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Copper in PDB 1nib: The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted

Enzymatic activity of The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted

All present enzymatic activity of The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted:
1.7.99.3;

Protein crystallography data

The structure of The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted, PDB code: 1nib was solved by E.T.Adman, J.W.Godden, S.Turley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.560, 115.360, 115.700, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / n/a

Copper Binding Sites:

The binding sites of Copper atom in the The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted (pdb code 1nib). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted, PDB code: 1nib:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1nib

Go back to Copper Binding Sites List in 1nib
Copper binding site 1 out of 6 in the The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:8.0
occ:1.00
 ND1 A:HIS145 1.9 10.2 1.0
ND1 A:HIS95 2.0 8.6 1.0
SG A:CYS136 2.1 7.6 1.0
SD A:MET150 2.5 8.4 1.0
CE1 A:HIS145 2.9 8.7 1.0
CE1 A:HIS95 3.0 5.2 1.0
CG A:HIS145 3.0 9.4 1.0
CG A:HIS95 3.1 7.7 1.0
CB A:CYS136 3.2 6.3 1.0
CE A:MET150 3.4 8.1 1.0
CB A:HIS145 3.4 6.0 1.0
CB A:HIS95 3.5 4.9 1.0
CG A:MET150 3.9 2.1 1.0
CA A:HIS95 4.0 5.7 1.0
NE2 A:HIS145 4.1 7.7 1.0
CG A:PRO138 4.1 10.7 1.0
CD2 A:HIS145 4.1 8.3 1.0
NE2 A:HIS95 4.2 4.9 1.0
CD2 A:HIS95 4.2 7.3 1.0
CB A:MET150 4.3 2.0 1.0
O A:LEU94 4.5 10.9 1.0
CA A:CYS136 4.6 3.0 1.0
CA A:HIS145 4.6 3.1 1.0
SD A:MET62 4.6 9.0 1.0
CD A:PRO138 4.6 6.8 1.0
N A:ASN96 4.8 6.1 1.0
CB A:MET62 4.8 6.9 1.0

Copper binding site 2 out of 6 in 1nib

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Copper binding site 2 out of 6 in the The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:13.3
occ:1.00
 NE2 B:HIS306 1.9 6.6 1.0
NE2 A:HIS135 2.0 7.4 1.0
NE2 A:HIS100 2.0 5.7 1.0
O A:HOH503 2.1 8.9 1.0
CE1 B:HIS306 2.8 2.0 1.0
CE1 A:HIS100 2.8 2.0 1.0
CE1 A:HIS135 3.0 6.4 1.0
CD2 A:HIS135 3.1 4.4 1.0
CD2 B:HIS306 3.1 5.3 1.0
CD2 A:HIS100 3.2 5.7 1.0
NE2 B:HIS255 3.9 5.1 1.0
OD2 A:ASP98 3.9 17.6 1.0
ND1 B:HIS306 4.0 5.2 1.0
ND1 A:HIS100 4.1 2.0 1.0
ND1 A:HIS135 4.1 6.0 1.0
CG B:HIS306 4.1 5.6 1.0
CG A:HIS135 4.2 5.4 1.0
CD2 B:HIS255 4.2 5.0 1.0
CG A:HIS100 4.3 4.8 1.0
CE1 B:HIS255 4.4 3.3 1.0
CG A:ASP98 4.6 17.5 1.0
O A:HOH521 4.7 19.9 1.1
CG B:HIS255 4.8 4.0 1.0
OD1 A:ASP98 4.9 20.2 1.0
ND1 B:HIS255 4.9 5.6 1.0
CD2 B:LEU308 4.9 2.0 1.0
CG1 B:ILE257 4.9 8.3 1.0

Copper binding site 3 out of 6 in 1nib

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Copper binding site 3 out of 6 in the The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:11.3
occ:1.00
 ND1 B:HIS145 2.0 9.1 1.0
ND1 B:HIS95 2.0 9.1 1.0
SG B:CYS136 2.2 7.5 1.0
SD B:MET150 2.5 6.5 1.0
CE1 B:HIS145 2.8 8.0 1.0
CG B:HIS95 3.0 6.9 1.0
CE1 B:HIS95 3.0 6.0 1.0
CG B:HIS145 3.1 8.9 1.0
CB B:CYS136 3.2 2.3 1.0
CB B:HIS95 3.3 4.9 1.0
CE B:MET150 3.4 2.0 1.0
CB B:HIS145 3.6 4.1 1.0
CA B:HIS95 3.8 5.9 1.0
CG B:MET150 3.9 3.1 1.0
NE2 B:HIS145 4.0 7.9 1.0
CG B:PRO138 4.1 8.0 1.0
CD2 B:HIS95 4.1 7.6 1.0
NE2 B:HIS95 4.1 6.3 1.0
CD2 B:HIS145 4.2 6.8 1.0
O B:LEU94 4.3 8.0 1.0
CB B:MET150 4.5 2.1 1.0
SD B:MET62 4.5 11.6 1.0
CD B:PRO138 4.5 6.7 1.0
N B:ASN96 4.6 7.5 1.0
CA B:CYS136 4.6 4.1 1.0
CA B:HIS145 4.7 3.8 1.0
C B:HIS95 4.8 6.8 1.0
N B:HIS95 4.8 6.0 1.0
CB B:MET62 4.9 4.8 1.0
C B:LEU94 5.0 7.1 1.0

Copper binding site 4 out of 6 in 1nib

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Copper binding site 4 out of 6 in the The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:8.9
occ:1.00
 NE2 B:HIS135 2.0 5.3 1.0
O B:HOH503 2.0 10.5 1.0
NE2 B:HIS100 2.0 5.6 1.0
NE2 C:HIS306 2.0 5.2 1.0
CE1 B:HIS100 2.9 4.8 1.0
CE1 C:HIS306 2.9 5.8 1.0
CE1 B:HIS135 2.9 2.0 1.0
CD2 C:HIS306 3.1 3.8 1.0
CD2 B:HIS135 3.1 5.5 1.0
CD2 B:HIS100 3.1 2.4 1.0
OD2 B:ASP98 3.5 17.6 1.0
NE2 C:HIS255 3.9 7.2 1.0
ND1 B:HIS100 4.1 2.0 1.0
ND1 C:HIS306 4.1 7.1 1.0
ND1 B:HIS135 4.1 2.8 1.0
CG C:HIS306 4.2 5.7 1.0
CG B:HIS135 4.2 2.4 1.0
CG B:HIS100 4.2 2.0 1.0
CD2 C:HIS255 4.2 6.8 1.0
CE1 C:HIS255 4.3 4.0 1.0
CG B:ASP98 4.6 16.7 1.0
O B:HOH518 4.7 16.6 1.0
CG1 C:ILE257 4.8 4.8 1.0
CG C:HIS255 4.9 6.7 1.0
ND1 C:HIS255 4.9 6.6 1.0

Copper binding site 5 out of 6 in 1nib

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Copper binding site 5 out of 6 in the The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:12.9
occ:1.00
 ND1 C:HIS95 1.9 8.6 1.0
ND1 C:HIS145 2.1 6.9 1.0
SG C:CYS136 2.1 4.6 1.0
SD C:MET150 2.5 4.9 1.0
CE1 C:HIS95 2.9 6.0 1.0
CE1 C:HIS145 2.9 8.2 1.0
CG C:HIS95 3.0 10.3 1.0
CB C:CYS136 3.2 4.6 1.0
CG C:HIS145 3.2 7.3 1.0
CB C:HIS95 3.3 6.2 1.0
CE C:MET150 3.4 2.5 1.0
CB C:HIS145 3.7 4.1 1.0
CA C:HIS95 3.8 5.6 1.0
CG C:MET150 4.0 3.8 1.0
NE2 C:HIS95 4.1 4.3 1.0
CD2 C:HIS95 4.1 7.4 1.0
CG C:PRO138 4.2 12.0 1.0
NE2 C:HIS145 4.2 6.8 1.0
O C:LEU94 4.2 6.5 1.0
CD2 C:HIS145 4.3 6.9 1.0
CB C:MET150 4.4 2.6 1.0
SD C:MET62 4.5 9.4 1.0
CD C:PRO138 4.6 12.6 1.0
CA C:CYS136 4.6 3.8 1.0
N C:ASN96 4.7 7.8 1.0
C C:HIS95 4.8 7.3 1.0
CA C:HIS145 4.8 4.4 1.0
N C:HIS95 4.8 5.6 1.0
CB C:MET62 4.9 6.0 1.0
C C:LEU94 4.9 5.4 1.0

Copper binding site 6 out of 6 in 1nib

Go back to Copper Binding Sites List in 1nib
Copper binding site 6 out of 6 in the The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of The Structure of Cu-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with Nitrite Bound and with Type II Cu Depleted within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:5.4
occ:1.00
 O A:HOH504 2.0 6.2 1.0
NE2 C:HIS100 2.0 7.5 1.0
NE2 C:HIS135 2.0 10.2 1.0
NE2 A:HIS306 2.0 8.7 1.0
CE1 C:HIS100 2.9 5.3 1.0
CE1 A:HIS306 2.9 5.5 1.0
CE1 C:HIS135 2.9 7.5 1.0
CD2 C:HIS100 3.1 6.0 1.0
CD2 C:HIS135 3.2 6.4 1.0
CD2 A:HIS306 3.2 5.8 1.0
NE2 A:HIS255 3.6 5.4 1.0
OD2 C:ASP98 4.0 23.6 1.0
ND1 C:HIS100 4.0 2.5 1.0
CE1 A:HIS255 4.1 7.8 1.0
ND1 A:HIS306 4.1 3.6 1.0
CD2 A:HIS255 4.1 6.2 1.0
ND1 C:HIS135 4.1 3.8 1.0
CG C:HIS100 4.2 4.5 1.0
CG C:HIS135 4.3 4.4 1.0
CG A:HIS306 4.3 5.9 1.0
CG C:ASP98 4.5 18.0 1.0
O C:HOH4306 4.6 24.9 1.1
OD1 C:ASP98 4.7 19.5 1.0
ND1 A:HIS255 4.8 9.5 1.0
CG A:HIS255 4.8 5.8 1.0
CG1 A:ILE257 4.9 8.2 1.0

Reference:

E.T.Adman, J.W.Godden, S.Turley. The Structure of Copper-Nitrite Reductase From Achromobacter Cycloclastes at Five pH Values, with NO2- Bound and with Type II Copper Depleted. J.Biol.Chem. V. 270 27458 1995.
ISSN: ISSN 0021-9258
PubMed: 7499203
DOI: 10.1074/JBC.270.46.27458
Page generated: Tue Jul 30 22:26:08 2024

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