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Sodium 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

Other elements in 2xgl:

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 also contains other interesting chemical elements:

Cadmium (Cd) 7 atoms
Chlorine (Cl) 11 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 14 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 2xgl

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Sodium binding site 1 out of 14 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 Sodium with other atoms in the Na 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:Na1122

b:45.6
occ:1.00
O A:GLU83 2.7 11.3 1.0
CL A:CL1129 3.0 45.2 1.0
OE1 A:GLU108 3.2 20.5 1.0
N A:CYS31 3.4 9.9 1.0
CA A:ALA30 3.6 12.1 1.0
CD A:GLU108 3.6 17.9 1.0
CD A:LYS84 3.6 10.4 1.0
CA A:LYS84 3.6 10.4 1.0
C A:GLU83 3.7 11.8 1.0
CG A:GLU108 3.8 13.8 1.0
CB A:ALA30 3.9 11.7 1.0
C A:ALA30 4.0 11.2 1.0
N A:LYS84 4.1 11.0 1.0
SG A:CYS31 4.2 10.8 1.0
CB A:CYS31 4.3 8.9 1.0
O A:LYS84 4.3 10.3 1.0
C A:LYS84 4.3 10.0 1.0
OE2 A:GLU108 4.4 21.3 1.0
CA A:CYS31 4.5 9.3 1.0
CB A:LYS84 4.5 10.9 1.0
CB A:GLU108 4.5 11.6 1.0
CE A:LYS84 4.5 10.9 1.0
CG A:LYS84 4.6 11.0 1.0
N A:ALA30 4.8 13.5 1.0
O A:PRO29 4.8 14.0 1.0
N A:GLU108 4.8 10.0 1.0
O A:ASP82 4.9 11.7 1.0
NZ A:LYS84 4.9 9.4 1.0

Sodium binding site 2 out of 14 in 2xgl

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Sodium binding site 2 out of 14 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 Sodium with other atoms in the Na 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:Na1123

b:35.0
occ:1.00
OH A:TYR105 3.0 10.8 1.0
O A:CYS107 3.3 10.8 1.0
CE1 A:PHE42 3.8 10.6 1.0
CZ A:TYR105 3.9 9.2 1.0
O A:LYS27 4.0 31.6 1.0
CE1 A:TYR105 4.1 9.1 1.0
CA A:GLY28 4.1 23.8 1.0
O A:GLU109 4.1 13.8 1.0
CA A:GLY110 4.1 13.4 1.0
CD A:PRO29 4.1 18.7 1.0
CZ A:PHE42 4.2 10.0 1.0
C A:CYS107 4.4 10.2 1.0
CD1 A:PHE42 4.5 10.0 1.0
C A:GLY110 4.9 12.5 1.0
C A:LYS27 4.9 31.2 1.0
C A:GLU109 4.9 13.8 1.0
CA A:CYS107 4.9 9.7 1.0
N A:PRO29 5.0 18.4 1.0

Sodium binding site 3 out of 14 in 2xgl

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Sodium binding site 3 out of 14 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 Sodium with other atoms in the Na 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:Na1124

b:25.9
occ:1.00
OD1 B:ASP82 2.9 22.5 1.0
OH A:TYR111 3.2 11.8 1.0
OE1 A:GLU109 3.6 20.0 1.0
CD A:GLU109 3.8 18.3 1.0
CG B:ASP82 3.8 15.1 1.0
CB B:ASP82 3.9 14.8 1.0
CA B:ASP82 4.1 13.9 1.0
CZ A:TYR111 4.1 12.3 1.0
CE2 A:TYR111 4.1 12.4 1.0
OE2 A:GLU109 4.2 23.6 1.0
CG A:GLU109 4.2 17.3 1.0
CD A:CD1116 4.2 29.8 1.0
O B:GLU81 4.6 15.0 1.0
NZ B:LYS84 4.6 10.3 1.0
N B:ASP82 4.7 14.6 1.0
C B:GLU81 4.8 15.5 1.0
OD2 B:ASP82 5.0 13.6 1.0

Sodium binding site 4 out of 14 in 2xgl

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Sodium binding site 4 out of 14 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 Sodium with other atoms in the Na 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:Na1127

b:39.2
occ:1.00
NH1 A:ARG40 3.7 22.9 1.0
CD A:ARG40 3.9 13.3 1.0
CG A:GLU37 4.0 36.2 1.0
CA A:GLU37 4.0 22.1 1.0
CB A:GLU37 4.1 26.1 1.0
CD A:GLU37 4.4 50.1 1.0
N A:GLU37 4.6 19.8 1.0
CZ A:ARG40 4.7 19.0 1.0
NE A:ARG40 4.8 16.3 1.0
OE2 A:GLU37 4.8 55.2 1.0
CB A:ARG40 4.8 10.8 1.0
OE1 A:GLU37 4.8 60.5 1.0
CG A:ARG40 4.9 10.6 1.0

Sodium binding site 5 out of 14 in 2xgl

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Sodium binding site 5 out of 14 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 Sodium with other atoms in the Na 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:Na1131

b:33.7
occ:1.00
O A:GLU74 3.0 24.8 1.0
OE2 A:GLU83 3.2 33.3 1.0
N A:LEU87 3.3 7.9 1.0
O A:THR85 3.6 9.8 1.0
CA A:LEU86 3.7 7.4 1.0
CD A:GLU83 3.8 29.8 1.0
C A:LEU86 4.0 7.3 1.0
OE1 A:GLU83 4.0 34.8 1.0
CB A:LEU87 4.1 9.9 1.0
CD2 A:LEU86 4.2 9.9 1.0
C A:GLU74 4.2 25.7 1.0
CA A:LEU87 4.3 8.4 1.0
C A:THR85 4.4 8.9 1.0
CL A:CL1125 4.4 46.4 1.0
CA A:ARG75 4.5 22.7 1.0
N A:LEU86 4.5 7.7 1.0
CB A:LEU86 4.6 7.2 1.0
CG A:GLU83 4.8 20.5 1.0
O A:LEU87 4.8 8.4 1.0
N A:ARG75 4.8 24.8 1.0
CG A:LEU86 5.0 7.8 1.0

Sodium binding site 6 out of 14 in 2xgl

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Sodium binding site 6 out of 14 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 Sodium with other atoms in the Na 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
A:Na1132

b:35.8
occ:1.00
OD2 A:ASP26 4.0 33.1 1.0
OD1 A:ASP26 4.2 35.3 1.0
CB A:GLU25 4.3 26.0 1.0
CG A:ASP26 4.3 34.1 1.0

Sodium binding site 7 out of 14 in 2xgl

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Sodium binding site 7 out of 14 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 Sodium with other atoms in the Na 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
A:Na1133

b:29.8
occ:1.00
OD1 A:ASP57 3.8 28.6 1.0
CB A:ASN56 4.0 27.6 1.0
ND2 A:ASN56 4.7 39.8 1.0
CB A:TRP54 4.8 21.1 1.0
CG A:TRP54 4.8 22.4 1.0
N A:ASN56 4.9 24.5 1.0
CD1 A:TRP54 4.9 25.4 1.0
CG A:ASN56 4.9 33.9 1.0
CG A:ASP57 5.0 20.6 1.0

Sodium binding site 8 out of 14 in 2xgl

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Sodium binding site 8 out of 14 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 Sodium with other atoms in the Na binding site number 8 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:Na1120

b:40.8
occ:1.00
OD1 B:ASP55 2.4 23.0 1.0
O B:LYS52 2.8 25.9 1.0
CG B:ASP55 3.5 24.9 1.0
C B:ARG53 3.7 22.8 1.0
O B:ARG53 3.8 24.0 1.0
CA B:ARG53 3.8 24.1 1.0
C B:LYS52 3.9 24.2 1.0
CA B:ASP55 4.2 22.0 1.0
N B:ASP55 4.2 21.6 1.0
N B:ARG53 4.3 23.6 1.0
OD2 B:ASP55 4.3 29.3 1.0
N B:TRP54 4.3 20.7 1.0
C B:TRP54 4.4 19.9 1.0
O B:HOH2005 4.4 30.1 1.0
CB B:ASP55 4.5 23.9 1.0
O B:TRP54 4.7 18.4 1.0
CA B:TRP54 5.0 20.1 1.0
CG2 B:VAL58 5.0 14.4 1.0

Sodium binding site 9 out of 14 in 2xgl

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Sodium binding site 9 out of 14 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 Sodium with other atoms in the Na binding site number 9 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:Na1124

b:44.7
occ:1.00
O B:HOH2005 3.3 30.1 1.0
OE1 B:GLU64 3.8 37.6 1.0
CG B:LYS52 3.9 26.0 1.0
CD B:LYS52 4.0 29.5 1.0
CB B:LYS52 4.1 24.8 1.0
OE2 B:GLU64 4.3 37.5 1.0
CD B:GLU64 4.4 33.3 1.0
CE B:LYS52 4.7 31.7 1.0

Sodium binding site 10 out of 14 in 2xgl

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Sodium binding site 10 out of 14 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 Sodium with other atoms in the Na binding site number 10 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:Na1125

b:49.1
occ:1.00
OE2 B:GLU108 3.2 21.0 1.0
OE1 B:GLU108 3.8 20.1 1.0
CD B:GLU108 3.9 18.0 1.0
OE1 A:GLU109 4.1 20.0 1.0
CE B:LYS84 4.1 11.5 1.0
OD1 A:ASP26 4.2 35.3 1.0
OE2 A:GLU108 4.4 21.3 1.0
NZ B:LYS84 4.9 10.3 1.0
CD A:GLU109 5.0 18.3 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: Tue Dec 15 05:59:17 2020

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