Sodium in PDB 3pdg: Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules

The structure of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules, PDB code: 3pdg was solved by P.M.Alahuhta, V.V.Lunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.78
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	42.316, 42.316, 116.756, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 27.1

The binding sites of Sodium atom in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules (pdb code 3pdg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules, PDB code: 3pdg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range: probe atom residue distance (Å) B Occ A:Na99 b:23.1 occ:1.00 O A:PRO50 2.2 23.4 1.0 O A:THR48 2.3 31.1 0.3 O A:THR48 2.3 31.9 0.7 OD2 A:ASP46 2.4 22.2 1.0 O A:HOH110 2.4 14.1 1.0 O A:HOH152 2.5 25.2 1.0 O A:HOH190 2.6 34.0 1.0 CG A:ASP46 3.1 26.6 1.0 OD1 A:ASP46 3.1 21.5 1.0 C A:PRO50 3.3 24.6 1.0 C A:THR48 3.4 31.4 0.7 C A:THR48 3.5 31.0 0.3 CA A:TYR51 4.0 22.8 1.0 C A:ALA49 4.0 30.7 1.0 N A:TYR51 4.0 22.9 1.0 N A:PRO50 4.0 28.8 1.0 O A:HOH109 4.1 7.4 1.0 CB A:THR48 4.1 32.5 0.7 O A:ALA49 4.2 31.6 1.0 N A:THR52 4.3 23.8 1.0 CA A:THR48 4.3 31.9 0.7 CA A:PRO50 4.3 26.8 1.0 N A:ALA49 4.3 31.3 1.0 CA A:ALA49 4.4 31.0 1.0 OG1 A:THR52 4.4 22.3 1.0 CB A:ASP46 4.5 26.6 1.0 CA A:THR48 4.5 31.4 0.3 C A:TYR51 4.5 23.2 1.0 N A:THR48 4.6 30.8 0.7 CD A:PRO50 4.7 30.6 1.0 N A:THR48 4.7 30.6 0.3 CG2 A:THR48 4.7 33.1 0.7 CG A:PRO50 4.9 29.5 1.0 CB A:THR48 4.9 32.1 0.3 CG2 A:THR52 4.9 23.2 1.0

Sodium binding site 2 out of 2 in the Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structures of Clostridium Thermocellum Cbha Fibronectin(III)-Like Modules within 5.0Å range: probe atom residue distance (Å) B Occ A:Na100 b:9.1 occ:0.25 O A:HOH169 3.1 13.6 1.0 NE A:ARG75 3.2 15.2 0.7 CD A:ARG75 3.6 14.7 0.7 NE A:ARG75 3.7 8.3 0.3 CD A:ARG75 3.9 8.5 0.3 CZ A:ARG75 4.1 15.9 0.7 NH1 A:ARG75 4.3 16.8 0.7 CZ A:ARG75 4.5 8.0 0.3 CG A:ARG75 4.8 13.6 0.7 NH1 A:ARG75 4.9 5.0 0.3 OD2 A:ASP73 4.9 19.6 1.0 O A:HOH182 5.0 2.0 0.3

R.Brunecky, M.Alahuhta, Y.J.Bomble, Q.Xu, J.O.Baker, S.Y.Ding, M.E.Himmel, V.V.Lunin. Structure and Function of the Clostridium Thermocellum Cellobiohydrolase A X1-Module Repeat: Enhancement Through Stabilization of the Cbha Complex. Acta Crystallogr.,Sect.D V. 68 292 2012.
ISSN: ISSN 0907-4449
PubMed: 22349231
DOI: 10.1107/S0907444912001680