Sodium in PDB 4cd4: The Structure of GH26 Beta-Mannanase CJMAN26C From Cellvibrio Japonicus in Complex with Manifg

All present enzymatic activity of The Structure of GH26 Beta-Mannanase CJMAN26C From Cellvibrio Japonicus in Complex with Manifg:
3.2.1.78;

The structure of The Structure of GH26 Beta-Mannanase CJMAN26C From Cellvibrio Japonicus in Complex with Manifg, PDB code: 4cd4 was solved by R.J.Williams, J.Iglesias-Fernandez, J.Stepper, A.Jackson, A.J.Thompson, E.C.Lowe, J.M.White, H.J.Gilbert, C.Rovira, G.J.Davies, S.J.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.19 / 1.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	84.518, 84.518, 244.491, 90.00, 90.00, 120.00
R / Rfree (%)	11.129 / 13.385

The binding sites of Sodium atom in the The Structure of GH26 Beta-Mannanase CJMAN26C From Cellvibrio Japonicus in Complex with Manifg (pdb code 4cd4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Structure of GH26 Beta-Mannanase CJMAN26C From Cellvibrio Japonicus in Complex with Manifg, PDB code: 4cd4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Structure of GH26 Beta-Mannanase CJMAN26C From Cellvibrio Japonicus in Complex with Manifg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of GH26 Beta-Mannanase CJMAN26C From Cellvibrio Japonicus in Complex with Manifg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1420 b:10.9 occ:1.00 O A:VAL408 2.2 10.8 1.0 O A:SER405 2.2 11.0 1.0 O A:TYR403 2.4 9.6 1.0 O A:HOH2722 2.4 17.6 1.0 O A:HOH2726 2.4 26.1 1.0 C A:SER405 3.4 9.4 1.0 C A:VAL408 3.4 9.4 1.0 C A:TYR403 3.5 8.9 1.0 C A:GLN404 3.7 9.7 1.0 O A:GLN404 3.7 13.2 1.0 N A:SER405 3.8 9.1 1.0 N A:VAL408 4.1 9.0 1.0 CA A:VAL408 4.1 9.1 1.0 CA A:GLN404 4.2 9.4 1.0 CA A:SER405 4.2 9.4 0.5 O A:HOH2731 4.2 11.7 1.0 CA A:SER405 4.2 9.5 0.5 N A:GLU406 4.3 10.5 1.0 N A:GLN404 4.3 9.3 1.0 CB A:VAL408 4.3 10.1 1.0 CA A:GLU406 4.4 11.9 1.0 C A:GLU406 4.4 10.9 1.0 N A:LEU409 4.4 8.5 1.0 OG A:SER405 4.5 12.8 0.5 O A:GLU406 4.5 12.6 1.0 OE1 A:GLU413 4.6 17.4 1.0 O A:HOH2723 4.6 31.6 0.5 CA A:TYR403 4.6 8.6 1.0 O A:PHE402 4.7 9.2 1.0 CA A:LEU409 4.7 8.0 1.0 O A:HOH2730 4.7 33.1 1.0 CB A:SER405 4.8 10.0 0.5 CD2 A:LEU409 4.9 13.0 1.0 CG1 A:VAL408 4.9 12.0 1.0 N A:VAL407 5.0 10.2 1.0 C A:VAL407 5.0 9.6 1.0 CB A:SER405 5.0 11.6 0.5

Sodium binding site 2 out of 2 in the The Structure of GH26 Beta-Mannanase CJMAN26C From Cellvibrio Japonicus in Complex with Manifg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of GH26 Beta-Mannanase CJMAN26C From Cellvibrio Japonicus in Complex with Manifg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1421 b:9.3 occ:1.00 O A:SER365 2.3 10.1 1.0 O A:ARG76 2.3 9.7 1.0 O A:HIS79 2.3 9.8 1.0 O A:ILE367 2.3 8.6 1.0 O A:HOH2079 2.5 17.5 1.0 C A:ARG76 3.3 9.2 1.0 C A:HIS79 3.3 8.9 1.0 C A:SER365 3.5 9.5 1.0 C A:ILE367 3.5 8.1 1.0 CA A:ARG76 3.7 9.5 1.0 C A:GLU366 3.9 8.6 1.0 CA A:GLU366 3.9 8.7 0.5 N A:ILE367 4.0 8.3 1.0 CA A:GLU366 4.1 9.4 0.5 N A:LEU80 4.1 9.8 1.0 N A:HIS79 4.1 9.7 1.0 N A:GLU366 4.2 9.2 1.0 CA A:LEU80 4.2 11.1 0.5 CA A:LEU80 4.2 10.9 0.5 O A:HOH2067 4.3 24.7 1.0 CA A:HIS79 4.3 9.8 1.0 CB A:ARG76 4.3 9.4 1.0 CA A:ILE367 4.4 8.2 1.0 CB A:LEU80 4.4 14.1 0.5 O A:GLU366 4.4 9.5 1.0 N A:TYR77 4.5 10.8 1.0 CB A:LEU80 4.5 14.0 0.5 N A:ALA368 4.5 7.4 1.0 CD1 A:LEU80 4.5 13.5 0.5 CA A:SER365 4.6 9.3 0.5 CA A:SER365 4.6 9.2 0.5 CA A:ALA368 4.6 7.4 1.0 C A:TYR77 4.7 13.1 1.0 CG1 A:ILE367 4.7 8.7 1.0 O A:TYR77 4.7 16.5 1.0 O A:HOH2068 4.8 22.6 0.5 O A:LEU75 4.8 10.7 1.0 CA A:TYR77 4.9 11.7 1.0 N A:LYS78 4.9 12.2 1.0 CB A:SER365 5.0 9.8 0.5 C A:LYS78 5.0 12.4 1.0 C A:ALA368 5.0 7.5 1.0

R.J.Williams, J.Iglesias-Fernandez, J.Stepper, A.Jackson, A.J.Thompson, E.C.Lowe, J.M.White, H.J.Gilbert, C.Rovira, G.J.Davies, S.J.Williams. Combined Inhibitor Free-Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate. Angew.Chem.Int.Ed.Engl. V. 53 1087 2014.
ISSN: ISSN 1433-7851
PubMed: 24339341
DOI: 10.1002/ANIE.201308334