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Vanadium in PDB 6dyl: Vanadyl-Bound Structure of the Engineered Cyt B562 Variant, CH3Y*

Protein crystallography data

The structure of Vanadyl-Bound Structure of the Engineered Cyt B562 Variant, CH3Y*, PDB code: 6dyl 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) 49.20 / 1.69
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 49.031, 98.405, 178.753, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.6

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Vanadyl-Bound Structure of the Engineered Cyt B562 Variant, CH3Y* (pdb code 6dyl). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Vanadyl-Bound Structure of the Engineered Cyt B562 Variant, CH3Y*, PDB code: 6dyl:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 6dyl

Go back to Vanadium Binding Sites List in 6dyl
Vanadium binding site 1 out of 2 in the Vanadyl-Bound Structure of the Engineered Cyt B562 Variant, CH3Y*


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Vanadyl-Bound Structure of the Engineered Cyt B562 Variant, CH3Y* within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V201

b:18.9
occ:1.00
O E:HOH227 2.0 15.9 1.0
NE2 E:HIS71 2.1 16.2 1.0
NE2 A:HIS71 2.1 17.6 1.0
NE2 E:HIS67 2.2 19.9 1.0
NE2 A:HIS67 2.2 20.7 1.0
NE2 E:HIS97 2.2 16.3 1.0
CE1 E:HIS71 3.0 17.0 1.0
CD2 A:HIS67 3.0 21.3 1.0
CE1 E:HIS67 3.0 20.1 1.0
HD2 A:HIS67 3.1 25.6 1.0
HE1 E:HIS71 3.1 20.4 1.0
CE1 E:HIS97 3.1 20.4 1.0
HE1 E:HIS67 3.1 24.1 1.0
CE1 A:HIS71 3.1 17.8 1.0
CD2 A:HIS71 3.2 16.6 1.0
CD2 E:HIS71 3.2 16.2 1.0
HE1 E:HIS97 3.2 24.5 1.0
CD2 E:HIS67 3.2 16.8 1.0
CD2 E:HIS97 3.2 17.8 1.0
CE1 A:HIS67 3.2 19.4 1.0
HE1 A:HIS71 3.3 21.3 1.0
HD2 A:HIS71 3.3 19.9 1.0
HD2 E:HIS71 3.4 19.5 1.0
HD2 E:HIS97 3.5 21.4 1.0
HD2 E:HIS67 3.5 20.2 1.0
HE1 A:HIS67 3.5 23.3 1.0
ND1 E:HIS71 4.1 20.1 1.0
ND1 E:HIS67 4.2 21.6 1.0
CG A:HIS67 4.2 19.2 1.0
ND1 E:HIS97 4.2 18.1 1.0
ND1 A:HIS71 4.2 19.0 1.0
CG E:HIS71 4.3 13.0 1.0
ND1 A:HIS67 4.3 18.8 1.0
CG A:HIS71 4.3 16.9 1.0
CG E:HIS67 4.3 16.7 1.0
CG E:HIS97 4.3 19.6 1.0
HD1 A:TYR70 4.4 31.2 1.0
O E:HOH254 4.4 26.6 1.0
HE1 A:HIS97 4.5 27.8 1.0
CD1 A:TYR70 4.6 26.0 1.0
HE1 A:TYR70 4.7 28.6 1.0
CE1 A:TYR70 4.8 23.8 1.0
HD1 E:TYR70 4.9 31.6 1.0
CE1 A:HIS97 4.9 23.1 1.0
HD1 E:HIS71 4.9 24.1 1.0
HD1 E:HIS67 4.9 26.0 1.0
HD1 E:HIS97 5.0 21.7 1.0
HB3 A:TYR70 5.0 19.9 1.0

Vanadium binding site 2 out of 2 in 6dyl

Go back to Vanadium Binding Sites List in 6dyl
Vanadium binding site 2 out of 2 in the Vanadyl-Bound Structure of the Engineered Cyt B562 Variant, CH3Y*


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Vanadyl-Bound Structure of the Engineered Cyt B562 Variant, CH3Y* within 5.0Å range:
probe atom residue distance (Å) B Occ
C:V201

b:12.0
occ:1.00
O G:HOH261 2.0 13.5 1.0
NE2 G:HIS71 2.1 10.2 1.0
NE2 C:HIS67 2.1 11.8 1.0
NE2 C:HIS71 2.2 10.7 1.0
NE2 G:HIS67 2.2 11.3 1.0
NE2 G:HIS97 2.3 13.2 1.0
CE1 G:HIS71 3.0 12.4 1.0
CE1 G:HIS67 3.0 16.2 1.0
CD2 C:HIS67 3.1 10.2 1.0
CE1 C:HIS71 3.1 20.7 1.0
HE1 G:HIS67 3.1 19.4 1.0
HE1 G:HIS71 3.1 14.9 1.0
CD2 C:HIS71 3.2 10.8 1.0
CE1 C:HIS67 3.2 13.7 1.0
CD2 G:HIS71 3.2 12.6 1.0
CE1 G:HIS97 3.2 11.3 1.0
HD2 C:HIS67 3.2 12.2 1.0
CD2 G:HIS67 3.2 13.2 1.0
CD2 G:HIS97 3.3 12.2 1.0
HE1 C:HIS71 3.3 24.8 1.0
HE1 G:HIS97 3.3 13.6 1.0
HD2 C:HIS71 3.3 13.0 1.0
HE1 C:HIS67 3.4 16.4 1.0
HD2 G:HIS71 3.4 15.1 1.0
HD2 G:HIS97 3.4 14.7 1.0
HD2 G:HIS67 3.5 15.8 1.0
HD1 C:TYR70 4.1 20.3 1.0
ND1 G:HIS71 4.2 12.8 1.0
ND1 G:HIS67 4.2 14.3 1.0
ND1 C:HIS71 4.2 15.4 1.0
CG C:HIS67 4.2 12.1 1.0
ND1 C:HIS67 4.3 11.6 1.0
CG G:HIS71 4.3 13.1 1.0
CG C:HIS71 4.3 9.5 1.0
ND1 G:HIS97 4.3 14.8 1.0
CG G:HIS67 4.3 11.0 1.0
O G:HOH307 4.4 20.3 1.0
CG G:HIS97 4.4 12.6 1.0
HE1 C:HIS97 4.6 22.6 1.0
CD1 C:TYR70 4.7 16.9 1.0
HD1 G:TYR70 4.7 21.4 1.0
HE1 C:TYR70 4.8 21.0 1.0
CE1 C:HIS97 4.9 18.8 1.0
HD1 G:HIS71 4.9 15.3 1.0
HD1 G:HIS67 4.9 17.2 1.0
HB3 C:TYR70 5.0 13.2 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: Wed Dec 16 02:31:43 2020

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