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Copper in PDB 6dyf: Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y

Protein crystallography data

The structure of Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y, PDB code: 6dyf was solved by F.A.Tezcan, J.Rittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.44 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.742, 82.882, 38.528, 90.00, 98.96, 90.00
R / Rfree (%) 14.7 / 16.5

Other elements in 6dyf:

The structure of Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Chlorine (Cl) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y (pdb code 6dyf). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total only one binding site of Copper was determined in the Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y, PDB code: 6dyf:

Copper binding site 1 out of 1 in 6dyf

Go back to Copper Binding Sites List in 6dyf
Copper binding site 1 out of 1 in the Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:13.1
occ:1.00
NE2 B:HIS67 2.0 13.0 1.0
NE2 A:HIS67 2.0 12.7 1.0
NE2 A:HIS71 2.1 13.1 1.0
NE2 B:HIS71 2.1 13.5 1.0
NE2 A:HIS97 2.2 12.3 1.0
CD2 B:HIS67 2.9 13.4 1.0
CE1 A:HIS67 2.9 13.2 1.0
CE1 B:HIS71 3.0 14.2 1.0
CE1 B:HIS67 3.0 13.6 1.0
CE1 A:HIS71 3.0 13.6 1.0
CE1 A:HIS97 3.0 13.2 1.0
CD2 A:HIS67 3.1 12.8 1.0
HD2 B:HIS67 3.1 16.1 1.0
CD2 A:HIS71 3.1 12.7 1.0
HE1 A:HIS67 3.1 15.8 1.0
CD2 B:HIS71 3.1 13.5 1.0
HE1 B:HIS71 3.1 17.1 1.0
HE1 A:HIS97 3.2 15.9 1.0
HE1 A:HIS71 3.2 16.3 1.0
CD2 A:HIS97 3.2 13.2 1.0
HE1 B:HIS67 3.2 16.3 1.0
HD2 A:HIS71 3.3 15.3 1.0
HD2 A:HIS67 3.3 15.4 1.0
HD2 B:HIS71 3.3 16.2 1.0
HD2 A:HIS97 3.5 15.9 1.0
CG B:HIS67 4.1 13.7 1.0
ND1 A:HIS67 4.1 14.2 1.0
ND1 B:HIS67 4.1 14.5 1.0
ND1 A:HIS97 4.1 14.0 1.0
HE1 B:HIS97 4.1 16.6 1.0
ND1 B:HIS71 4.1 14.5 1.0
ND1 A:HIS71 4.2 13.2 1.0
CG A:HIS67 4.2 13.6 1.0
CG A:HIS71 4.2 13.1 1.0
CG B:HIS71 4.2 14.1 1.0
CG A:HIS97 4.2 13.5 1.0
HD1 B:TYR70 4.4 18.5 1.0
HD1 A:TYR70 4.5 18.7 1.0
HE1 A:TYR70 4.5 19.6 1.0
CE1 B:HIS97 4.5 13.8 1.0
HD1 A:HIS67 4.9 17.0 1.0
NE2 B:HIS97 4.9 14.5 1.0
HD1 A:HIS97 4.9 16.8 1.0
HB3 A:GLN93 4.9 18.1 1.0
HD1 B:HIS67 4.9 17.4 1.0
HD1 B:HIS71 4.9 17.4 1.0
HD1 A:HIS71 4.9 15.8 1.0
O A:GLN93 5.0 15.4 1.0
CD1 B:TYR70 5.0 15.4 1.0

Reference:

J.Rittle, M.J.Field, M.T.Green, F.A.Tezcan. An Efficient, Step-Economical Strategy For the Design of Functional Metalloproteins. Nat.Chem. V. 11 434 2019.
ISSN: ESSN 1755-4349
PubMed: 30778140
DOI: 10.1038/S41557-019-0218-9
Page generated: Sun Dec 13 11:22:10 2020

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