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Cadmium in PDB 4cvs: Structure of Apobacterioferritin Y45F Variant

Enzymatic activity of Structure of Apobacterioferritin Y45F Variant

All present enzymatic activity of Structure of Apobacterioferritin Y45F Variant:
1.16.3.1;

Protein crystallography data

The structure of Structure of Apobacterioferritin Y45F Variant, PDB code: 4cvs was solved by K.Hingorani, R.Pace, S.Whitney, J.W.Murray, T.Wydrzynski, M.H.Cheah, P.Smith, W.Hillier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.557 / 1.39
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.490, 27.840, 56.760, 90.00, 119.18, 90.00
R / Rfree (%) 20.3 / 22.49

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Apobacterioferritin Y45F Variant (pdb code 4cvs). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Structure of Apobacterioferritin Y45F Variant, PDB code: 4cvs:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 4cvs

Go back to Cadmium Binding Sites List in 4cvs
Cadmium binding site 1 out of 3 in the Structure of Apobacterioferritin Y45F Variant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Apobacterioferritin Y45F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1157

b:14.1
occ:1.00
OE2 A:GLU84 2.1 8.1 1.0
O A:HOH2078 2.2 15.9 1.0
O A:HOH2077 2.4 15.0 1.0
O A:HOH2079 2.4 18.0 1.0
O A:HOH2081 2.5 15.8 1.0
CD A:GLU84 3.1 8.4 1.0
OE1 A:GLU84 3.4 9.0 1.0
NH1 A:ARG88 4.1 15.2 1.0
O A:HOH2080 4.1 19.6 1.0
O A:HOH2127 4.2 23.3 1.0
OE1 A:GLN142 4.2 17.6 1.0
O A:HOH2129 4.4 18.1 1.0
CG A:GLU84 4.5 7.7 1.0
CZ A:ARG88 4.9 13.2 1.0

Cadmium binding site 2 out of 3 in 4cvs

Go back to Cadmium Binding Sites List in 4cvs
Cadmium binding site 2 out of 3 in the Structure of Apobacterioferritin Y45F Variant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Apobacterioferritin Y45F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1158

b:8.8
occ:1.00
OE2 A:GLU51 2.1 11.7 1.0
ND1 A:HIS130 2.3 8.6 1.0
OE1 A:GLU127 2.3 12.2 1.0
OE1 A:GLU94 2.4 9.2 1.0
OE2 A:GLU94 2.4 9.6 1.0
O A:HOH2016 2.6 15.2 1.0
CD A:GLU94 2.7 10.1 1.0
CD A:GLU51 2.9 14.0 1.0
OE1 A:GLU51 2.9 11.8 1.0
CE1 A:HIS130 3.2 9.1 1.0
CD A:GLU127 3.3 10.6 1.0
CG A:HIS130 3.4 8.1 1.0
CD A:CD1159 3.6 10.1 1.0
CB A:HIS130 3.7 8.1 1.0
OE2 A:GLU127 3.9 10.4 1.0
O A:HOH2089 3.9 22.0 1.0
CG A:GLU94 4.2 8.2 1.0
O A:HOH2088 4.2 12.2 1.0
CG A:GLU51 4.3 13.9 1.0
NE2 A:HIS130 4.3 9.7 1.0
CA A:GLU127 4.4 7.9 1.0
CG A:GLU127 4.5 9.1 1.0
CD2 A:HIS130 4.5 8.8 1.0
O A:HOH2115 4.5 16.8 1.0
CB A:GLU127 4.6 8.1 1.0
CE2 A:TYR25 4.6 11.3 1.0
OH A:TYR25 4.7 11.1 1.0
O A:HOH2024 5.0 18.4 1.0

Cadmium binding site 3 out of 3 in 4cvs

Go back to Cadmium Binding Sites List in 4cvs
Cadmium binding site 3 out of 3 in the Structure of Apobacterioferritin Y45F Variant


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Apobacterioferritin Y45F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1159

b:10.1
occ:1.00
OE2 A:GLU127 2.3 10.4 1.0
OE1 A:GLU18 2.3 10.2 1.0
OE1 A:GLU51 2.4 11.8 1.0
ND1 A:HIS54 2.4 10.8 1.0
OE2 A:GLU18 2.4 12.7 1.0
O A:HOH2016 2.5 15.2 1.0
CD A:GLU18 2.7 10.3 1.0
OE1 A:GLU127 2.9 12.2 1.0
CD A:GLU127 3.0 10.6 1.0
CE1 A:HIS54 3.2 10.1 1.0
CD A:GLU51 3.2 14.0 1.0
CG A:HIS54 3.4 10.5 1.0
CD A:CD1158 3.6 8.8 1.0
OE2 A:GLU51 3.7 11.7 1.0
CB A:HIS54 3.7 10.8 1.0
CA A:GLU51 4.2 14.1 1.0
O A:HOH2017 4.2 11.4 1.0
CG A:GLU18 4.2 12.1 1.0
CB A:GLU51 4.3 13.7 1.0
CG A:GLU51 4.3 13.9 1.0
NE2 A:HIS54 4.4 10.2 1.0
CG A:GLU127 4.4 9.1 1.0
O A:HOH2115 4.4 16.8 1.0
CD2 A:HIS54 4.5 10.4 1.0
CG2 A:ILE123 4.5 9.7 1.0
CE1 A:HIS130 4.8 9.1 1.0
ND1 A:HIS130 4.9 8.6 1.0
N A:GLU51 4.9 14.4 1.0
O A:GLU51 5.0 14.2 1.0

Reference:

K.Hingorani, R.Pace, S.Whitney, J.W.Murray, P.Smith, M.H.Cheah, T.Wydrzynski, W.Hillier. Photo-Oxidation of Tyrosine in A Bio-Engineered Bacterioferritin 'Reaction Centre'-A Protein Model For Artificial Photosynthesis. Biochim.Biophys.Acta V.1837 1821 2014.
ISSN: ISSN 0006-3002
PubMed: 25107631
DOI: 10.1016/J.BBABIO.2014.07.019
Page generated: Sat Dec 12 08:24:18 2020

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