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Copper in PDB 1nds: Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans

Enzymatic activity of Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans

All present enzymatic activity of Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans:
1.7.99.3;

Protein crystallography data

The structure of Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 1nds was solved by F.E.Dodd, S.S.Hasnain, Z.H.L.Abraham, R.R.Eady, B.E.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.890, 102.200, 151.880, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 28

Copper Binding Sites:

The binding sites of Copper atom in the Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans (pdb code 1nds). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 1nds:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1nds

Go back to Copper Binding Sites List in 1nds
Copper binding site 1 out of 6 in the Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:10.2
occ:1.00
 ND1 A:HIS145 2.0 3.9 1.0
SG A:CYS136 2.1 4.5 1.0
ND1 A:HIS95 2.1 6.4 1.0
SD A:MET150 2.7 5.2 1.0
CE1 A:HIS145 2.9 3.9 1.0
CE1 A:HIS95 3.1 6.4 1.0
CG A:HIS145 3.1 3.9 1.0
CG A:HIS95 3.2 6.4 1.0
CB A:CYS136 3.3 4.5 1.0
CB A:HIS145 3.5 3.9 1.0
CB A:HIS95 3.6 6.4 1.0
CA A:HIS95 3.9 6.4 1.0
CG A:MET150 4.0 5.2 1.0
NE2 A:HIS145 4.0 3.9 1.0
CE A:MET150 4.1 5.2 1.0
CD2 A:HIS145 4.2 3.9 1.0
NE2 A:HIS95 4.2 6.4 1.0
CD2 A:HIS95 4.3 6.4 1.0
CB A:MET150 4.6 5.2 1.0
CA A:HIS145 4.7 3.9 1.0
CA A:CYS136 4.7 4.5 1.0
N A:HIS95 4.9 6.4 1.0
C A:HIS95 5.0 6.4 1.0

Copper binding site 2 out of 6 in 1nds

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Copper binding site 2 out of 6 in the Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:2.0
occ:1.00
 O2 A:NO2503 1.7 29.3 1.0
NE2 A:HIS135 2.0 2.6 1.0
NE2 B:HIS306 2.1 2.0 1.0
NE2 A:HIS100 2.2 2.8 1.0
O1 A:NO2503 2.4 29.3 1.0
N A:NO2503 2.5 29.3 1.0
CE1 A:HIS135 2.9 2.6 1.0
CE1 B:HIS306 3.0 2.0 1.0
CE1 A:HIS100 3.0 2.8 1.0
CD2 A:HIS135 3.1 2.6 1.0
CD2 B:HIS306 3.2 2.0 1.0
CD2 A:HIS100 3.3 2.8 1.0
ND1 A:HIS135 4.0 2.6 1.0
ND1 B:HIS306 4.1 2.0 1.0
CG A:HIS135 4.2 2.6 1.0
ND1 A:HIS100 4.2 2.8 1.0
CG B:HIS306 4.3 2.0 1.0
CG A:HIS100 4.4 2.8 1.0

Copper binding site 3 out of 6 in 1nds

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Copper binding site 3 out of 6 in the Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:10.2
occ:1.00
 ND1 B:HIS145 2.0 3.9 1.0
ND1 B:HIS95 2.1 6.4 1.0
SG B:CYS136 2.2 4.5 1.0
SD B:MET150 2.6 5.2 1.0
CE1 B:HIS145 2.9 3.9 1.0
CE1 B:HIS95 3.0 6.4 1.0
CG B:HIS95 3.1 6.4 1.0
CG B:HIS145 3.1 3.9 1.0
CB B:CYS136 3.3 4.5 1.0
CB B:HIS95 3.5 6.4 1.0
CB B:HIS145 3.6 3.9 1.0
CA B:HIS95 3.9 6.4 1.0
CG B:MET150 4.0 5.2 1.0
CE B:MET150 4.0 5.2 1.0
NE2 B:HIS145 4.1 3.9 1.0
NE2 B:HIS95 4.1 6.4 1.0
CD2 B:HIS145 4.2 3.9 1.0
CD2 B:HIS95 4.2 6.4 1.0
CB B:MET150 4.6 5.2 1.0
CA B:CYS136 4.7 4.5 1.0
CA B:HIS145 4.7 3.9 1.0
N B:HIS95 4.9 6.4 1.0
C B:HIS95 5.0 6.4 1.0

Copper binding site 4 out of 6 in 1nds

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Copper binding site 4 out of 6 in the Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:2.0
occ:1.00
 O2 B:NO2503 1.8 29.3 1.0
NE2 C:HIS306 2.0 2.0 1.0
NE2 B:HIS135 2.1 2.6 1.0
NE2 B:HIS100 2.1 2.8 1.0
O1 B:NO2503 2.4 29.3 1.0
N B:NO2503 2.5 29.3 1.0
CE1 C:HIS306 2.9 2.0 1.0
CE1 B:HIS100 2.9 2.8 1.0
CE1 B:HIS135 3.0 2.6 1.0
CD2 C:HIS306 3.0 2.0 1.0
CD2 B:HIS135 3.1 2.6 1.0
CD2 B:HIS100 3.3 2.8 1.0
ND1 C:HIS306 4.0 2.0 1.0
CG C:HIS306 4.1 2.0 1.0
ND1 B:HIS135 4.1 2.6 1.0
ND1 B:HIS100 4.1 2.8 1.0
CG B:HIS135 4.2 2.6 1.0
CG B:HIS100 4.3 2.8 1.0

Copper binding site 5 out of 6 in 1nds

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Copper binding site 5 out of 6 in the Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:10.2
occ:1.00
 ND1 C:HIS145 1.9 3.9 1.0
ND1 C:HIS95 2.1 6.4 1.0
SG C:CYS136 2.2 4.5 1.0
SD C:MET150 2.6 5.2 1.0
CE1 C:HIS145 2.8 3.9 1.0
CE1 C:HIS95 3.0 6.4 1.0
CG C:HIS145 3.0 3.9 1.0
CG C:HIS95 3.2 6.4 1.0
CB C:CYS136 3.3 4.5 1.0
CB C:HIS145 3.5 3.9 1.0
CB C:HIS95 3.6 6.4 1.0
CA C:HIS95 3.9 6.4 1.0
CG C:MET150 4.0 5.2 1.0
NE2 C:HIS145 4.0 3.9 1.0
CE C:MET150 4.0 5.2 1.0
CD2 C:HIS145 4.1 3.9 1.0
NE2 C:HIS95 4.2 6.4 1.0
CD2 C:HIS95 4.3 6.4 1.0
CB C:MET150 4.6 5.2 1.0
CA C:HIS145 4.7 3.9 1.0
CA C:CYS136 4.7 4.5 1.0
N C:HIS95 4.9 6.4 1.0
C C:HIS95 5.0 6.4 1.0

Copper binding site 6 out of 6 in 1nds

Go back to Copper Binding Sites List in 1nds
Copper binding site 6 out of 6 in the Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystallographic Structure of A Substrate Bound Blue Copper Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:2.0
occ:1.00
 O2 C:NO2503 1.7 29.3 1.0
NE2 A:HIS306 2.0 2.0 1.0
NE2 C:HIS135 2.0 2.6 1.0
NE2 C:HIS100 2.1 2.8 1.0
O1 C:NO2503 2.4 29.3 1.0
N C:NO2503 2.5 29.3 1.0
CE1 A:HIS306 2.9 2.0 1.0
CE1 C:HIS135 2.9 2.6 1.0
CE1 C:HIS100 3.0 2.8 1.0
CD2 A:HIS306 3.1 2.0 1.0
CD2 C:HIS135 3.1 2.6 1.0
CD2 C:HIS100 3.3 2.8 1.0
ND1 A:HIS306 4.1 2.0 1.0
ND1 C:HIS135 4.1 2.6 1.0
ND1 C:HIS100 4.2 2.8 1.0
CG A:HIS306 4.2 2.0 1.0
CG C:HIS135 4.2 2.6 1.0
CG C:HIS100 4.3 2.8 1.0

Reference:

F.E.Dodd, S.S.Hasnain, Z.H.Abraham, R.R.Eady, B.E.Smith. Structures of A Blue-Copper Nitrite Reductase and Its Substrate-Bound Complex. Acta Crystallogr.,Sect.D V. 53 406 1997.
ISSN: ISSN 0907-4449
PubMed: 15299906
DOI: 10.1107/S0907444997002667
Page generated: Tue Jul 30 22:25:26 2024

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