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Cadmium in PDB 2xgl: The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential

Protein crystallography data

The structure of The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential, PDB code: 2xgl was solved by F.Gerard, M.A.Brooks, H.Barreteau, T.Touze, M.Graille, A.Bouhss, D.Blanot, H.V.Tilbeurgh, D.Mengin-Lecreulx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.24 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 52.000, 101.100, 43.520, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 26.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential (pdb code 2xgl). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential, PDB code: 2xgl:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 2xgl

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Cadmium binding site 1 out of 7 in the The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1116

b:29.8
occ:1.00
OE2 A:GLU109 2.2 23.6 1.0
OD1 B:ASP82 2.2 22.5 1.0
ND1 A:HIS106 2.3 17.7 1.0
CL B:CL1118 2.4 27.6 1.0
CG B:ASP82 2.9 15.1 1.0
OD2 B:ASP82 2.9 13.6 1.0
OH A:TYR111 3.0 11.8 1.0
CD A:GLU109 3.1 18.3 1.0
CG A:HIS106 3.2 12.4 1.0
CE1 A:HIS106 3.2 14.2 1.0
OE1 A:GLU109 3.4 20.0 1.0
CB A:HIS106 3.4 10.9 1.0
NZ B:LYS84 3.6 10.3 1.0
CZ A:TYR111 3.8 12.3 1.0
NE2 A:HIS106 4.2 14.1 1.0
CD2 A:HIS106 4.2 13.9 1.0
NA A:NA1124 4.2 25.9 1.0
CB B:ASP82 4.4 14.8 1.0
CE2 A:TYR111 4.4 12.4 1.0
CG A:GLU109 4.4 17.3 1.0
CE1 A:TYR111 4.6 12.1 1.0
CE B:LYS84 4.7 11.5 1.0
CB A:GLU109 4.7 14.6 1.0
O B:ASP82 4.7 12.9 1.0
CA A:HIS106 4.7 9.7 1.0
CG2 A:THR85 4.9 11.1 1.0

Cadmium binding site 2 out of 7 in 2xgl

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Cadmium binding site 2 out of 7 in the The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1117

b:38.5
occ:1.00
OD1 A:ASP79 2.2 28.0 1.0
OE1 B:GLU113 2.2 29.3 1.0
OE2 B:GLU113 2.8 24.3 1.0
CD B:GLU113 2.8 20.8 1.0
OD2 A:ASP79 2.8 24.5 1.0
CG A:ASP79 2.9 21.4 1.0
CG B:GLU113 4.3 15.6 1.0
CB A:ASP79 4.4 19.1 1.0
CB B:GLU113 4.9 12.2 1.0
CA A:ASP79 5.0 18.5 1.0

Cadmium binding site 3 out of 7 in 2xgl

Go back to Cadmium Binding Sites List in 2xgl
Cadmium binding site 3 out of 7 in the The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1118

b:38.3
occ:1.00
OD1 B:ASP79 2.2 29.7 1.0
OE1 A:GLU113 2.2 32.1 1.0
OD2 B:ASP79 2.7 25.1 1.0
CG B:ASP79 2.8 22.7 1.0
CD A:GLU113 2.9 23.4 1.0
OE2 A:GLU113 3.1 25.2 1.0
CB B:ASP79 4.3 20.5 1.0
CG A:GLU113 4.4 17.5 1.0
O A:HOH2008 4.8 5.9 1.0
CA B:ASP79 4.9 20.4 1.0

Cadmium binding site 4 out of 7 in 2xgl

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Cadmium binding site 4 out of 7 in the The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1119

b:48.2
occ:1.00
CL A:CL1128 2.4 49.8 1.0
OE2 A:GLU71 2.5 40.0 1.0
SD A:MET100 3.0 25.1 1.0
CD A:GLU71 3.2 35.6 1.0
CE A:MET100 3.3 22.1 1.0
OE1 A:GLU71 3.9 43.5 1.0
CG A:MET100 4.0 20.0 1.0
CG A:GLU71 4.0 27.1 1.0
CE A:LYS91 4.4 28.9 1.0
CG A:LYS91 4.9 18.3 1.0

Cadmium binding site 5 out of 7 in 2xgl

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Cadmium binding site 5 out of 7 in the The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1120

b:55.2
occ:1.00
OE2 A:GLU93 2.2 36.1 1.0
CD A:GLU93 3.0 26.8 1.0
OE1 A:GLU93 3.1 31.8 1.0
CG A:GLU93 4.4 19.4 1.0
CE A:LYS98 4.5 20.5 1.0
NZ A:LYS98 4.8 22.7 1.0

Cadmium binding site 6 out of 7 in 2xgl

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Cadmium binding site 6 out of 7 in the The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1116

b:27.8
occ:1.00
OE1 B:GLU109 2.2 17.7 1.0
OD1 A:ASP82 2.2 20.3 1.0
ND1 B:HIS106 2.3 16.1 1.0
CL A:CL1126 2.4 24.6 1.0
OD2 A:ASP82 2.9 12.4 1.0
CG A:ASP82 2.9 13.3 1.0
CD B:GLU109 3.0 13.9 1.0
OH B:TYR111 3.1 11.5 1.0
CE1 B:HIS106 3.2 13.2 1.0
CG B:HIS106 3.2 11.8 1.0
OE2 B:GLU109 3.2 15.5 1.0
CB B:HIS106 3.5 10.0 1.0
NZ A:LYS84 3.6 9.4 1.0
CZ B:TYR111 3.9 11.2 1.0
NA B:NA1126 4.1 54.1 1.0
CE2 B:TYR111 4.2 11.3 1.0
NE2 B:HIS106 4.2 13.3 1.0
CD2 B:HIS106 4.2 12.2 1.0
CG B:GLU109 4.4 12.6 1.0
CB A:ASP82 4.4 12.9 1.0
CE A:LYS84 4.7 10.9 1.0
O A:ASP82 4.7 11.7 1.0
CA B:HIS106 4.7 9.2 1.0
CB B:GLU109 4.8 11.2 1.0
CG2 B:THR85 4.8 10.7 1.0
CE1 B:TYR111 4.8 10.6 1.0

Cadmium binding site 7 out of 7 in 2xgl

Go back to Cadmium Binding Sites List in 2xgl
Cadmium binding site 7 out of 7 in the The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of The X-Ray Structure of the Escherichia Coli Colicin M Immunity Protein Demonstrates the Presence of A Disulphide Bridge, Which Is Functionally Essential within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1117

b:45.3
occ:1.00
CL B:CL1122 2.5 50.1 1.0
OE2 B:GLU71 2.7 36.9 1.0
SD B:MET100 3.0 25.4 1.0
CE B:MET100 3.3 23.4 1.0
CD B:GLU71 3.4 32.7 1.0
CG B:MET100 3.7 19.6 1.0
OE1 B:GLU71 4.1 40.3 1.0
CG B:GLU71 4.2 24.6 1.0
CE B:LYS91 4.5 25.9 1.0
O B:HOH2007 4.6 16.7 1.0
CB B:MET100 4.9 17.3 1.0
CG B:LYS91 5.0 15.9 1.0

Reference:

F.Gerard, M.A.Brooks, H.Barreteau, T.Touze, M.Graille, A.Bouhss, D.Blanot, H.V.Tilbeurgh, D.Mengin-Lecreulx. X-Ray Structure and Site-Directed Mutagenesis Analysis of the Escherichia Coli Colicin M Immunity Protein. J.Bacteriol. V. 193 205 2011.
ISSN: ISSN 0021-9193
PubMed: 21037007
DOI: 10.1128/JB.01119-10
Page generated: Fri Aug 28 13:15:37 2020
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