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Cadmium in PDB 1c6r: Crystal Structure of Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus

Protein crystallography data

The structure of Crystal Structure of Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus, PDB code: 1c6r was solved by J.Schnackenberg, M.E.Than, K.Mann, G.Wiegand, R.Huber, W.Reuter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 35.560, 48.470, 43.920, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 26

Other elements in 1c6r:

The structure of Crystal Structure of Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus also contains other interesting chemical elements:

Iron (Fe) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus (pdb code 1c6r). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus, PDB code: 1c6r:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 1c6r

Go back to Cadmium Binding Sites List in 1c6r
Cadmium binding site 1 out of 4 in the Crystal Structure of Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus


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 Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd91

b:7.0
occ:0.50
O A:HOH149 1.8 14.6 1.0
O A:HOH120 1.9 16.1 1.0
OD2 A:ASP3 2.0 10.6 1.0
CG A:ASP3 3.1 8.8 1.0
OD1 A:ASP3 3.4 8.2 1.0
O A:HOH106 4.2 12.3 1.0
CB A:ASP3 4.4 8.7 1.0
O A:HOH103 4.5 7.0 1.0
CB A:LEU6 4.6 7.6 1.0
CD2 A:LEU6 5.0 7.0 1.0

Cadmium binding site 2 out of 4 in 1c6r

Go back to Cadmium Binding Sites List in 1c6r
Cadmium binding site 2 out of 4 in the Crystal Structure of Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus


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 Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd92

b:7.0
occ:1.00
OD2 A:ASP69 2.0 11.6 1.0
OD1 A:ASP71 2.2 9.1 1.0
OD2 A:ASP71 2.3 8.5 1.0
CG A:ASP71 2.6 9.6 1.0
O A:HOH151 2.7 15.0 1.0
CG A:ASP69 2.8 11.7 1.0
OD1 A:ASP69 2.9 11.1 1.0
CB A:ASP71 4.1 9.1 1.0
CB A:ASP69 4.3 11.3 1.0
CG A:GLU72 4.3 7.8 1.0
OE2 A:GLU72 4.4 8.1 1.0
O A:HOH136 4.4 22.1 1.0
CD A:GLU72 4.5 8.4 1.0
O A:HOH143 4.6 27.2 1.0
N A:GLU72 4.8 8.0 1.0
O A:HOH103 4.8 7.0 1.0
N A:ASP71 4.8 8.4 1.0
CA A:ASP71 4.8 8.8 1.0

Cadmium binding site 3 out of 4 in 1c6r

Go back to Cadmium Binding Sites List in 1c6r
Cadmium binding site 3 out of 4 in the Crystal Structure of Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus


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 Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd93

b:30.0
occ:1.00
O A:HOH148 1.6 17.4 1.0
NE2 A:HIS30 2.7 9.5 1.0
O1D A:HEM90 3.1 11.9 1.0
CD2 A:HIS30 3.3 10.1 1.0
CE1 A:HIS30 3.8 8.9 1.0
CGD A:HEM90 4.0 9.6 1.0
O2D A:HEM90 4.1 10.9 1.0
O A:PHE40 4.4 15.5 1.0
CG A:HIS30 4.5 9.7 1.0
CD1 A:PHE40 4.6 16.6 1.0
CB A:PHE40 4.7 15.6 1.0
ND1 A:HIS30 4.7 9.2 1.0
O A:HOH134 4.8 21.7 1.0

Cadmium binding site 4 out of 4 in 1c6r

Go back to Cadmium Binding Sites List in 1c6r
Cadmium binding site 4 out of 4 in the Crystal Structure of Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Reduced Cytochrome C6 From the Green Algae Scenedesmus Obliquus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd94

b:34.3
occ:0.50
O A:TRP89 1.6 19.2 1.0
C A:TRP89 2.6 14.7 1.0
O A:HOH162 2.6 29.0 1.0
OXT A:TRP89 2.9 17.6 1.0
CA A:TRP89 4.0 15.7 1.0
CB A:TRP89 4.7 13.5 1.0
O A:HOH163 4.8 26.1 1.0
N A:TRP89 4.9 14.1 1.0

Reference:

J.Schnackenberg, M.E.Than, K.Mann, G.Wiegand, R.Huber, W.Reuter. Amino Acid Sequence, Crystallization and Structure Determination of Reduced and Oxidized Cytochrome C6 From the Green Alga Scenedesmus Obliquus. J.Mol.Biol. V. 290 1019 1999.
ISSN: ISSN 0022-2836
PubMed: 10438600
DOI: 10.1006/JMBI.1999.2944
Page generated: Sat Dec 12 08:08:29 2020

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