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Copper in PDB 6tfo: Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1

Enzymatic activity of Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1

All present enzymatic activity of Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1, PDB code: 6tfo was solved by D.Sasaki, T.F.Watanabe, R.R.Eady, R.C.Garratt, S.V.Antonyuk, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.58 / 2.05
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 77.072, 77.072, 754.548, 90.00, 90.00, 120.00
R / Rfree (%) 22.7 / 27.9

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1 (pdb code 6tfo). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1, PDB code: 6tfo:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 6tfo

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Copper binding site 1 out of 9 in the Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1


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 Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:41.8
occ:1.00
 ND1 A:HIS222 2.0 45.7 1.0
ND1 A:HIS271 2.1 42.8 1.0
SG A:CYS263 2.2 47.5 1.0
SD A:MET276 2.5 41.5 1.0
CE1 A:HIS222 2.8 51.0 1.0
CE1 A:HIS271 3.0 46.0 1.0
CG A:HIS271 3.1 43.7 1.0
CB A:CYS263 3.1 44.7 1.0
CG A:HIS222 3.2 47.2 1.0
CE A:MET276 3.5 44.4 1.0
CB A:HIS271 3.5 42.8 1.0
CB A:HIS222 3.6 47.5 1.0
CA A:HIS222 3.8 46.1 1.0
CG A:MET276 4.0 38.8 1.0
NE2 A:HIS222 4.0 48.2 1.0
NE2 A:HIS271 4.1 45.2 1.0
O A:ILE221 4.1 39.3 1.0
CD2 A:HIS271 4.2 44.8 1.0
CD2 A:HIS222 4.2 46.3 1.0
N A:SER223 4.5 39.7 1.0
CA A:HIS271 4.5 39.8 1.0
CB A:MET276 4.5 40.4 1.0
CA A:CYS263 4.6 43.5 1.0
CB A:THR265 4.6 43.4 1.0
CE3 A:TRP189 4.6 39.3 1.0
C A:HIS222 4.7 42.0 1.0
N A:HIS222 4.8 45.7 1.0
OG1 A:THR265 4.9 42.2 1.0
C A:ILE221 4.9 44.6 1.0

Copper binding site 2 out of 9 in 6tfo

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Copper binding site 2 out of 9 in the Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1


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 Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:49.7
occ:0.65
 NE2 C:HIS419 2.1 46.8 1.0
NE2 A:HIS227 2.1 57.5 1.0
NE2 A:HIS262 2.1 42.0 1.0
CE1 A:HIS262 3.0 40.6 1.0
CE1 A:HIS227 3.0 59.3 1.0
CD2 C:HIS419 3.1 47.8 1.0
CE1 C:HIS419 3.1 50.0 1.0
CD2 A:HIS227 3.2 52.2 1.0
OD2 A:ASP225 3.2 56.7 1.0
CD2 A:HIS262 3.2 41.4 1.0
NE2 C:HIS368 3.7 47.0 1.0
CD2 C:HIS368 4.0 48.4 1.0
CG A:ASP225 4.0 53.1 1.0
ND1 A:HIS227 4.2 53.3 1.0
ND1 A:HIS262 4.2 38.4 1.0
ND1 C:HIS419 4.2 45.1 1.0
CG C:HIS419 4.2 44.9 1.0
CG A:HIS227 4.3 53.4 1.0
CG A:HIS262 4.3 40.2 1.0
CE1 C:HIS368 4.4 46.6 1.0
OD1 A:ASP225 4.5 53.1 1.0
O A:HOH682 4.6 38.2 1.0
CG1 C:ILE370 4.7 55.3 1.0
CG C:HIS368 4.8 45.6 1.0
CD1 C:ILE370 5.0 53.3 1.0
ND1 C:HIS368 5.0 44.6 1.0
CD1 C:LEU421 5.0 39.9 1.0

Copper binding site 3 out of 9 in 6tfo

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Copper binding site 3 out of 9 in the Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1


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 Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu503

b:49.0
occ:1.00
 ND1 A:HIS80 2.0 45.0 1.0
SG A:CYS117 2.2 44.5 1.0
ND1 A:HIS122 2.3 48.5 1.0
SD A:MET127 2.6 48.9 1.0
CE1 A:HIS80 2.9 53.0 1.0
CG A:HIS80 3.1 48.2 1.0
CG A:HIS122 3.1 46.3 1.0
O A:GLN79 3.2 42.7 1.0
CB A:CYS117 3.2 43.0 1.0
CB A:HIS122 3.2 42.7 1.0
CE1 A:HIS122 3.3 42.2 1.0
CA A:HIS80 3.4 46.1 1.0
CB A:HIS80 3.5 50.1 1.0
CE A:MET127 3.7 52.9 1.0
C A:GLN79 4.0 42.2 1.0
NE2 A:HIS80 4.0 47.1 1.0
CD2 A:HIS80 4.1 48.0 1.0
CG A:MET127 4.2 46.2 1.0
N A:HIS80 4.2 43.9 1.0
CD2 A:HIS122 4.3 49.7 1.0
CB A:LEU119 4.3 47.6 1.0
NE2 A:HIS122 4.4 47.6 1.0
N A:ASP81 4.6 45.3 1.0
C A:HIS80 4.6 45.0 1.0
CA A:CYS117 4.6 43.0 1.0
CB A:MET127 4.7 46.9 1.0
CA A:HIS122 4.7 44.0 1.0
CE A:MET43 4.7 57.8 1.0
CG A:LEU119 4.8 50.6 1.0
CD2 A:LEU119 4.8 50.8 1.0
O A:ASP81 5.0 41.0 1.0

Copper binding site 4 out of 9 in 6tfo

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Copper binding site 4 out of 9 in the Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1


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 Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:46.2
occ:1.00
 ND1 B:HIS222 2.0 55.3 1.0
ND1 B:HIS271 2.1 46.8 1.0
SG B:CYS263 2.2 49.1 1.0
SD B:MET276 2.4 46.1 1.0
CE1 B:HIS222 2.8 57.4 1.0
CE1 B:HIS271 3.0 45.6 1.0
CG B:HIS222 3.1 61.2 1.0
CG B:HIS271 3.1 43.1 1.0
CB B:CYS263 3.2 45.2 1.0
OG1 B:THR265 3.2 71.5 1.0
CE B:MET276 3.4 48.9 1.0
CB B:HIS271 3.5 45.0 1.0
CB B:HIS222 3.6 57.3 1.0
CA B:HIS222 3.8 55.5 1.0
CG B:MET276 4.0 46.5 1.0
NE2 B:HIS222 4.0 58.3 1.0
NE2 B:HIS271 4.1 45.6 1.0
O B:ILE221 4.2 45.8 1.0
CD2 B:HIS222 4.2 62.8 1.0
CD2 B:HIS271 4.2 48.1 1.0
CA B:HIS271 4.5 44.7 1.0
CB B:MET276 4.5 45.4 1.0
N B:SER223 4.5 48.4 1.0
CE3 B:TRP189 4.6 40.9 1.0
CA B:CYS263 4.6 44.9 1.0
CB B:THR265 4.7 52.7 1.0
C B:HIS222 4.8 51.5 1.0
N B:HIS222 4.8 51.5 1.0
C B:ILE221 4.9 46.4 1.0

Copper binding site 5 out of 9 in 6tfo

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Copper binding site 5 out of 9 in the Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1


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 As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:48.0
occ:0.70
 NE2 B:HIS262 1.9 43.4 1.0
NE2 B:HIS227 2.0 57.5 1.0
NE2 A:HIS419 2.1 48.3 1.0
O A:HOH728 2.1 45.7 1.0
CE1 B:HIS262 2.9 47.9 1.0
CE1 B:HIS227 2.9 54.6 1.0
CD2 B:HIS262 3.0 42.6 1.0
CE1 A:HIS419 3.0 49.1 1.0
CD2 B:HIS227 3.1 52.2 1.0
CD2 A:HIS419 3.1 50.4 1.0
OD2 B:ASP225 3.3 55.7 1.0
NE2 A:HIS368 3.8 53.2 1.0
ND1 B:HIS262 4.0 47.0 1.0
CG B:HIS262 4.1 45.8 1.0
ND1 B:HIS227 4.1 59.1 1.0
CG B:ASP225 4.1 57.1 1.0
ND1 A:HIS419 4.1 49.4 1.0
CD2 A:HIS368 4.1 50.5 1.0
CG B:HIS227 4.2 59.3 1.0
CG A:HIS419 4.2 45.1 1.0
CE1 A:HIS368 4.4 50.7 1.0
O B:HOH645 4.5 39.1 1.0
OD1 B:ASP225 4.6 54.3 1.0
CG A:HIS368 4.9 43.2 1.0
CD1 A:LEU421 5.0 41.1 1.0
CG1 A:ILE370 5.0 47.9 1.0

Copper binding site 6 out of 9 in 6tfo

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Copper binding site 6 out of 9 in the Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1


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 As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu503

b:46.2
occ:1.00
 ND1 B:HIS80 2.0 48.5 1.0
SG B:CYS117 2.3 45.6 1.0
ND1 B:HIS122 2.3 46.6 1.0
SD B:MET127 2.5 43.7 1.0
CE1 B:HIS80 2.9 49.6 1.0
CG B:HIS80 3.1 51.6 1.0
CG B:HIS122 3.1 46.8 1.0
CB B:CYS117 3.2 40.6 1.0
CB B:HIS122 3.2 44.6 1.0
O B:GLN79 3.2 43.3 1.0
CE1 B:HIS122 3.3 49.0 1.0
CB B:HIS80 3.5 50.0 1.0
CA B:HIS80 3.5 47.3 1.0
CE B:MET127 3.6 43.5 1.0
NE2 B:HIS80 4.0 50.3 1.0
C B:GLN79 4.1 45.6 1.0
CG B:MET127 4.1 40.7 1.0
CD2 B:HIS80 4.1 49.5 1.0
N B:HIS80 4.2 42.7 1.0
CD2 B:HIS122 4.3 52.8 1.0
CB B:LEU119 4.4 50.8 1.0
NE2 B:HIS122 4.4 52.8 1.0
CA B:CYS117 4.6 41.3 1.0
CB B:MET127 4.6 41.7 1.0
N B:ASP81 4.6 44.4 1.0
C B:HIS80 4.6 46.2 1.0
CA B:HIS122 4.7 42.3 1.0
CG B:LEU119 4.9 53.5 1.0
CD2 B:LEU119 4.9 50.0 1.0
O B:ASP81 4.9 44.5 1.0
SD B:MET43 5.0 58.3 1.0

Copper binding site 7 out of 9 in 6tfo

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Copper binding site 7 out of 9 in the Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1


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 As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:45.6
occ:1.00
 ND1 C:HIS222 2.0 45.9 1.0
ND1 C:HIS271 2.1 47.5 1.0
SG C:CYS263 2.1 53.7 1.0
SD C:MET276 2.5 41.8 1.0
CE1 C:HIS222 2.9 49.5 1.0
CE1 C:HIS271 3.0 47.1 1.0
CB C:CYS263 3.1 48.5 1.0
CG C:HIS271 3.1 43.2 1.0
CG C:HIS222 3.1 51.2 1.0
CE C:MET276 3.5 46.0 1.0
CB C:HIS271 3.5 44.0 1.0
CB C:HIS222 3.6 52.6 1.0
CA C:HIS222 3.8 49.7 1.0
CG C:MET276 4.1 49.0 1.0
NE2 C:HIS222 4.1 46.6 1.0
NE2 C:HIS271 4.1 45.9 1.0
O C:ILE221 4.1 49.6 1.0
CD2 C:HIS271 4.2 42.9 1.0
CD2 C:HIS222 4.2 48.9 1.0
N C:SER223 4.4 44.9 1.0
CA C:CYS263 4.5 46.9 1.0
CB C:MET276 4.6 46.4 1.0
CA C:HIS271 4.6 45.9 1.0
CB C:THR265 4.6 50.2 1.0
C C:HIS222 4.7 49.3 1.0
CE3 C:TRP189 4.7 43.2 1.0
N C:HIS222 4.8 51.2 1.0
OG1 C:THR265 4.8 46.4 1.0
C C:ILE221 4.9 48.8 1.0

Copper binding site 8 out of 9 in 6tfo

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Copper binding site 8 out of 9 in the Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1


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 As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:53.2
occ:0.70
 NE2 B:HIS419 2.0 46.2 1.0
NE2 C:HIS262 2.0 52.9 1.0
NE2 C:HIS227 2.0 69.5 1.0
O C:HOH661 2.1 56.7 1.0
CE1 B:HIS419 2.9 44.5 1.0
CE1 C:HIS227 2.9 70.7 1.0
CE1 C:HIS262 3.0 48.8 1.0
CD2 B:HIS419 3.0 47.1 1.0
CD2 C:HIS262 3.0 52.5 1.0
CD2 C:HIS227 3.1 63.8 1.0
OD2 C:ASP225 3.4 62.1 1.0
NE2 B:HIS368 3.8 65.9 1.0
ND1 B:HIS419 4.0 43.2 1.0
ND1 C:HIS262 4.1 48.2 1.0
ND1 C:HIS227 4.1 67.4 1.0
CD2 B:HIS368 4.1 58.9 1.0
CG B:HIS419 4.1 42.5 1.0
CG C:HIS262 4.1 47.3 1.0
CG C:ASP225 4.2 55.1 1.0
CG C:HIS227 4.2 64.8 1.0
CE1 B:HIS368 4.4 62.1 1.0
OD1 C:ASP225 4.6 64.3 1.0
O C:HOH656 4.8 51.9 1.0
CG B:HIS368 4.8 56.7 1.0
CD1 B:LEU421 4.9 41.2 1.0
CG1 B:ILE370 5.0 58.1 1.0
ND1 B:HIS368 5.0 57.9 1.0

Copper binding site 9 out of 9 in 6tfo

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Copper binding site 9 out of 9 in the Crystal Structure of As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1


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 As Isolated Three-Domain Copper-Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu503

b:44.0
occ:1.00
 ND1 C:HIS80 2.0 40.3 1.0
SG C:CYS117 2.2 46.1 1.0
ND1 C:HIS122 2.4 52.1 1.0
SD C:MET127 2.6 45.1 1.0
CE1 C:HIS80 2.9 45.4 1.0
CG C:HIS80 3.1 41.5 1.0
CB C:CYS117 3.1 42.5 1.0
CG C:HIS122 3.2 48.3 1.0
O C:GLN79 3.2 42.7 1.0
CB C:HIS122 3.3 48.6 1.0
CE1 C:HIS122 3.4 49.6 1.0
CB C:HIS80 3.4 44.7 1.0
CA C:HIS80 3.5 46.3 1.0
CE C:MET127 3.6 48.9 1.0
NE2 C:HIS80 4.1 47.1 1.0
C C:GLN79 4.1 46.1 1.0
CG C:MET127 4.1 41.2 1.0
CD2 C:HIS80 4.1 43.4 1.0
N C:HIS80 4.2 43.3 1.0
CB C:LEU119 4.3 54.9 1.0
CD2 C:HIS122 4.4 47.9 1.0
NE2 C:HIS122 4.5 49.7 1.0
CA C:CYS117 4.5 42.4 1.0
N C:ASP81 4.6 40.9 1.0
CB C:MET127 4.6 40.4 1.0
C C:HIS80 4.6 42.9 1.0
CA C:HIS122 4.7 41.9 1.0
CG C:LEU119 4.8 58.4 1.0
CD2 C:LEU119 4.8 60.1 1.0
O C:ASP81 4.9 39.0 1.0

Reference:

D.Sasaki, T.F.Watanabe, R.R.Eady, R.C.Garratt, S.V.Antonyuk, S.S.Hasnain. Structures of Substrate- and Product-Bound Forms of A Multi-Domain Copper Nitrite Reductase Shed Light on the Role of Domain Tethering in Protein Complexes. Iucrj V. 7 557 2020.
ISSN: ESSN 2052-2525
PubMed: 32431838
DOI: 10.1107/S2052252520005230
Page generated: Wed Jul 31 07:33:14 2024

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