS114 4.1 21.0 1.0
CG A:HIS80 4.2 19.1 1.0
CG C:HIS267 4.2 18.9 1.0
CE1 C:HIS216 4.2 22.1 1.0
CZ C:PHE269 4.5 18.7 1.0
O A:HOH851 4.5 32.6 1.0
CB A:SER78 4.6 22.5 1.0
CG C:HIS216 4.7 20.5 1.0
ND1 C:HIS216 4.9 21.5 1.0

Copper binding site 3 out of 9 in 6hbe

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Copper binding site 3 out of 9 in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:24.7
occ:1.00
 OE1 A:GLN130 2.0 26.0 1.0
ND1 A:HIS125 2.0 25.5 1.0
ND1 A:HIS75 2.0 23.7 1.0
SG A:CYS115 2.2 24.0 1.0
CE1 A:HIS75 2.9 23.1 1.0
CE1 A:HIS125 3.0 24.8 1.0
CG A:HIS125 3.0 23.4 1.0
CD A:GLN130 3.0 24.6 1.0
CG A:HIS75 3.1 23.4 1.0
CB A:CYS115 3.3 23.4 1.0
CB A:HIS125 3.4 23.2 1.0
NE2 A:GLN130 3.4 25.2 1.0
CB A:HIS75 3.6 23.6 1.0
CA A:HIS75 3.8 23.4 1.0
NE2 A:HIS75 4.1 23.5 1.0
NE2 A:HIS125 4.1 24.7 1.0
CD2 A:HIS125 4.2 23.6 1.0
CD2 A:HIS75 4.2 23.1 1.0
CG A:PRO117 4.2 25.4 1.0
O A:THR74 4.3 22.7 1.0
CG A:GLN130 4.5 24.9 1.0
CD A:PRO117 4.6 25.7 1.0
N A:GLY76 4.6 23.6 1.0
CA A:CYS115 4.7 22.6 1.0
C A:HIS75 4.7 23.8 1.0
CA A:HIS125 4.8 22.4 1.0
N A:HIS75 4.8 23.2 1.0
CB A:GLN130 4.9 22.4 1.0
C A:THR74 5.0 23.5 1.0

Copper binding site 4 out of 9 in 6hbe

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Copper binding site 4 out of 9 in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu500

b:25.3
occ:1.00
 ND1 B:HIS431 2.0 21.3 1.0
ND1 B:HIS390 2.0 22.6 1.0
SG B:CYS428 2.3 26.7 1.0
CE1 B:HIS390 2.9 23.9 1.0
CE1 B:HIS431 2.9 22.3 1.0
SD B:MET434 3.1 25.1 1.0
CG B:HIS431 3.1 23.6 1.0
CG B:HIS390 3.1 22.8 1.0
CB B:CYS428 3.2 24.7 1.0
CB B:HIS431 3.5 24.4 1.0
O B:ARG389 3.6 22.4 1.0
CB B:HIS390 3.6 22.6 1.0
CA B:HIS390 3.7 23.0 1.0
N B:HIS431 3.9 24.8 1.0
CE B:MET434 3.9 22.8 1.0
NE2 B:HIS390 4.1 21.9 1.0
NE2 B:HIS431 4.1 22.8 1.0
CB B:ILE430 4.2 26.0 1.0
CD2 B:HIS431 4.2 21.9 1.0
CD2 B:HIS390 4.2 22.9 1.0
CA B:HIS431 4.3 24.7 1.0
C B:ARG389 4.4 25.1 1.0
N B:HIS390 4.5 22.4 1.0
CG B:MET434 4.5 26.7 1.0
CA B:CYS428 4.6 25.6 1.0
C B:ILE430 4.7 25.9 1.0
N B:ASP391 4.7 24.8 1.0
C B:HIS390 4.8 24.4 1.0
O B:HIS431 4.8 24.2 1.0
CG2 B:ILE430 4.8 24.9 1.0
CA B:ILE430 4.8 26.3 1.0
N B:ILE430 4.9 25.3 1.0
CG1 B:ILE430 5.0 27.4 1.0

Copper binding site 5 out of 9 in 6hbe

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Copper binding site 5 out of 9 in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:23.4
occ:1.00
 O B:HOH702 2.0 28.9 1.0
NE2 B:HIS114 2.0 23.2 1.0
NE2 B:HIS80 2.0 19.8 1.0
NE2 A:HIS267 2.1 21.1 1.0
CE1 B:HIS80 2.8 21.0 1.0
CD2 B:HIS114 3.0 22.4 1.0
CE1 A:HIS267 3.0 19.5 1.0
CE1 B:HIS114 3.1 23.1 1.0
CD2 A:HIS267 3.1 19.6 1.0
CD2 B:HIS80 3.2 22.7 1.0
NE2 A:HIS216 3.5 24.0 1.0
CD2 A:HIS216 3.8 21.8 1.0
OG B:SER78 3.8 26.0 1.0
ND1 B:HIS80 4.0 21.0 1.0
ND1 A:HIS267 4.1 17.9 1.0
CG B:HIS114 4.1 21.6 1.0
ND1 B:HIS114 4.1 23.1 1.0
CE1 A:HIS216 4.2 24.9 1.0
CG B:HIS80 4.2 19.4 1.0
CG A:HIS267 4.2 17.9 1.0
CZ A:PHE269 4.5 18.9 1.0
CB B:SER78 4.5 23.1 1.0
O B:HOH863 4.6 32.2 1.0
CG A:HIS216 4.7 21.9 1.0
ND1 A:HIS216 4.8 24.3 1.0

Copper binding site 6 out of 9 in 6hbe

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Copper binding site 6 out of 9 in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:25.0
occ:1.00
 ND1 B:HIS125 2.0 22.8 1.0
ND1 B:HIS75 2.0 22.0 1.0
OE1 B:GLN130 2.0 26.1 1.0
SG B:CYS115 2.2 24.7 1.0
CE1 B:HIS75 2.9 23.7 1.0
CE1 B:HIS125 3.0 25.6 1.0
CG B:HIS125 3.0 22.8 1.0
CD B:GLN130 3.1 25.6 1.0
CG B:HIS75 3.1 22.6 1.0
CB B:CYS115 3.3 23.0 1.0
CB B:HIS125 3.3 23.1 1.0
NE2 B:GLN130 3.4 25.5 1.0
CB B:HIS75 3.5 23.3 1.0
CA B:HIS75 3.8 22.6 1.0
NE2 B:HIS75 4.1 24.8 1.0
NE2 B:HIS125 4.1 23.6 1.0
CD2 B:HIS125 4.1 23.5 1.0
CD2 B:HIS75 4.2 23.2 1.0
CG B:PRO117 4.2 26.3 1.0
O B:THR74 4.3 22.1 1.0
CG B:GLN130 4.5 25.9 1.0
CD B:PRO117 4.6 25.4 1.0
CA B:CYS115 4.6 21.8 1.0
N B:GLY76 4.7 22.0 1.0
C B:HIS75 4.7 23.2 1.0
CA B:HIS125 4.7 23.2 1.0
N B:HIS75 4.8 22.5 1.0
CB B:GLN130 4.9 24.0 1.0
C B:THR74 5.0 23.5 1.0

Copper binding site 7 out of 9 in 6hbe

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Copper binding site 7 out of 9 in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu500

b:26.9
occ:1.00
 ND1 C:HIS431 2.0 25.2 1.0
ND1 C:HIS390 2.1 26.5 1.0
SG C:CYS428 2.3 27.4 1.0
CE1 C:HIS390 2.9 25.6 1.0
CE1 C:HIS431 2.9 25.2 1.0
SD C:MET434 3.0 27.9 1.0
CG C:HIS431 3.1 25.0 1.0
CG C:HIS390 3.2 24.7 1.0
CB C:CYS428 3.2 27.9 1.0
CB C:HIS431 3.5 25.4 1.0
O C:ARG389 3.6 25.0 1.0
CB C:HIS390 3.6 25.3 1.0
CA C:HIS390 3.7 24.8 1.0
N C:HIS431 3.9 26.7 1.0
CE C:MET434 4.0 27.5 1.0
NE2 C:HIS431 4.1 25.0 1.0
NE2 C:HIS390 4.1 24.5 1.0
CB C:ILE430 4.1 27.8 1.0
CD2 C:HIS431 4.2 25.1 1.0
CD2 C:HIS390 4.2 25.7 1.0
CA C:HIS431 4.3 25.7 1.0
C C:ARG389 4.4 24.8 1.0
CG C:MET434 4.5 28.4 1.0
N C:HIS390 4.5 22.6 1.0
CA C:CYS428 4.7 27.3 1.0
C C:ILE430 4.7 27.7 1.0
N C:ASP391 4.7 28.8 1.0
CG2 C:ILE430 4.7 28.4 1.0
O C:HIS431 4.8 26.6 1.0
CA C:ILE430 4.8 27.4 1.0
C C:HIS390 4.8 26.7 1.0
N C:ILE430 4.9 27.1 1.0
C C:HIS431 5.0 27.2 1.0

Copper binding site 8 out of 9 in 6hbe

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Copper binding site 8 out of 9 in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:23.6
occ:1.00
 O B:HOH713 1.9 28.9 1.0
NE2 C:HIS114 2.0 23.7 1.0
NE2 C:HIS80 2.1 22.6 1.0
NE2 B:HIS267 2.1 22.0 1.0
CE1 C:HIS80 2.9 20.7 1.0
CD2 C:HIS114 3.0 21.6 1.0
CE1 B:HIS267 3.0 20.7 1.0
CE1 C:HIS114 3.0 22.7 1.0
CD2 B:HIS267 3.1 21.2 1.0
CD2 C:HIS80 3.2 21.3 1.0
NE2 B:HIS216 3.5 25.3 1.0
CD2 B:HIS216 3.8 23.5 1.0
OG C:SER78 3.9 26.6 1.0
ND1 C:HIS80 4.1 21.8 1.0
CG C:HIS114 4.1 21.7 1.0
ND1 C:HIS114 4.1 22.6 1.0
ND1 B:HIS267 4.1 21.2 1.0
CE1 B:HIS216 4.2 23.8 1.0
CG B:HIS267 4.2 20.4 1.0
CG C:HIS80 4.3 20.1 1.0
CB C:SER78 4.5 24.5 1.0
CZ B:PHE269 4.5 19.4 1.0
O C:HOH850 4.5 29.9 1.0
CG B:HIS216 4.7 23.2 1.0
ND1 B:HIS216 4.8 24.3 1.0

Copper binding site 9 out of 9 in 6hbe

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Copper binding site 9 out of 9 in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:25.0
occ:1.00
 ND1 C:HIS125 2.0 28.5 1.0
OE1 C:GLN130 2.0 25.8 1.0
ND1 C:HIS75 2.1 24.0 1.0
SG C:CYS115 2.1 23.9 1.0
CE1 C:HIS75 3.0 21.4 1.0
CE1 C:HIS125 3.0 27.9 1.0
CG C:HIS125 3.0 26.8 1.0
CD C:GLN130 3.0 27.6 1.0
CG C:HIS75 3.1 22.9 1.0
CB C:CYS115 3.2 23.1 1.0
CB C:HIS125 3.4 25.3 1.0
NE2 C:GLN130 3.4 28.3 1.0
CB C:HIS75 3.5 23.9 1.0
CA C:HIS75 3.8 23.9 1.0
NE2 C:HIS75 4.1 23.5 1.0
NE2 C:HIS125 4.1 29.8 1.0
CD2 C:HIS125 4.1 28.2 1.0
CD2 C:HIS75 4.2 23.3 1.0
CG C:PRO117 4.2 24.8 1.0
O C:THR74 4.3 26.0 1.0
CG C:GLN130 4.5 26.8 1.0
CD C:PRO117 4.6 24.4 1.0
N C:GLY76 4.6 22.5 1.0
CA C:CYS115 4.7 22.1 1.0
C C:HIS75 4.7 24.7 1.0
CA C:HIS125 4.8 23.0 1.0
N C:HIS75 4.9 25.1 1.0
CB C:GLN130 4.9 24.6 1.0
CD2 C:PHE44 5.0 27.5 1.0

Reference:

D.J.Opperman, D.H.Murgida, S.D.Dalosto, C.D.Brondino, F.M.Ferroni. A Three-Domain Copper-Nitrite Reductase with A Unique Sensing Loop. Iucrj V. 6 248 2019.
ISSN: ESSN 2052-2525
PubMed: 30867922
DOI: 10.1107/S2052252519000241
Page generated: Wed Jul 31 06:10:31 2024

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