Sodium in PDB 4zmh: Crystal Structure of A Five-Domain GH115 Alpha-Glucuronidase From the Marine Bacterium Saccharophagus Degradans 2-40T

The structure of Crystal Structure of A Five-Domain GH115 Alpha-Glucuronidase From the Marine Bacterium Saccharophagus Degradans 2-40T, PDB code: 4zmh was solved by B.Nocek, H.Cui, W.Wang, A.Savchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.15 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	116.442, 124.294, 180.027, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 17

The binding sites of Sodium atom in the Crystal Structure of A Five-Domain GH115 Alpha-Glucuronidase From the Marine Bacterium Saccharophagus Degradans 2-40T (pdb code 4zmh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Five-Domain GH115 Alpha-Glucuronidase From the Marine Bacterium Saccharophagus Degradans 2-40T, PDB code: 4zmh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Five-Domain GH115 Alpha-Glucuronidase From the Marine Bacterium Saccharophagus Degradans 2-40T


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Five-Domain GH115 Alpha-Glucuronidase From the Marine Bacterium Saccharophagus Degradans 2-40T within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1004 b:28.6 occ:1.00 OD2 A:ASP471 2.1 23.1 1.0 O A:HOH1176 2.1 21.7 1.0 O A:HOH1301 2.2 23.5 1.0 O A:ARG439 2.2 19.7 1.0 O A:HOH1542 2.2 21.6 1.0 O A:HOH1450 2.3 22.9 1.0 CG A:ASP471 3.3 21.8 1.0 C A:ARG439 3.3 16.5 1.0 HB3 A:ARG439 3.4 18.5 1.0 HE21 A:GLN648 3.7 24.2 1.0 H A:ASP471 3.7 15.2 1.0 HA A:ARG439 3.8 15.9 1.0 HB2 A:ASP471 3.9 22.2 1.0 OD1 A:ASP430 3.9 27.1 1.0 O A:HOH1146 4.0 23.4 1.0 CA A:ARG439 4.0 13.2 1.0 HB2 A:GLN648 4.0 17.9 1.0 HA A:TRP440 4.0 17.7 1.0 O A:HOH1250 4.1 16.0 1.0 OD1 A:ASP471 4.1 24.1 1.0 CB A:ARG439 4.1 15.4 1.0 HG2 A:GLN648 4.1 22.8 1.0 CB A:ASP471 4.2 18.5 1.0 HB3 A:ALA219 4.3 23.1 1.0 O A:HOH1812 4.3 23.7 1.0 OD2 A:ASP430 4.3 22.6 1.0 N A:TRP440 4.4 14.5 1.0 N A:ASP471 4.4 12.7 1.0 NE2 A:GLN648 4.5 20.2 1.0 O A:ASP215 4.5 16.9 1.0 CG A:ASP430 4.5 28.5 1.0 HB2 A:ARG439 4.5 18.5 1.0 HA3 A:GLY470 4.6 18.2 1.0 O A:TRP440 4.6 20.9 1.0 CA A:TRP440 4.6 14.8 1.0 O A:HOH1233 4.6 24.3 1.0 HE A:ARG439 4.6 34.3 1.0 CB A:GLN648 4.7 15.0 1.0 HB3 A:GLN648 4.8 17.9 1.0 CG A:GLN648 4.8 19.0 1.0 HB2 A:ALA219 4.9 23.1 1.0 C A:TRP440 4.9 17.5 1.0 HB3 A:ASP471 4.9 22.2 1.0 HE22 A:GLN648 5.0 24.2 1.0 HB2 A:ASP215 5.0 25.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Five-Domain GH115 Alpha-Glucuronidase From the Marine Bacterium Saccharophagus Degradans 2-40T


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Five-Domain GH115 Alpha-Glucuronidase From the Marine Bacterium Saccharophagus Degradans 2-40T within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1002 b:30.3 occ:1.00 OD2 B:ASP471 2.1 19.6 1.0 O B:HOH1204 2.1 22.0 1.0 O B:ARG439 2.2 19.0 1.0 O B:HOH1554 2.3 19.9 1.0 O B:HOH1253 2.3 23.5 1.0 O B:HOH1425 2.5 23.0 1.0 CG B:ASP471 3.3 20.1 1.0 C B:ARG439 3.3 16.5 1.0 HB3 B:ARG439 3.5 23.5 1.0 H B:ASP471 3.7 13.5 1.0 HE21 B:GLN648 3.8 19.6 1.0 HA B:ARG439 3.9 17.6 1.0 HA B:TRP440 4.0 17.2 1.0 HB2 B:GLN648 4.0 15.2 1.0 O B:HOH1239 4.0 18.8 1.0 HB2 B:ASP471 4.0 22.3 1.0 OD1 B:ASP430 4.0 27.8 1.0 CA B:ARG439 4.0 14.7 1.0 O B:HOH1213 4.1 17.7 1.0 HG2 B:GLN648 4.1 14.6 1.0 OD1 B:ASP471 4.1 19.1 1.0 CB B:ARG439 4.2 19.6 1.0 CB B:ASP471 4.3 18.6 1.0 HB3 B:ALA219 4.3 21.0 1.0 O B:HOH1672 4.3 22.9 1.0 N B:TRP440 4.3 13.9 1.0 OD2 B:ASP430 4.4 23.1 1.0 O B:HOH1332 4.4 19.4 1.0 N B:ASP471 4.4 11.3 1.0 O B:TRP440 4.5 20.6 1.0 CA B:TRP440 4.5 14.4 1.0 HA3 B:GLY470 4.6 17.6 1.0 O B:ASP215 4.6 16.2 1.0 NE2 B:GLN648 4.6 16.3 1.0 CG B:ASP430 4.6 27.5 1.0 HB2 B:ARG439 4.6 23.5 1.0 CB B:GLN648 4.7 12.6 1.0 HB3 B:GLN648 4.7 15.2 1.0 HE B:ARG439 4.8 28.7 1.0 CG B:GLN648 4.8 12.2 1.0 HB2 B:ALA219 4.8 21.0 1.0 C B:TRP440 4.9 17.3 1.0 CB B:ALA219 5.0 17.5 1.0 HB2 B:ASP215 5.0 21.5 1.0

W.Wang, R.Yan, B.P.Nocek, T.V.Vuong, R.Di Leo, X.Xu, H.Cui, P.Gatenholm, G.Toriz, M.Tenkanen, A.Savchenko, E.R.Master. Biochemical and Structural Characterization of A Five-Domain GH115 Alpha-Glucuronidase From the Marine Bacterium Saccharophagus Degradans 2-40T. J.Biol.Chem. V. 291 14120 2016.
ISSN: ESSN 1083-351X
PubMed: 27129264
DOI: 10.1074/JBC.M115.702944