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Copper in PDB 6tfd: Crystal Structure of Nitrite and No Bound Three-Domain Copper- Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1

Enzymatic activity of Crystal Structure of Nitrite and No Bound Three-Domain Copper- Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1

All present enzymatic activity of Crystal Structure of Nitrite and No Bound Three-Domain Copper- Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of Nitrite and No Bound Three-Domain Copper- Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1, PDB code: 6tfd 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) 126.37 / 2.25
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 77.722, 77.722, 758.201, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 22.7

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Nitrite and No Bound Three-Domain Copper- Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1 (pdb code 6tfd). 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 Nitrite and No Bound Three-Domain Copper- Containing Nitrite Reductase From Hyphomicrobium Denitrificans Strain 1NES1, PDB code: 6tfd:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 6tfd

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Copper binding site 1 out of 9 in the Crystal Structure of Nitrite and No Bound 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 Nitrite and No Bound 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:45.8
occ:1.00
 ND1 A:HIS222 2.1 49.0 1.0
ND1 A:HIS271 2.1 46.7 1.0
SG A:CYS263 2.2 47.5 1.0
SD A:MET276 2.4 42.8 1.0
CE1 A:HIS222 2.9 52.7 1.0
CE1 A:HIS271 3.0 46.9 1.0
CB A:CYS263 3.1 44.0 1.0
CG A:HIS222 3.1 48.2 1.0
CG A:HIS271 3.1 44.8 1.0
CE A:MET276 3.3 43.1 1.0
CB A:HIS222 3.5 46.8 1.0
CB A:HIS271 3.5 43.5 1.0
CA A:HIS222 3.8 47.8 1.0
CG A:MET276 4.0 43.7 1.0
NE2 A:HIS271 4.1 45.6 1.0
NE2 A:HIS222 4.1 49.9 1.0
O A:ILE221 4.1 40.3 1.0
CD2 A:HIS271 4.2 48.8 1.0
CD2 A:HIS222 4.2 51.4 1.0
N A:SER223 4.5 45.8 1.0
CA A:CYS263 4.5 44.8 1.0
CA A:HIS271 4.6 43.4 1.0
CE3 A:TRP189 4.6 40.8 1.0
CB A:MET276 4.6 42.3 1.0
C A:HIS222 4.7 47.8 1.0
CB A:THR265 4.7 47.8 1.0
N A:HIS222 4.8 51.8 1.0
OG1 A:THR265 4.8 44.5 1.0
C A:ILE221 4.9 47.3 1.0

Copper binding site 2 out of 9 in 6tfd

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Copper binding site 2 out of 9 in the Crystal Structure of Nitrite and No Bound 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 Nitrite and No Bound 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:50.8
occ:1.00
 N A:NO2504 1.9 68.9 1.0
O2 A:NO2504 1.9 66.0 1.0
NE2 A:HIS262 2.1 42.0 1.0
NE2 A:HIS227 2.1 50.7 1.0
NE2 C:HIS419 2.1 48.7 1.0
O1 A:NO2504 2.8 53.0 1.0
CD2 A:HIS262 2.9 38.4 1.0
CE1 A:HIS227 2.9 51.1 1.0
CE1 C:HIS419 3.0 45.1 1.0
CD2 C:HIS419 3.1 44.5 1.0
CD2 A:HIS227 3.2 42.9 1.0
CE1 A:HIS262 3.2 39.3 1.0
OD2 A:ASP225 3.7 71.9 1.0
NE2 C:HIS368 3.9 48.5 1.0
ND1 A:HIS227 4.1 47.3 1.0
CG A:HIS262 4.1 37.5 1.0
ND1 C:HIS419 4.1 42.4 1.0
CD2 C:HIS368 4.2 47.0 1.0
ND1 A:HIS262 4.2 38.7 1.0
CG C:HIS419 4.2 46.2 1.0
CG A:HIS227 4.2 48.8 1.0
CG A:ASP225 4.4 55.4 1.0
CE1 C:HIS368 4.6 50.2 1.0
OD1 A:ASP225 4.7 51.1 1.0
O A:HOH733 4.9 47.9 1.0

Copper binding site 3 out of 9 in 6tfd

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Copper binding site 3 out of 9 in the Crystal Structure of Nitrite and No Bound 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 Nitrite and No Bound 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:48.3
occ:1.00
 ND1 A:HIS80 2.0 49.0 1.0
ND1 A:HIS122 2.2 52.5 1.0
SG A:CYS117 2.3 47.0 1.0
SD A:MET127 2.6 51.7 1.0
CE1 A:HIS80 2.8 52.4 1.0
CG A:HIS122 3.1 49.0 1.0
CG A:HIS80 3.1 46.0 1.0
CB A:CYS117 3.2 42.7 1.0
CE1 A:HIS122 3.2 49.5 1.0
CB A:HIS122 3.3 46.5 1.0
O A:GLN79 3.3 46.9 1.0
CB A:HIS80 3.5 46.2 1.0
CA A:HIS80 3.5 47.8 1.0
CE A:MET127 3.6 58.6 1.0
NE2 A:HIS80 4.0 52.7 1.0
CD2 A:HIS80 4.1 49.7 1.0
C A:GLN79 4.2 44.9 1.0
CG A:MET127 4.2 44.9 1.0
CD2 A:HIS122 4.2 52.4 1.0
NE2 A:HIS122 4.3 48.7 1.0
N A:HIS80 4.3 49.0 1.0
CB A:LEU119 4.4 50.4 1.0
CA A:CYS117 4.6 49.5 1.0
N A:ASP81 4.6 43.9 1.0
C A:HIS80 4.7 45.9 1.0
CB A:MET127 4.7 46.0 1.0
CA A:HIS122 4.7 47.0 1.0
CE A:MET43 4.7 55.4 1.0
CG A:LEU119 4.9 55.4 1.0
CD2 A:LEU119 5.0 51.8 1.0

Copper binding site 4 out of 9 in 6tfd

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Copper binding site 4 out of 9 in the Crystal Structure of Nitrite and No Bound 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 Nitrite and No Bound 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:49.9
occ:1.00
 ND1 B:HIS222 2.1 57.0 1.0
SG B:CYS263 2.1 50.2 1.0
ND1 B:HIS271 2.1 48.6 1.0
SD B:MET276 2.3 49.6 1.0
CE1 B:HIS222 3.0 56.8 1.0
CE1 B:HIS271 3.1 46.5 1.0
CG B:HIS271 3.1 45.5 1.0
CG B:HIS222 3.2 61.9 1.0
CB B:CYS263 3.2 55.4 1.0
CE B:MET276 3.3 47.3 1.0
OG1 B:THR265 3.4 88.2 1.0
CB B:HIS271 3.4 46.0 1.0
CB B:HIS222 3.5 56.5 1.0
CA B:HIS222 3.8 60.4 1.0
CG B:MET276 3.9 47.6 1.0
O B:ILE221 4.1 43.2 1.0
NE2 B:HIS222 4.2 58.7 1.0
NE2 B:HIS271 4.2 46.4 1.0
CD2 B:HIS271 4.2 48.2 1.0
CD2 B:HIS222 4.3 59.0 1.0
CB B:MET276 4.5 49.6 1.0
N B:SER223 4.5 54.4 1.0
CA B:HIS271 4.6 45.3 1.0
CA B:CYS263 4.6 54.4 1.0
CE3 B:TRP189 4.6 53.5 1.0
C B:HIS222 4.7 56.1 1.0
N B:HIS222 4.8 57.6 1.0
CB B:THR265 4.8 61.9 1.0
C B:ILE221 4.8 51.9 1.0

Copper binding site 5 out of 9 in 6tfd

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Copper binding site 5 out of 9 in the Crystal Structure of Nitrite and No Bound 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 Nitrite and No Bound 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:49.2
occ:1.00
 N A:NO2505 1.8 49.0 1.0
NE2 B:HIS262 2.0 46.5 1.0
NE2 B:HIS227 2.0 55.1 1.0
NE2 A:HIS419 2.1 47.3 1.0
O2 A:NO2505 2.1 55.7 1.0
CE1 B:HIS227 2.9 58.5 1.0
O1 A:NO2505 2.9 47.5 1.0
CE1 A:HIS419 2.9 51.3 1.0
CD2 B:HIS262 3.0 49.7 1.0
CE1 B:HIS262 3.0 50.3 1.0
CD2 A:HIS419 3.1 45.9 1.0
CD2 B:HIS227 3.1 51.5 1.0
OD2 B:ASP225 3.8 62.3 1.0
ND1 B:HIS227 4.1 57.7 1.0
NE2 A:HIS368 4.1 49.1 1.0
ND1 B:HIS262 4.1 48.2 1.0
ND1 A:HIS419 4.1 48.1 1.0
CG B:HIS262 4.1 50.0 1.0
CG B:HIS227 4.2 54.0 1.0
CG A:HIS419 4.2 44.4 1.0
CD2 A:HIS368 4.4 45.0 1.0
CG B:ASP225 4.4 58.8 1.0
CE1 A:HIS368 4.5 51.3 1.0
OD1 B:ASP225 4.7 55.9 1.0
O A:HOH650 4.8 48.3 1.0
CD1 A:LEU421 4.9 44.7 1.0
CG A:HIS368 4.9 44.7 1.0

Copper binding site 6 out of 9 in 6tfd

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Copper binding site 6 out of 9 in the Crystal Structure of Nitrite and No Bound 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 Nitrite and No Bound 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:48.5
occ:1.00
 ND1 B:HIS80 2.1 52.8 1.0
ND1 B:HIS122 2.1 48.3 1.0
SG B:CYS117 2.2 46.8 1.0
SD B:MET127 2.6 47.2 1.0
CE1 B:HIS80 2.9 54.0 1.0
CG B:HIS122 3.0 44.4 1.0
CG B:HIS80 3.1 49.8 1.0
CE1 B:HIS122 3.2 46.1 1.0
CB B:CYS117 3.2 43.2 1.0
CB B:HIS122 3.2 45.9 1.0
O B:GLN79 3.3 46.6 1.0
CB B:HIS80 3.5 49.3 1.0
CA B:HIS80 3.5 47.3 1.0
CE B:MET127 3.6 48.7 1.0
NE2 B:HIS80 4.1 51.4 1.0
CG B:MET127 4.1 48.0 1.0
CD2 B:HIS80 4.1 47.9 1.0
C B:GLN79 4.2 47.7 1.0
CD2 B:HIS122 4.2 50.4 1.0
NE2 B:HIS122 4.2 51.8 1.0
N B:HIS80 4.3 47.6 1.0
CB B:LEU119 4.3 50.7 1.0
N B:ASP81 4.6 45.9 1.0
CA B:CYS117 4.6 44.0 1.0
C B:HIS80 4.6 45.0 1.0
CA B:HIS122 4.7 45.3 1.0
CB B:MET127 4.7 45.0 1.0
CG B:LEU119 4.8 51.7 1.0
SD B:MET43 4.9 59.3 1.0

Copper binding site 7 out of 9 in 6tfd

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Copper binding site 7 out of 9 in the Crystal Structure of Nitrite and No Bound 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 Nitrite and No Bound 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:48.3
occ:1.00
 ND1 C:HIS271 2.1 50.9 1.0
ND1 C:HIS222 2.2 50.9 1.0
SG C:CYS263 2.2 50.5 1.0
SD C:MET276 2.5 47.3 1.0
CE1 C:HIS271 2.9 53.3 1.0
CE1 C:HIS222 3.1 56.6 1.0
CB C:CYS263 3.1 49.0 1.0
CG C:HIS271 3.1 47.3 1.0
CG C:HIS222 3.2 56.3 1.0
CE C:MET276 3.4 49.9 1.0
CB C:HIS222 3.6 58.3 1.0
CB C:HIS271 3.6 47.5 1.0
CA C:HIS222 3.8 57.8 1.0
NE2 C:HIS271 4.0 55.9 1.0
CG C:MET276 4.1 49.3 1.0
CD2 C:HIS271 4.1 51.5 1.0
O C:ILE221 4.2 51.1 1.0
NE2 C:HIS222 4.2 62.6 1.0
CD2 C:HIS222 4.3 57.8 1.0
N C:SER223 4.5 54.8 1.0
CA C:CYS263 4.5 48.6 1.0
CA C:HIS271 4.6 47.7 1.0
CB C:MET276 4.6 51.1 1.0
CE3 C:TRP189 4.7 48.1 1.0
CB C:THR265 4.7 50.2 1.0
C C:HIS222 4.7 56.7 1.0
N C:HIS222 4.8 54.9 1.0
OG1 C:THR265 4.9 45.1 1.0
C C:ILE221 4.9 50.2 1.0

Copper binding site 8 out of 9 in 6tfd

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Copper binding site 8 out of 9 in the Crystal Structure of Nitrite and No Bound 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 Nitrite and No Bound 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:49.6
occ:1.00
 N B:NO504 2.0 57.6 1.0
NE2 B:HIS419 2.0 46.9 1.0
NE2 C:HIS262 2.1 46.9 1.0
NE2 C:HIS227 2.1 55.5 1.0
O B:NO504 2.5 52.6 1.0
CE1 C:HIS227 3.0 59.7 1.0
CD2 B:HIS419 3.0 45.1 1.0
CE1 C:HIS262 3.0 47.8 1.0
CE1 B:HIS419 3.1 52.8 1.0
CD2 C:HIS262 3.1 47.1 1.0
CD2 C:HIS227 3.2 56.4 1.0
OD2 C:ASP225 3.5 65.5 1.0
NE2 B:HIS368 3.9 58.1 1.0
ND1 C:HIS227 4.1 57.7 1.0
ND1 B:HIS419 4.1 47.0 1.0
CG B:HIS419 4.2 46.0 1.0
ND1 C:HIS262 4.2 45.0 1.0
CD2 B:HIS368 4.2 52.9 1.0
CG C:HIS262 4.2 43.3 1.0
CG C:HIS227 4.3 57.2 1.0
CG C:ASP225 4.3 60.3 1.0
CE1 B:HIS368 4.5 53.4 1.0
O C:HOH661 4.8 52.8 1.0
OD1 C:ASP225 4.9 65.3 1.0
CD1 B:LEU421 4.9 47.5 1.0
CG B:HIS368 5.0 50.1 1.0

Copper binding site 9 out of 9 in 6tfd

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Copper binding site 9 out of 9 in the Crystal Structure of Nitrite and No Bound 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 Nitrite and No Bound 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:49.4
occ:1.00
 ND1 C:HIS80 2.0 49.2 1.0
SG C:CYS117 2.2 47.1 1.0
ND1 C:HIS122 2.2 49.5 1.0
SD C:MET127 2.6 42.0 1.0
CE1 C:HIS80 2.9 45.9 1.0
CG C:HIS80 3.1 46.8 1.0
CG C:HIS122 3.1 49.9 1.0
CB C:CYS117 3.2 43.8 1.0
CB C:HIS122 3.2 50.5 1.0
CE1 C:HIS122 3.3 51.0 1.0
O C:GLN79 3.3 52.1 1.0
CB C:HIS80 3.5 49.6 1.0
CA C:HIS80 3.5 48.1 1.0
CE C:MET127 3.7 49.7 1.0
NE2 C:HIS80 4.1 46.6 1.0
CD2 C:HIS80 4.1 48.8 1.0
CG C:MET127 4.1 42.0 1.0
C C:GLN79 4.2 50.7 1.0
CD2 C:HIS122 4.3 52.8 1.0
CB C:LEU119 4.3 55.7 1.0
N C:HIS80 4.3 45.0 1.0
NE2 C:HIS122 4.3 50.0 1.0
N C:ASP81 4.6 42.3 1.0
CA C:CYS117 4.6 46.1 1.0
CB C:MET127 4.6 43.1 1.0
C C:HIS80 4.7 46.4 1.0
CA C:HIS122 4.7 47.3 1.0
CG C:LEU119 4.7 59.9 1.0
CD2 C:LEU119 4.9 61.9 1.0
O C:ASP81 5.0 41.6 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 07:32:46 2024

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