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Copper in PDB 5onx: Resting State Copper Nitrite Reductase Determined By Serial Femtosecond Rotation Crystallography

Enzymatic activity of Resting State Copper Nitrite Reductase Determined By Serial Femtosecond Rotation Crystallography

All present enzymatic activity of Resting State Copper Nitrite Reductase Determined By Serial Femtosecond Rotation Crystallography:
1.7.2.1;

Protein crystallography data

The structure of Resting State Copper Nitrite Reductase Determined By Serial Femtosecond Rotation Crystallography, PDB code: 5onx 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) 19.84 / 1.60
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 89.970, 89.970, 143.560, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 22.6

Other elements in 5onx:

The structure of Resting State Copper Nitrite Reductase Determined By Serial Femtosecond Rotation Crystallography also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Resting State Copper Nitrite Reductase Determined By Serial Femtosecond Rotation Crystallography (pdb code 5onx). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Resting State Copper Nitrite Reductase Determined By Serial Femtosecond Rotation Crystallography, PDB code: 5onx:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 5onx

Go back to Copper Binding Sites List in 5onx
Copper binding site 1 out of 2 in the Resting State Copper Nitrite Reductase Determined By Serial Femtosecond Rotation Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Resting State Copper Nitrite Reductase Determined By Serial Femtosecond Rotation Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:27.9
occ:1.00
ND1 A:HIS139 2.0 25.4 1.0
ND1 A:HIS89 2.0 26.8 1.0
SG A:CYS130 2.1 27.0 1.0
SD A:MET144 2.7 25.5 1.0
CE1 A:HIS139 2.9 28.4 1.0
CE1 A:HIS89 2.9 28.8 1.0
CG A:HIS139 3.0 27.2 1.0
CG A:HIS89 3.0 29.9 1.0
CB A:CYS130 3.2 26.0 1.0
CB A:HIS89 3.4 29.3 1.0
CB A:HIS139 3.5 25.8 1.0
CE A:MET144 3.7 29.9 1.0
CA A:HIS89 3.8 29.1 1.0
CG A:PRO132 3.9 29.6 1.0
O A:PRO88 4.0 29.4 1.0
NE2 A:HIS139 4.0 29.8 1.0
NE2 A:HIS89 4.0 31.3 1.0
CD2 A:HIS139 4.1 26.4 1.0
CD2 A:HIS89 4.1 27.9 1.0
CG A:MET144 4.2 24.2 1.0
CD A:PRO132 4.3 29.4 1.0
SD A:MET56 4.5 27.1 1.0
CA A:CYS130 4.6 24.5 1.0
N A:ASN90 4.7 28.1 1.0
CB A:MET144 4.7 24.0 1.0
CA A:HIS139 4.7 22.6 1.0
N A:HIS89 4.7 29.8 1.0
C A:PRO88 4.8 31.8 1.0
C A:HIS89 4.8 30.8 1.0

Copper binding site 2 out of 2 in 5onx

Go back to Copper Binding Sites List in 5onx
Copper binding site 2 out of 2 in the Resting State Copper Nitrite Reductase Determined By Serial Femtosecond Rotation Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Resting State Copper Nitrite Reductase Determined By Serial Femtosecond Rotation Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:24.3
occ:1.00
O1 A:OXY504 1.8 29.9 1.0
NE2 A:HIS129 2.0 25.8 1.0
NE2 A:HIS94 2.0 20.4 1.0
O2 A:OXY504 2.6 34.3 1.0
CE1 A:HIS94 2.9 21.1 1.0
CD2 A:HIS129 3.0 20.7 1.0
CE1 A:HIS129 3.0 24.5 1.0
CD2 A:HIS94 3.1 21.3 1.0
OD2 A:ASP92 3.6 27.5 1.0
ND1 A:HIS94 4.1 22.2 1.0
ND1 A:HIS129 4.1 23.9 1.0
CG A:HIS129 4.2 23.9 1.0
CG A:HIS94 4.2 22.4 1.0
CG A:ASP92 4.3 27.3 1.0
OD1 A:ASP92 4.6 25.1 1.0
O A:HOH612 4.9 26.0 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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