Sodium in PDB 4cd5: The Structure of GH26 Beta-Mannanase CJMAN26C From Cellvibrio Japonicus in Complex with Manmim

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

The structure of The Structure of GH26 Beta-Mannanase CJMAN26C From Cellvibrio Japonicus in Complex with Manmim, PDB code: 4cd5 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 / 1.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	84.507, 84.507, 244.941, 90.00, 90.00, 120.00
R / Rfree (%)	15.171 / 17.213

The binding sites of Sodium atom in the The Structure of GH26 Beta-Mannanase CJMAN26C From Cellvibrio Japonicus in Complex with Manmim (pdb code 4cd5). 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 Manmim, PDB code: 4cd5:
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 Manmim


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 Manmim within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1420 b:8.7 occ:1.00 O A:SER365 2.3 9.8 1.0 O A:ARG76 2.3 9.4 1.0 O A:HIS79 2.3 9.5 1.0 O A:ILE367 2.3 8.6 1.0 O A:HOH2057 2.5 18.1 1.0 C A:ARG76 3.3 8.7 1.0 C A:HIS79 3.3 8.7 1.0 C A:SER365 3.5 9.6 1.0 C A:ILE367 3.5 7.2 1.0 CA A:ARG76 3.7 8.9 1.0 C A:GLU366 3.9 8.4 1.0 CA A:GLU366 4.0 8.4 0.5 N A:ILE367 4.0 7.8 1.0 CA A:GLU366 4.0 9.0 0.5 N A:HIS79 4.1 9.1 1.0 N A:LEU80 4.1 9.2 1.0 N A:GLU366 4.2 8.6 1.0 CA A:LEU80 4.2 10.1 1.0 O A:HOH2049 4.2 27.6 1.0 CB A:ARG76 4.3 8.5 1.0 CA A:HIS79 4.3 8.7 1.0 CA A:ILE367 4.4 7.6 1.0 O A:GLU366 4.4 8.8 1.0 CB A:LEU80 4.5 12.6 1.0 N A:TYR77 4.5 9.7 1.0 N A:ALA368 4.5 7.0 1.0 CA A:SER365 4.6 9.4 0.5 CA A:SER365 4.6 9.8 0.5 CA A:ALA368 4.6 7.5 1.0 CD1 A:LEU80 4.6 17.8 1.0 C A:TYR77 4.7 13.0 1.0 CG1 A:ILE367 4.7 8.6 1.0 O A:TYR77 4.8 16.9 1.0 O A:HOH2050 4.8 22.4 0.5 O A:LEU75 4.8 10.7 1.0 CA A:TYR77 4.9 11.7 1.0 N A:LYS78 5.0 11.8 1.0 C A:LYS78 5.0 11.2 1.0 CB A:SER365 5.0 9.3 0.5

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


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 Manmim within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1421 b:11.1 occ:1.00 O A:VAL408 2.2 10.9 1.0 O A:SER405 2.3 10.5 1.0 O A:TYR403 2.4 9.1 1.0 O A:HOH2479 2.4 18.4 1.0 O A:HOH2484 2.4 27.1 1.0 C A:SER405 3.4 9.4 1.0 C A:VAL408 3.4 8.9 1.0 C A:TYR403 3.5 8.6 1.0 C A:GLN404 3.7 10.0 1.0 O A:GLN404 3.8 13.0 1.0 N A:SER405 3.8 9.4 1.0 O A:HOH2482 4.1 30.0 1.0 N A:VAL408 4.1 8.5 1.0 CA A:VAL408 4.1 7.8 1.0 CA A:SER405 4.2 8.2 0.5 O A:HOH2496 4.2 46.0 0.5 CA A:GLN404 4.2 9.4 1.0 CA A:SER405 4.2 9.3 0.5 O A:HOH2489 4.2 12.6 1.0 N A:GLN404 4.3 8.1 1.0 N A:GLU406 4.3 10.4 1.0 CB A:VAL408 4.3 9.3 1.0 CA A:GLU406 4.4 12.1 1.0 C A:GLU406 4.4 10.2 1.0 N A:LEU409 4.5 7.9 1.0 OG A:SER405 4.5 10.0 0.5 O A:GLU406 4.5 12.4 1.0 CA A:TYR403 4.6 8.7 1.0 OE1 A:GLU413 4.6 20.6 1.0 O A:PHE402 4.6 9.7 1.0 O A:HOH2488 4.6 37.8 1.0 CA A:LEU409 4.7 8.6 1.0 CB A:SER405 4.8 11.0 0.5 CD2 A:LEU409 4.9 13.3 1.0 N A:VAL407 5.0 9.5 1.0 CG1 A:VAL408 5.0 12.1 1.0 C A:VAL407 5.0 9.2 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