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Cadmium in PDB 4i7z: Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain

Enzymatic activity of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain

All present enzymatic activity of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain:
1.10.9.1;

Protein crystallography data

The structure of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain, PDB code: 4i7z was solved by S.S.Hasan, J.T.Stofleth, E.Yamashita, W.A.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.52 / 2.80
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 159.451, 159.451, 362.746, 90.00, 90.00, 120.00
R / Rfree (%) 24.8 / 27.2

Other elements in 4i7z:

The structure of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain (pdb code 4i7z). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain, PDB code: 4i7z:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 4i7z

Go back to Cadmium Binding Sites List in 4i7z
Cadmium binding site 1 out of 3 in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd309

b:85.8
occ:1.00
OE2 A:GLU75 2.5 91.7 1.0
NE2 C:HIS143 2.5 71.8 1.0
O C:HOH401 2.5 91.2 1.0
O A:HOH404 3.3 68.3 1.0
CD A:GLU75 3.3 87.7 1.0
CD2 C:HIS143 3.3 72.4 1.0
HD2 C:HIS143 3.3 86.8 1.0
OE1 A:GLU75 3.4 89.3 1.0
CE1 C:HIS143 3.5 72.5 1.0
HE1 C:HIS143 3.7 86.9 1.0
O C:LYS140 3.9 94.4 1.0
O A:ASN74 3.9 63.3 1.0
HB3 A:ASN74 3.9 81.0 1.0
CG C:HIS143 4.5 71.8 1.0
ND1 C:HIS143 4.6 71.6 1.0
HA A:GLU75 4.6 79.9 1.0
CG A:GLU75 4.7 81.5 1.0
C A:ASN74 4.7 64.1 1.0
HG3 A:GLU75 4.8 97.8 1.0
CB A:ASN74 4.9 67.5 1.0

Cadmium binding site 2 out of 3 in 4i7z

Go back to Cadmium Binding Sites List in 4i7z
Cadmium binding site 2 out of 3 in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:0.1
occ:1.00
OD1 B:ASP58 2.4 89.5 1.0
OE2 F:GLU4 2.5 0.3 1.0
HZ1 C:LYS146 2.8 84.5 1.0
HZ2 C:LYS146 3.1 84.5 1.0
OE1 G:GLU3 3.1 0.0 1.0
OD2 B:ASP58 3.1 90.8 1.0
CG B:ASP58 3.1 89.2 1.0
NZ C:LYS146 3.3 70.4 1.0
OE2 G:GLU3 3.5 0.9 1.0
CD G:GLU3 3.6 0.3 1.0
CD F:GLU4 3.7 0.8 1.0
HB2 G:LEU5 3.7 87.8 1.0
HE3 C:LYS146 3.8 83.0 1.0
HD2 G:PRO4 4.0 0.8 1.0
HZ3 C:LYS146 4.0 84.5 1.0
OE1 F:GLU4 4.1 0.3 1.0
CE C:LYS146 4.2 69.2 1.0
HE21 C:GLN38 4.2 78.2 1.0
HB3 G:LEU5 4.2 87.8 1.0
H G:LEU5 4.3 99.1 1.0
HD22 G:LEU5 4.3 81.4 1.0
HA G:GLU3 4.3 0.0 1.0
CB G:LEU5 4.4 73.1 1.0
CB B:ASP58 4.6 82.7 1.0
HE2 C:LYS146 4.7 83.0 1.0
HG2 C:GLN38 4.7 82.0 1.0
HB2 B:ASP58 4.8 99.2 1.0
HG2 F:GLU4 4.8 0.6 1.0
NE2 C:GLN38 4.9 65.2 1.0
CG F:GLU4 4.9 0.9 1.0
CD G:PRO4 4.9 86.5 1.0
HD13 G:LEU5 4.9 86.8 1.0
HG3 C:GLN38 5.0 82.0 1.0
CG G:GLU3 5.0 0.6 1.0
HZ2 A:TRP88 5.0 75.4 1.0

Cadmium binding site 3 out of 3 in 4i7z

Go back to Cadmium Binding Sites List in 4i7z
Cadmium binding site 3 out of 3 in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd302

b:0.1
occ:1.00
HE2 C:HIS150 2.3 80.3 1.0
NE2 C:HIS150 2.9 66.9 1.0
HD2 C:HIS150 3.3 83.2 1.0
CD2 C:HIS150 3.4 69.3 1.0
HB3 C:ALA148 3.7 68.8 1.0
CE1 C:HIS150 4.0 69.5 1.0
HE1 C:HIS150 4.3 83.4 1.0
HD3 C:ARG14 4.4 92.2 1.0
HB3 B:GLU64 4.4 0.6 1.0
HH11 C:ARG14 4.6 91.2 1.0
CB C:ALA148 4.6 57.4 1.0
HB1 C:ALA148 4.6 68.8 1.0
NH1 C:ARG14 4.6 76.0 1.0
CG C:HIS150 4.6 71.1 1.0
CZ C:ARG14 4.8 78.5 1.0
HH12 C:ARG14 4.8 91.2 1.0
ND1 C:HIS150 4.9 70.1 1.0
OE1 B:GLU64 4.9 0.4 1.0
NE C:ARG14 5.0 79.2 1.0
HD2 C:ARG14 5.0 92.2 1.0
HB2 C:ALA148 5.0 68.8 1.0

Reference:

S.S.Hasan, J.T.Stofleth, E.Yamashita, W.A.Cramer. Lipid-Induced Conformational Changes Within the Cytochrome B6F Complex of Oxygenic Photosynthesis. Biochemistry V. 52 2649 2013.
ISSN: ISSN 0006-2960
PubMed: 23514009
DOI: 10.1021/BI301638H
Page generated: Fri Jul 19 17:28:37 2024

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