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Sodium in PDB 1w9s: Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans

Protein crystallography data

The structure of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans, PDB code: 1w9s was solved by A.B.Boraston, A.L.Van Bueren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.59
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 30.795, 40.834, 56.118, 108.95, 105.93, 90.00
R / Rfree (%) 11.7 / 16.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans (pdb code 1w9s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans, PDB code: 1w9s:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 1w9s

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Sodium binding site 1 out of 6 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1141

b:12.6
occ:1.00
OD1 A:ASN134 2.3 12.6 1.0
O A:ASP38 2.3 14.3 1.0
OE1 A:GLN16 2.4 13.6 1.0
O A:HOH2028 2.4 17.4 1.0
O A:ASN134 2.5 11.8 1.0
OE1 A:GLU18 2.5 12.7 1.0
C A:ASN134 3.4 11.2 1.0
CD A:GLU18 3.4 13.5 1.0
CG A:ASN134 3.5 13.3 1.0
C A:ASP38 3.5 14.5 1.0
CD A:GLN16 3.6 13.7 1.0
OE2 A:GLU18 3.6 15.4 1.0
CA A:ASN134 3.8 10.6 1.0
CB A:GLN16 3.9 12.2 1.0
O A:HOH2025 4.0 22.2 1.0
N A:ASP38 4.0 16.1 1.0
CG A:GLN16 4.2 12.1 1.0
N A:ALA17 4.2 11.0 1.0
CB A:ASN134 4.2 11.7 1.0
CA A:ASP38 4.3 14.9 1.0
CA A:GLN16 4.3 11.1 1.0
N A:ASN39 4.5 12.9 1.0
N A:TRP135 4.5 10.7 1.0
ND2 A:ASN134 4.5 13.4 1.0
O A:HOH2024 4.6 26.6 1.0
CA A:ASN39 4.6 12.3 1.0
C A:GLN16 4.6 11.9 1.0
NE2 A:GLN16 4.7 15.4 1.0
CG A:GLU18 4.8 14.8 1.0
N A:GLU18 4.8 12.0 1.0
CB A:TRP135 4.9 10.6 1.0
CD1 A:TRP135 4.9 12.7 1.0
CB A:ASP38 4.9 15.4 1.0
CA A:TRP135 5.0 9.7 1.0

Sodium binding site 2 out of 6 in 1w9s

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Sodium binding site 2 out of 6 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1142

b:12.2
occ:1.00
O A:TRP42 2.2 11.7 1.0
OD2 A:ASP47 2.3 11.2 1.0
O A:GLY25 2.3 12.4 1.0
O B:THR84 2.3 12.4 1.0
OD1 A:ASN44 2.4 12.6 1.0
CG A:ASN44 3.3 10.8 1.0
C A:GLY25 3.3 11.4 1.0
C B:THR84 3.4 12.6 1.0
C A:TRP42 3.4 10.8 1.0
CG A:ASP47 3.4 10.3 1.0
N A:ASN44 3.4 10.6 1.0
CB B:THR84 3.6 13.2 1.0
CB A:ASN44 3.7 10.8 1.0
O A:HOH2078 3.8 16.1 1.0
CA B:THR84 3.8 11.8 1.0
C A:ILE43 3.9 11.4 1.0
OD1 A:ASP47 3.9 10.8 1.0
CA A:ILE43 3.9 11.2 1.0
CA A:GLY25 4.0 11.3 1.0
N A:ILE43 4.1 10.7 1.0
NH1 B:ARG79 4.1 11.7 1.0
CA A:ASN44 4.2 10.9 1.0
N A:ILE26 4.4 11.8 1.0
OG1 B:THR84 4.4 12.7 1.0
CA A:TRP42 4.5 11.8 1.0
N B:GLY85 4.5 12.9 1.0
ND2 A:ASN44 4.6 14.6 1.0
CA A:ILE26 4.6 11.6 1.0
CB A:ASP47 4.6 9.4 1.0
CG2 B:THR84 4.6 12.9 1.0
CB A:TRP42 4.6 13.7 1.0
O B:GLY85 4.7 11.4 1.0
CG2 A:ILE26 4.8 12.1 1.0
C B:GLY85 4.8 11.9 1.0
O A:ILE43 4.8 11.3 1.0
O A:HOH2085 4.9 12.4 1.0
CA B:GLY85 5.0 12.3 1.0

Sodium binding site 3 out of 6 in 1w9s

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Sodium binding site 3 out of 6 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1143

b:25.8
occ:1.00
OD2 A:ASP90 2.2 21.0 1.0
O A:HOH2123 2.2 25.0 1.0
O A:HOH2149 2.3 18.8 1.0
O A:ASP90 2.4 13.0 1.0
O A:HOH2150 2.5 17.0 1.0
C A:ASP90 3.2 13.6 1.0
CG A:ASP90 3.4 21.8 1.0
N A:ASP90 3.8 12.5 1.0
CA A:ASP90 3.9 13.7 1.0
O A:HOH2147 4.1 35.1 1.0
N A:VAL91 4.1 13.7 1.0
O A:HOH2126 4.1 39.2 1.0
CB A:ASP90 4.2 15.8 1.0
OD1 A:ASP90 4.3 31.9 1.0
N A:ASN108 4.3 14.4 1.0
O A:HOH2070 4.4 45.5 1.0
CA A:GLY107 4.4 13.8 1.0
O A:ASN108 4.5 15.3 1.0
CA A:VAL91 4.6 14.2 1.0
O A:HOH2148 4.6 16.8 1.0
C A:GLY107 4.8 13.7 1.0
O A:HOH2122 4.9 36.8 1.0

Sodium binding site 4 out of 6 in 1w9s

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Sodium binding site 4 out of 6 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1141

b:12.5
occ:1.00
O B:ASP38 2.3 13.7 1.0
OD1 B:ASN134 2.3 12.6 1.0
O B:ASN134 2.5 12.0 1.0
OE1 B:GLU18 2.5 12.0 1.0
OE1 B:GLN16 2.5 14.2 1.0
O B:HOH2037 2.5 15.2 1.0
C B:ASN134 3.4 11.2 1.0
CD B:GLU18 3.4 14.0 1.0
C B:ASP38 3.5 13.4 1.0
CG B:ASN134 3.5 13.5 1.0
OE2 B:GLU18 3.6 16.8 1.0
CD B:GLN16 3.6 13.9 1.0
CA B:ASN134 3.8 11.1 1.0
CB B:GLN16 3.9 12.6 1.0
O B:HOH2033 4.0 21.5 1.0
N B:ASP38 4.1 14.9 1.0
N B:ALA17 4.2 10.3 1.0
CG B:GLN16 4.2 12.4 1.0
CB B:ASN134 4.2 11.4 1.0
CA B:GLN16 4.3 12.0 1.0
CA B:ASP38 4.3 14.8 1.0
N B:ASN39 4.5 11.2 1.0
N B:TRP135 4.5 10.4 1.0
ND2 B:ASN134 4.6 14.3 1.0
CA B:ASN39 4.6 11.6 1.0
C B:GLN16 4.6 12.3 1.0
O B:HOH2018 4.6 25.0 1.0
NE2 B:GLN16 4.7 15.9 1.0
CG B:GLU18 4.8 13.2 1.0
N B:GLU18 4.8 11.3 1.0
CB B:TRP135 4.8 12.3 1.0
CB B:ASP38 4.9 16.0 1.0
CD1 B:TRP135 4.9 14.3 1.0
CA B:TRP135 5.0 10.3 1.0

Sodium binding site 5 out of 6 in 1w9s

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Sodium binding site 5 out of 6 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1142

b:11.7
occ:1.00
OD2 B:ASP47 2.3 12.8 1.0
O B:TRP42 2.3 11.8 1.0
O B:GLY25 2.3 12.0 1.0
OD1 B:ASN44 2.4 13.0 1.0
CG B:ASN44 3.3 10.9 1.0
C B:TRP42 3.4 11.8 1.0
C B:GLY25 3.4 11.0 1.0
CG B:ASP47 3.4 10.2 1.0
N B:ASN44 3.5 11.2 1.0
CB B:ASN44 3.7 11.2 1.0
C B:ILE43 3.9 12.2 1.0
CA B:ILE43 3.9 11.9 1.0
OD1 B:ASP47 3.9 9.4 1.0
CA B:GLY25 4.0 11.1 1.0
N B:ILE43 4.1 11.5 1.0
CA B:ASN44 4.2 10.9 1.0
N B:ILE26 4.4 11.3 1.0
CA B:TRP42 4.5 12.1 1.0
ND2 B:ASN44 4.5 15.2 1.0
CA B:ILE26 4.6 11.7 1.0
CB B:ASP47 4.6 8.3 1.0
CB B:TRP42 4.6 13.0 1.0
O B:ILE43 4.7 11.0 1.0
CG2 B:ILE26 4.8 13.3 1.0
O B:HOH2093 5.0 12.2 1.0

Sodium binding site 6 out of 6 in 1w9s

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Sodium binding site 6 out of 6 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1143

b:24.6
occ:1.00
OD2 B:ASP90 2.2 18.9 1.0
O B:HOH2127 2.2 23.1 1.0
O B:HOH2149 2.3 19.2 1.0
O B:ASP90 2.5 12.5 1.0
O B:HOH2150 2.5 17.5 1.0
C B:ASP90 3.3 13.0 1.0
CG B:ASP90 3.4 18.7 1.0
N B:ASP90 3.8 12.1 1.0
CA B:ASP90 3.9 13.0 1.0
O B:HOH2128 4.0 41.2 1.0
N B:VAL91 4.2 13.2 1.0
CB B:ASP90 4.3 14.8 1.0
OD1 B:ASP90 4.3 25.5 1.0
O B:HOH2145 4.3 29.9 1.0
N B:ASN108 4.3 15.0 1.0
CA B:GLY107 4.4 14.0 1.0
O B:ASN108 4.5 16.2 1.0
O B:HOH2146 4.6 16.7 1.0
CA B:VAL91 4.6 14.2 1.0
O B:HOH2086 4.7 43.9 1.0
C B:GLY107 4.8 13.8 1.0

Reference:

A.L.Van Bueren, C.Moreland, H.J.Gilbert, A.B.Boraston. Family 6 Carbohydrate Binding Modules Recognize the Non-Reducing End of Beta-1,3-Linked Glucans By Presenting A Unique Ligand Binding Surface J.Biol.Chem. V. 280 530 2005.
ISSN: ISSN 0021-9258
PubMed: 15501830
DOI: 10.1074/JBC.M410113200
Page generated: Tue Dec 15 05:41:05 2020

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