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Copper in PDB 6qpt: Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331)

Enzymatic activity of Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331)

All present enzymatic activity of Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331):
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331), PDB code: 6qpt was solved by S.V.Antonyuk, T.M.Hedison, R.R.Eady, S.S.Hasnain, N.S.Scrutton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 165.910, 167.553, 143.973, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.4

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331) (pdb code 6qpt). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331), PDB code: 6qpt:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in 6qpt

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Copper binding site 1 out of 12 in the Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331)


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 Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:23.8
occ:1.00
 ND1 A:HIS94 2.0 26.0 1.0
ND1 A:HIS143 2.2 24.7 1.0
SG A:CYS135 2.2 23.0 1.0
SD A:MET148 2.6 22.4 1.0
CE1 A:HIS94 2.9 26.4 1.0
CG A:HIS94 3.0 26.9 1.0
CG A:HIS143 3.1 23.8 1.0
CB A:CYS135 3.1 22.8 1.0
CE1 A:HIS143 3.1 25.2 1.0
CB A:HIS143 3.4 23.2 1.0
CB A:HIS94 3.4 27.0 1.0
CE A:MET148 3.5 23.4 1.0
CA A:HIS94 3.8 27.6 1.0
NE2 A:HIS94 4.1 27.2 1.0
CD2 A:HIS94 4.1 27.5 1.0
OG1 A:THR137 4.1 27.4 1.0
CG A:MET148 4.1 21.8 1.0
NE2 A:HIS143 4.2 24.9 1.0
CD2 A:HIS143 4.2 24.4 1.0
O A:PRO93 4.2 30.0 1.0
CB A:THR137 4.2 27.3 1.0
CE3 A:TRP61 4.5 26.4 1.0
CA A:CYS135 4.5 22.1 1.0
CA A:HIS143 4.6 23.1 1.0
N A:ASN95 4.7 26.4 1.0
CB A:MET148 4.7 20.9 1.0
N A:HIS94 4.8 29.4 1.0
C A:HIS94 4.8 27.3 1.0
CZ3 A:TRP61 4.9 26.6 1.0
C A:PRO93 4.9 31.1 1.0

Copper binding site 2 out of 12 in 6qpt

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Copper binding site 2 out of 12 in the Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331)


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 Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:19.9
occ:1.00
 NE2 B:HIS289 2.0 17.8 1.0
O A:HOH606 2.0 27.1 1.0
NE2 A:HIS134 2.0 19.2 1.0
NE2 A:HIS99 2.1 17.9 1.0
O B:HOH746 2.4 27.5 1.0
CE1 A:HIS99 2.9 17.2 1.0
CE1 B:HIS289 3.0 17.9 1.0
CD2 A:HIS134 3.0 19.6 1.0
CD2 B:HIS289 3.0 17.7 1.0
CE1 A:HIS134 3.0 20.3 1.0
CD2 A:HIS99 3.2 18.2 1.0
OD2 A:ASP97 3.8 22.2 1.0
NE2 B:HIS240 4.0 18.0 1.0
ND1 A:HIS99 4.1 17.0 1.0
ND1 B:HIS289 4.1 17.1 1.0
CD2 B:HIS240 4.1 17.5 1.0
ND1 A:HIS134 4.1 20.6 1.0
CG B:HIS289 4.1 17.0 1.0
CG A:HIS134 4.1 20.0 1.0
CG A:HIS99 4.2 17.8 1.0
CG A:ASP97 4.4 21.6 1.0
CE1 B:HIS240 4.7 18.0 1.0
OD1 A:ASP97 4.8 22.1 1.0
CG B:HIS240 4.9 17.2 1.0
O B:HOH720 5.0 24.4 1.0

Copper binding site 3 out of 12 in 6qpt

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Copper binding site 3 out of 12 in the Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331)


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 Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:26.0
occ:1.00
 ND1 B:HIS143 2.0 27.4 1.0
ND1 B:HIS94 2.0 27.5 1.0
SG B:CYS135 2.2 25.1 1.0
SD B:MET148 2.6 24.7 1.0
CE1 B:HIS143 2.9 28.6 1.0
CE1 B:HIS94 3.0 27.7 1.0
CG B:HIS94 3.1 28.7 1.0
CB B:CYS135 3.1 24.6 1.0
CG B:HIS143 3.1 27.0 1.0
CB B:HIS94 3.4 29.3 1.0
CB B:HIS143 3.5 25.6 1.0
CE B:MET148 3.5 25.3 1.0
CA B:HIS94 3.8 30.2 1.0
NE2 B:HIS143 4.0 28.2 1.0
CG B:MET148 4.1 23.9 1.0
OG1 B:THR137 4.1 31.5 1.0
CD2 B:HIS143 4.1 27.4 1.0
NE2 B:HIS94 4.1 28.5 1.0
CB B:THR137 4.2 31.1 1.0
CD2 B:HIS94 4.2 29.1 1.0
O B:PRO93 4.3 32.6 1.0
CE3 B:TRP61 4.5 27.5 1.0
CA B:CYS135 4.5 24.2 1.0
CA B:HIS143 4.6 25.4 1.0
CB B:MET148 4.6 23.0 1.0
N B:ASN95 4.7 28.6 1.0
C B:HIS94 4.8 30.0 1.0
N B:HIS94 4.9 32.4 1.0
CZ3 B:TRP61 4.9 27.9 1.0

Copper binding site 4 out of 12 in 6qpt

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Copper binding site 4 out of 12 in the Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331)


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 Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:22.4
occ:1.00
 O1 B:NO2503 2.0 40.6 1.0
NE2 B:HIS99 2.1 19.4 1.0
NE2 B:HIS134 2.1 19.4 1.0
NE2 C:HIS289 2.1 19.1 1.0
N B:NO2503 2.2 41.2 1.0
O2 B:NO2503 2.5 40.1 1.0
CE1 B:HIS99 2.9 18.5 1.0
CD2 C:HIS289 3.0 18.9 1.0
CD2 B:HIS134 3.0 20.1 1.0
CE1 B:HIS134 3.1 20.4 1.0
CE1 C:HIS289 3.2 19.2 1.0
CD2 B:HIS99 3.2 19.8 1.0
OD2 B:ASP97 3.9 23.1 1.0
NE2 C:HIS240 3.9 20.2 1.0
CD2 C:HIS240 4.0 19.9 1.0
ND1 B:HIS99 4.1 18.6 1.0
CG C:HIS289 4.2 18.1 1.0
CG B:HIS134 4.2 20.4 1.0
ND1 B:HIS134 4.2 20.6 1.0
CG B:HIS99 4.2 19.7 1.0
ND1 C:HIS289 4.2 18.1 1.0
CG B:ASP97 4.3 23.1 1.0
OD1 B:ASP97 4.6 23.2 1.0
CE1 C:HIS240 4.7 20.0 1.0
O B:HOH713 4.8 22.6 1.0
CG C:HIS240 4.9 19.0 1.0
O B:HOH781 4.9 37.8 1.0

Copper binding site 5 out of 12 in 6qpt

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Copper binding site 5 out of 12 in the Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331)


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 Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:19.9
occ:1.00
 ND1 C:HIS94 2.0 20.6 1.0
ND1 C:HIS143 2.1 21.6 1.0
SG C:CYS135 2.2 18.5 1.0
SD C:MET148 2.6 18.9 1.0
CE1 C:HIS94 3.0 21.2 1.0
CE1 C:HIS143 3.0 22.1 1.0
CG C:HIS94 3.0 21.0 1.0
CG C:HIS143 3.1 20.5 1.0
CB C:CYS135 3.2 17.9 1.0
CB C:HIS94 3.4 20.6 1.0
CE C:MET148 3.4 18.9 1.0
CB C:HIS143 3.4 19.9 1.0
CA C:HIS94 3.8 21.0 1.0
O C:PRO93 4.0 22.8 1.0
NE2 C:HIS94 4.1 21.8 1.0
NE2 C:HIS143 4.1 22.2 1.0
CG C:MET148 4.1 18.1 1.0
CD2 C:HIS94 4.1 21.6 1.0
CD2 C:HIS143 4.2 21.3 1.0
CB C:THR137 4.2 21.4 1.0
OG1 C:THR137 4.2 20.5 1.0
CE3 C:TRP61 4.4 22.3 1.0
CA C:HIS143 4.5 19.8 1.0
CA C:CYS135 4.6 17.4 1.0
CB C:MET148 4.7 17.4 1.0
N C:ASN95 4.7 19.6 1.0
N C:HIS94 4.8 22.2 1.0
C C:PRO93 4.8 23.6 1.0
C C:HIS94 4.8 20.4 1.0
CZ3 C:TRP61 4.8 22.7 1.0
CG2 C:THR137 5.0 22.2 1.0

Copper binding site 6 out of 12 in 6qpt

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Copper binding site 6 out of 12 in the Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331)


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 Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:17.3
occ:1.00
 N C:NO2503 1.6 22.9 0.8
NE2 C:HIS134 2.0 15.9 1.0
NE2 C:HIS99 2.0 14.6 1.0
NE2 A:HIS289 2.1 15.2 1.0
O2 C:NO2503 2.1 22.3 0.8
O1 C:NO2503 2.5 21.6 0.8
CD2 C:HIS134 2.9 15.7 1.0
CE1 C:HIS99 3.0 14.3 1.0
CD2 A:HIS289 3.0 15.3 1.0
CE1 C:HIS134 3.1 16.4 1.0
CE1 A:HIS289 3.1 15.7 1.0
CD2 C:HIS99 3.1 14.7 1.0
OD2 C:ASP97 3.8 19.2 1.0
NE2 A:HIS240 3.9 15.9 1.0
CD2 A:HIS240 4.1 15.5 1.0
CG C:HIS134 4.1 16.1 1.0
ND1 C:HIS99 4.1 14.2 1.0
ND1 C:HIS134 4.1 16.2 1.0
CG A:HIS289 4.2 15.2 1.0
ND1 A:HIS289 4.2 15.0 1.0
CG C:HIS99 4.2 14.7 1.0
CG C:ASP97 4.3 18.1 1.0
OD1 C:ASP97 4.6 18.5 1.0
CE1 A:HIS240 4.6 15.8 1.0
O C:HOH756 4.8 17.5 1.0
CG A:HIS240 4.8 15.5 1.0
O C:HOH610 5.0 36.2 1.0

Copper binding site 7 out of 12 in 6qpt

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Copper binding site 7 out of 12 in the Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331)


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 Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu501

b:24.3
occ:1.00
 ND1 D:HIS94 2.0 27.3 1.0
ND1 D:HIS143 2.0 27.6 1.0
SG D:CYS135 2.2 23.1 1.0
SD D:MET148 2.5 25.1 1.0
CE1 D:HIS94 2.9 28.2 1.0
CE1 D:HIS143 2.9 28.2 1.0
CG D:HIS143 3.0 27.1 1.0
CG D:HIS94 3.1 28.0 1.0
CB D:CYS135 3.1 23.9 1.0
CB D:HIS143 3.5 26.1 1.0
CE D:MET148 3.5 25.3 1.0
CB D:HIS94 3.5 27.8 1.0
CA D:HIS94 3.8 28.1 1.0
NE2 D:HIS143 4.0 28.1 1.0
NE2 D:HIS94 4.1 28.4 1.0
CG D:MET148 4.1 24.5 1.0
CD2 D:HIS143 4.1 27.1 1.0
O D:PRO93 4.2 29.3 1.0
CD2 D:HIS94 4.2 28.8 1.0
OG1 D:THR137 4.2 26.8 1.0
CB D:THR137 4.2 27.4 1.0
CE3 D:TRP61 4.5 26.7 1.0
CA D:CYS135 4.5 23.2 1.0
CA D:HIS143 4.6 26.1 1.0
CB D:MET148 4.6 23.8 1.0
N D:ASN95 4.7 27.0 1.0
N D:HIS94 4.8 29.1 1.0
C D:HIS94 4.8 27.5 1.0
C D:PRO93 4.9 30.2 1.0
CZ3 D:TRP61 5.0 26.8 1.0

Copper binding site 8 out of 12 in 6qpt

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Copper binding site 8 out of 12 in the Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331)


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 Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu502

b:21.1
occ:1.00
 NE2 D:HIS99 2.0 18.6 1.0
O2 D:NO2503 2.0 24.6 0.8
NE2 E:HIS289 2.0 18.2 1.0
N D:NO2503 2.1 25.7 0.8
NE2 D:HIS134 2.1 20.5 1.0
O1 D:NO2503 2.5 25.0 0.8
CE1 D:HIS99 2.8 18.2 1.0
CD2 E:HIS289 3.0 17.3 1.0
CE1 E:HIS289 3.1 18.1 1.0
CD2 D:HIS134 3.1 20.9 1.0
CE1 D:HIS134 3.1 21.3 1.0
CD2 D:HIS99 3.1 18.6 1.0
OD2 D:ASP97 3.8 24.8 1.0
NE2 E:HIS240 4.0 16.6 1.0
ND1 D:HIS99 4.0 17.9 1.0
CD2 E:HIS240 4.1 16.4 1.0
CG E:HIS289 4.1 17.2 1.0
ND1 E:HIS289 4.2 17.7 1.0
CG D:HIS99 4.2 18.7 1.0
ND1 D:HIS134 4.2 21.3 1.0
CG D:HIS134 4.2 21.1 1.0
CG D:ASP97 4.3 23.3 1.0
OD1 D:ASP97 4.6 23.0 1.0
CE1 E:HIS240 4.8 16.4 1.0
O D:HOH716 4.8 24.4 1.0
O D:HOH601 4.9 17.2 0.5
CG E:HIS240 4.9 16.3 1.0

Copper binding site 9 out of 12 in 6qpt

Go back to Copper Binding Sites List in 6qpt
Copper binding site 9 out of 12 in the Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331)


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 Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu501

b:22.2
occ:1.00
 ND1 E:HIS143 2.0 23.6 1.0
ND1 E:HIS94 2.0 21.5 1.0
SG E:CYS135 2.2 21.0 1.0
SD E:MET148 2.6 21.4 1.0
CE1 E:HIS143 2.8 24.4 1.0
CE1 E:HIS94 3.0 22.4 1.0
CG E:HIS143 3.0 23.3 1.0
CG E:HIS94 3.0 22.3 1.0
CB E:CYS135 3.1 20.1 1.0
CB E:HIS94 3.4 22.2 1.0
CE E:MET148 3.4 21.5 1.0
CB E:HIS143 3.5 22.2 1.0
CA E:HIS94 3.8 23.0 1.0
NE2 E:HIS143 4.0 24.7 1.0
O E:PRO93 4.1 24.1 1.0
CD2 E:HIS143 4.1 24.1 1.0
OG1 E:THR137 4.1 23.4 1.0
NE2 E:HIS94 4.2 22.9 1.0
CB E:THR137 4.2 23.9 1.0
CG E:MET148 4.2 20.6 1.0
CD2 E:HIS94 4.2 22.9 1.0
CE3 E:TRP61 4.5 24.8 1.0
CA E:CYS135 4.5 19.4 1.0
CA E:HIS143 4.5 22.1 1.0
N E:ASN95 4.6 21.9 1.0
CB E:MET148 4.7 20.0 1.0
N E:HIS94 4.8 24.2 1.0
C E:HIS94 4.8 22.8 1.0
C E:PRO93 4.8 25.8 1.0
CZ3 E:TRP61 4.9 25.7 1.0
N E:THR137 5.0 22.0 1.0

Copper binding site 10 out of 12 in 6qpt

Go back to Copper Binding Sites List in 6qpt
Copper binding site 10 out of 12 in the Crystal Structure of Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331)


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 Nitrite Bound Synthetic Core Domain of Nitrite Reductase From Ralstonia Pickettii (Residues 1-331) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu502

b:19.1
occ:1.00
 N E:NO2503 1.9 21.1 0.5
NE2 E:HIS99 2.1 15.3 1.0
NE2 E:HIS134 2.1 15.2 1.0
O2 E:NO2503 2.1 21.0 0.8
NE2 F:HIS289 2.1 16.6 1.0
O1 E:NO2503 2.4 20.2 0.8
CE1 E:HIS99 3.0 14.7 1.0
CD2 E:HIS134 3.0 15.5 1.0
CD2 F:HIS289 3.1 16.5 1.0
CE1 E:HIS134 3.1 16.1 1.0
CD2 E:HIS99 3.1 15.5 1.0
CE1 F:HIS289 3.2 16.5 1.0
OD2 E:ASP97 3.6 18.9 1.0
NE2 F:HIS240 3.9 17.1 1.0
CD2 F:HIS240 4.1 17.0 1.0
ND1 E:HIS99 4.1 14.8 1.0
CG E:HIS134 4.2 16.0 1.0
ND1 E:HIS134 4.2 16.3 1.0
CG E:HIS99 4.2 15.2 1.0
CG F:HIS289 4.2 16.0 1.0
ND1 F:HIS289 4.3 15.7 1.0
CG E:ASP97 4.3 18.1 1.0
OD1 E:ASP97 4.6 17.8 1.0
CE1 F:HIS240 4.7 16.6 1.0
O E:HOH676 4.8 36.4 1.0
O E:HOH755 4.8 21.9 1.0
CG F:HIS240 4.9 16.2 1.0
O E:HOH789 5.0 30.6 1.0

Reference:

T.M.Hedison, R.T.Shenoy, A.I.Iorgu, D.J.Heyes, K.Fisher, G.Wright, S.Hay, R.R.Eady, S.S.Hasnain, N.S.Scrutton. Unexpected Roles of A Tether Harboring A Tyrosine Gatekeeper Residue in Modular Nitrite Reductase Catalysis Acs Catalysis 2019.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.9B01266
Page generated: Wed Jul 31 06:47:01 2024

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