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Copper in PDB 5ony: As-Isolated Resting State Copper Nitrite Reductase From Achromobacter Xylosoxidans

Enzymatic activity of As-Isolated Resting State Copper Nitrite Reductase From Achromobacter Xylosoxidans

All present enzymatic activity of As-Isolated Resting State Copper Nitrite Reductase From Achromobacter Xylosoxidans:
1.7.2.1;

Protein crystallography data

The structure of As-Isolated Resting State Copper Nitrite Reductase From Achromobacter Xylosoxidans, PDB code: 5ony was solved by T.P.Halsted, K.Yamashita, K.Hirata, H.Ago, G.Ueno, T.Tosha, R.R.Eady, S.V.Antonyuk, M.Yamamoto, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.86 / 1.60
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 90.347, 90.347, 143.580, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 22.3

Other elements in 5ony:

The structure of As-Isolated Resting State Copper Nitrite Reductase From Achromobacter Xylosoxidans also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the As-Isolated Resting State Copper Nitrite Reductase From Achromobacter Xylosoxidans (pdb code 5ony). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the As-Isolated Resting State Copper Nitrite Reductase From Achromobacter Xylosoxidans, PDB code: 5ony:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 5ony

Go back to Copper Binding Sites List in 5ony
Copper binding site 1 out of 2 in the As-Isolated Resting State Copper Nitrite Reductase From Achromobacter Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of As-Isolated Resting State Copper Nitrite Reductase From Achromobacter Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:30.3
occ:1.00
ND1 A:HIS139 2.0 24.8 1.0
ND1 A:HIS89 2.1 25.7 1.0
SG A:CYS130 2.1 26.9 1.0
SD A:MET144 2.7 28.2 1.0
CE1 A:HIS139 2.9 25.7 1.0
CE1 A:HIS89 3.0 29.4 1.0
CG A:HIS139 3.1 24.0 1.0
CG A:HIS89 3.1 29.6 1.0
CB A:CYS130 3.2 27.5 1.0
CB A:HIS89 3.5 29.7 1.0
CE A:MET144 3.6 32.6 1.0
CB A:HIS139 3.6 21.9 1.0
CA A:HIS89 3.8 28.2 1.0
NE2 A:HIS139 4.0 26.9 1.0
O A:PRO88 4.1 31.6 1.0
CD A:PRO132 4.1 32.1 1.0
NE2 A:HIS89 4.2 27.9 1.0
CD2 A:HIS139 4.2 26.9 1.0
CG A:MET144 4.2 26.5 1.0
CD2 A:HIS89 4.2 28.2 1.0
CG A:PRO132 4.3 34.7 1.0
CA A:CYS130 4.5 24.8 1.0
SD A:MET56 4.6 28.3 1.0
CB A:MET144 4.6 24.4 1.0
N A:ASN90 4.7 26.0 1.0
N A:HIS89 4.8 29.7 1.0
CA A:HIS139 4.8 19.6 1.0
C A:HIS89 4.8 30.4 1.0
C A:PRO88 4.9 34.7 1.0

Copper binding site 2 out of 2 in 5ony

Go back to Copper Binding Sites List in 5ony
Copper binding site 2 out of 2 in the As-Isolated Resting State Copper Nitrite Reductase From Achromobacter Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of As-Isolated Resting State Copper Nitrite Reductase From Achromobacter Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:21.4
occ:1.00
O A:HOH660 1.7 29.1 1.0
NE2 A:HIS129 2.0 23.1 1.0
NE2 A:HIS94 2.0 20.4 1.0
CE1 A:HIS94 2.9 20.5 1.0
CD2 A:HIS129 2.9 19.1 1.0
CE1 A:HIS129 3.1 22.2 1.0
CD2 A:HIS94 3.1 19.9 1.0
OD2 A:ASP92 3.6 27.6 1.0
ND1 A:HIS94 4.1 19.9 1.0
CG A:HIS129 4.1 20.9 1.0
ND1 A:HIS129 4.1 22.5 1.0
CG A:HIS94 4.2 18.4 1.0
CG A:ASP92 4.3 28.0 1.0
OD1 A:ASP92 4.6 26.4 1.0
O A:HOH716 4.9 25.3 1.0

Reference:

T.P.Halsted, K.Yamashita, K.Hirata, H.Ago, G.Ueno, T.Tosha, R.R.Eady, S.V.Antonyuk, M.Yamamoto, S.S.Hasnain. An Unprecedented Dioxygen Species Revealed By Serial Femtosecond Rotation Crystallography in Copper Nitrite Reductase. Iucrj V. 5 22 2018.
ISSN: ESSN 2052-2525
PubMed: 29354268
DOI: 10.1107/S2052252517016128
Page generated: Sun Dec 13 11:19:34 2020

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