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Copper in PDB 5akr: Atomic Resolution Structure of Nitrite Bound State of the Achromobacter Cycloclastes Cu Nitrite Reductase at 0.87 A Resolution

Enzymatic activity of Atomic Resolution Structure of Nitrite Bound State of the Achromobacter Cycloclastes Cu Nitrite Reductase at 0.87 A Resolution

All present enzymatic activity of Atomic Resolution Structure of Nitrite Bound State of the Achromobacter Cycloclastes Cu Nitrite Reductase at 0.87 A Resolution:
1.7.2.1;

Protein crystallography data

The structure of Atomic Resolution Structure of Nitrite Bound State of the Achromobacter Cycloclastes Cu Nitrite Reductase at 0.87 A Resolution, PDB code: 5akr was solved by M.P.Blakeley, S.S.Hasnain, S.V.Antonyuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.41 / 0.87
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 94.948, 94.948, 94.948, 90.00, 90.00, 90.00
R / Rfree (%) 10.892 / 12.714

Copper Binding Sites:

The binding sites of Copper atom in the Atomic Resolution Structure of Nitrite Bound State of the Achromobacter Cycloclastes Cu Nitrite Reductase at 0.87 A Resolution (pdb code 5akr). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Atomic Resolution Structure of Nitrite Bound State of the Achromobacter Cycloclastes Cu Nitrite Reductase at 0.87 A Resolution, PDB code: 5akr:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 5akr

Go back to Copper Binding Sites List in 5akr
Copper binding site 1 out of 2 in the Atomic Resolution Structure of Nitrite Bound State of the Achromobacter Cycloclastes Cu Nitrite Reductase at 0.87 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Atomic Resolution Structure of Nitrite Bound State of the Achromobacter Cycloclastes Cu Nitrite Reductase at 0.87 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:6.0
occ:1.00
ND1 A:HIS145 2.0 5.9 1.0
ND1 A:HIS95 2.0 5.8 1.0
SG A:CYS136 2.2 6.5 1.0
SD A:MET150 2.5 6.2 1.0
CE1 A:HIS145 3.0 6.5 1.0
HB3 A:HIS145 3.0 5.5 1.0
CE1 A:HIS95 3.0 6.0 1.0
HE1 A:HIS145 3.1 6.4 1.0
CG A:HIS95 3.1 5.8 1.0
HB3 A:HIS95 3.1 5.8 1.0
CG A:HIS145 3.1 5.8 1.0
HE1 A:HIS95 3.1 5.9 1.0
HB3 A:CYS136 3.2 5.8 1.0
CB A:CYS136 3.2 5.9 1.0
HA A:HIS95 3.2 5.9 1.0
HE3 A:MET150 3.3 7.0 1.0
CE A:MET150 3.3 7.2 1.0
HB2 A:CYS136 3.3 5.9 1.0
HE2 A:MET150 3.4 6.8 1.0
CB A:HIS95 3.5 5.9 1.0
CB A:HIS145 3.5 5.6 1.0
CA A:HIS95 3.9 5.7 1.0
CG A:MET150 3.9 5.8 1.0
H A:ASN96 3.9 5.8 1.0
HG2 A:PRO138 4.0 7.2 1.0
HG2 A:MET150 4.0 5.8 1.0
HB3 A:MET150 4.0 5.5 1.0
HB2 A:HIS145 4.1 5.6 1.0
HB3 A:MET62 4.1 6.5 1.0
HD3 A:PRO138 4.1 6.6 1.0
NE2 A:HIS145 4.1 6.9 1.0
NE2 A:HIS95 4.2 6.0 1.0
CD2 A:HIS145 4.2 6.9 1.0
O A:LEU94 4.2 7.7 1.0
HE1 A:MET150 4.2 6.9 1.0
CD2 A:HIS95 4.2 6.0 1.0
HB2 A:MET150 4.3 5.6 1.0
CG A:PRO138 4.3 7.3 1.0
CB A:MET150 4.3 5.5 1.0
SD A:MET62 4.4 7.7 1.0
HB2 A:HIS95 4.4 5.8 1.0
HA A:HIS145 4.6 5.4 1.0
CA A:CYS136 4.6 5.3 1.0
HG3 A:MET150 4.6 5.9 1.0
CD A:PRO138 4.7 6.5 1.0
N A:ASN96 4.7 5.8 1.0
CA A:HIS145 4.7 5.3 1.0
N A:HIS95 4.8 6.5 1.0
HE2 A:HIS145 4.9 6.6 1.0
C A:HIS95 4.9 5.9 1.0
CB A:MET62 4.9 6.7 1.0
HB2 A:MET62 4.9 6.8 1.0
C A:LEU94 4.9 6.6 1.0
HE2 A:HIS95 4.9 5.9 1.0
HA A:CYS136 4.9 5.3 1.0

Copper binding site 2 out of 2 in 5akr

Go back to Copper Binding Sites List in 5akr
Copper binding site 2 out of 2 in the Atomic Resolution Structure of Nitrite Bound State of the Achromobacter Cycloclastes Cu Nitrite Reductase at 0.87 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Atomic Resolution Structure of Nitrite Bound State of the Achromobacter Cycloclastes Cu Nitrite Reductase at 0.87 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:6.2
occ:1.00
NE2 A:HIS100 2.0 5.4 1.0
NE2 A:HIS135 2.0 6.2 1.0
N A:NO2508 2.1 8.0 0.5
O A:HOH2698 2.2 27.8 0.5
O1 A:NO2508 2.3 21.5 0.5
O2 A:NO2508 2.3 17.0 0.5
CE1 A:HIS100 2.9 5.3 1.0
CD2 A:HIS135 3.0 6.0 1.0
CE1 A:HIS135 3.0 6.3 1.0
CD2 A:HIS100 3.1 5.2 1.0
HD2 A:HIS135 3.2 5.8 1.0
HD2 A:HIS100 3.3 5.2 1.0
OD2 A:ASP98 3.8 13.1 0.5
ND1 A:HIS100 4.1 5.2 1.0
CG A:HIS135 4.2 5.2 1.0
ND1 A:HIS135 4.2 5.7 1.0
O A:HOH2476 4.2 15.5 0.5
CG A:HIS100 4.2 4.7 1.0
O A:HOH2169 4.2 8.9 0.4
CG A:ASP98 4.4 8.4 0.5
OD1 A:ASP98 4.6 8.2 0.5
HG13 A:VAL133 4.6 5.9 1.0
HD1 A:HIS100 4.9 5.0 1.0
HD1 A:HIS135 4.9 5.6 1.0

Reference:

M.P.Blakeley, S.S.Hasnain, S.V.Antonyuk. Sub-Atomic Resolution X-Ray Crystallography and Neutron Crystallography: Promise, Challenges and Potential. Iucrj V. 2 464 2015.
ISSN: ISSN 2052-2525
PubMed: 26175905
DOI: 10.1107/S2052252515011239
Page generated: Sun Dec 13 11:16:58 2020

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