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Sodium in PDB 1gmm: Carbohydrate Binding Module CBM6 From Xylanase U Clostridium Thermocellum

Enzymatic activity of Carbohydrate Binding Module CBM6 From Xylanase U Clostridium Thermocellum

All present enzymatic activity of Carbohydrate Binding Module CBM6 From Xylanase U Clostridium Thermocellum:
3.2.1.8;

Protein crystallography data

The structure of Carbohydrate Binding Module CBM6 From Xylanase U Clostridium Thermocellum, PDB code: 1gmm was solved by M.Czjzek, A.Mosbah, D.Bolam, J.Allouch, V.Zamboni, B.Henrissat, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.00 / 2.0
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 59.650, 59.650, 157.450, 90.00, 90.00, 120.00
R / Rfree (%) 20.77 / 21.59

Other elements in 1gmm:

The structure of Carbohydrate Binding Module CBM6 From Xylanase U Clostridium Thermocellum also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Carbohydrate Binding Module CBM6 From Xylanase U Clostridium Thermocellum (pdb code 1gmm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Carbohydrate Binding Module CBM6 From Xylanase U Clostridium Thermocellum, PDB code: 1gmm:

Sodium binding site 1 out of 1 in 1gmm

Go back to Sodium Binding Sites List in 1gmm
Sodium binding site 1 out of 1 in the Carbohydrate Binding Module CBM6 From Xylanase U Clostridium Thermocellum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Carbohydrate Binding Module CBM6 From Xylanase U Clostridium Thermocellum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1131

b:10.9
occ:1.00
 O A:VAL119 2.9 6.7 1.0
N A:ILE35 2.9 9.6 1.0
N A:VAL119 3.0 7.0 1.0
N A:TYR34 3.2 9.0 1.0
O A:HOH2174 3.3 21.3 1.0
C A:VAL119 3.5 6.3 1.0
CA A:PRO118 3.5 7.6 1.0
CB A:PRO118 3.6 7.5 1.0
CA A:TYR34 3.7 9.7 1.0
O A:ILE35 3.7 9.6 1.0
OD1 A:ASN120 3.7 6.3 1.0
C A:PRO118 3.7 8.0 1.0
CB A:ILE35 3.7 9.5 1.0
CA A:ILE35 3.7 9.1 1.0
C A:TYR34 3.8 10.1 1.0
CA A:VAL119 3.8 5.8 1.0
C A:GLY33 3.9 10.8 1.0
CG1 A:ILE35 4.2 8.7 1.0
C A:ILE35 4.2 9.8 1.0
CA A:GLY33 4.2 10.8 1.0
CZ3 A:TRP92 4.4 7.1 1.0
N A:ASN120 4.4 5.8 1.0
CG A:ASN120 4.7 5.9 1.0
CD1 A:ILE35 4.7 10.5 1.0
O A:GLY33 4.8 9.8 1.0
O A:PRO118 4.8 7.5 1.0
CA A:ASN120 4.9 6.0 1.0
N A:PRO118 4.9 7.7 1.0
O A:TYR34 5.0 10.1 1.0
CE3 A:TRP92 5.0 6.6 1.0
CH2 A:TRP92 5.0 7.5 1.0
CG2 A:ILE35 5.0 8.8 1.0

Reference:

M.Czjzek, D.Bolam, A.Mosbah, J.Allouch, C.M.Fontes, L.M.Ferreira, O.Bornet, V.Zamboni, H.Darbon, N.L.Smith, G.W.Black, B.Henrissat, H.J.Gilbert. The Location of the Ligand-Binding Site of Carbohydrate-Binding Modules That Have Evolved From A Common Sequence Is Not Conserved. J.Biol.Chem. V. 276 48580 2001.
ISSN: ISSN 0021-9258
PubMed: 11673472
DOI: 10.1074/JBC.M109142200
Page generated: Tue Dec 15 05:24:49 2020

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