Magnesium in PDB 2yhg: Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism

The structure of Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism, PDB code: 2yhg was solved by J.H.Hehemann, C.Marsters, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.73 / 1.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.580, 61.580, 125.460, 90.00, 90.00, 90.00
R / Rfree (%)	13.3 / 15.1

The structure of Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Magnesium atom in the Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism (pdb code 2yhg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism, PDB code: 2yhg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1937 b:14.4 occ:1.00 OD1 A:ASP879 2.2 12.5 1.0 O A:TYR881 2.3 13.1 1.0 O A:HOH2387 2.3 18.2 1.0 O A:GLY876 2.3 12.1 1.0 O A:ASP879 2.7 10.8 1.0 O A:HOH2386 2.7 19.3 1.0 C A:GLY876 3.4 10.1 1.0 C A:ASP879 3.4 9.1 1.0 CG A:ASP879 3.4 9.6 1.0 C A:TYR881 3.5 12.2 1.0 CA A:GLY876 3.8 11.3 1.0 N A:ASP879 4.0 8.9 1.0 N A:TYR881 4.0 10.8 1.0 CA A:ASP879 4.0 8.6 1.0 O A:HOH2392 4.1 20.8 1.0 C A:SER880 4.2 10.8 1.0 N A:SER880 4.3 8.9 1.0 CB A:ASP879 4.3 8.8 1.0 CA A:TYR881 4.3 11.2 1.0 OD2 A:ASP879 4.3 9.7 1.0 O A:HOH2388 4.4 24.9 1.0 N A:SER882 4.5 12.6 1.0 CA A:SER882 4.5 14.3 1.0 N A:GLU877 4.5 10.2 1.0 CA A:SER880 4.6 10.2 1.0 O A:SER880 4.7 12.0 1.0 CB A:TYR881 4.8 10.8 1.0 C A:GLU877 4.9 10.9 1.0 CA A:GLU877 5.0 10.8 1.0 C A:SER882 5.0 14.6 1.0

Magnesium binding site 2 out of 3 in the Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1938 b:17.2 occ:0.70 O A:GLN721 2.8 11.3 1.0 O A:GLY724 2.8 12.2 1.0 C A:SER722 3.4 11.8 1.0 N A:GLY724 3.5 13.0 1.0 N A:ALA728 3.6 10.7 1.0 O A:SER722 3.6 13.3 1.0 C A:GLY724 3.7 11.5 1.0 CA A:SER722 3.8 11.8 1.0 C A:GLN721 3.8 10.3 1.0 N A:HIS723 3.8 11.0 1.0 CB A:ALA728 3.9 12.6 1.0 CA A:GLY724 3.9 13.7 1.0 CA A:ALA728 4.0 11.0 1.0 C A:GLY727 4.0 9.5 1.0 C A:HIS723 4.0 11.0 1.0 O A:HOH2211 4.1 20.1 1.0 N A:SER722 4.2 10.8 1.0 CA A:GLY727 4.3 10.5 1.0 CA A:HIS723 4.5 11.1 1.0 O A:HIS723 4.6 12.5 1.0 O A:GLY727 4.7 10.1 1.0 N A:GLY727 4.8 10.2 1.0 N A:ALA725 4.9 12.4 1.0

Magnesium binding site 3 out of 3 in the Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1939 b:11.0 occ:0.70 O A:SER799 2.7 9.1 1.0 N A:GLY762 3.0 7.9 1.0 NE1 A:TRP803 3.1 8.0 1.0 O A:GLY762 3.2 7.4 1.0 OH A:TYR875 3.2 10.7 1.0 CL A:CL1935 3.4 11.3 1.0 CA A:GLY761 3.4 7.7 1.0 C A:GLY761 3.6 7.0 1.0 C A:GLY765 3.7 6.6 1.0 CB A:SER799 3.8 8.1 1.0 C A:SER799 3.8 7.2 1.0 N A:ARG766 3.9 6.9 1.0 CB A:ARG766 3.9 7.3 1.0 CA A:GLY765 3.9 7.0 1.0 C A:GLY762 3.9 7.2 1.0 O A:GLY765 4.0 6.9 1.0 CA A:GLY762 4.0 7.7 1.0 CE2 A:TRP803 4.0 7.9 1.0 CD1 A:TRP803 4.0 8.3 1.0 CZ2 A:TRP803 4.2 9.3 1.0 CA A:SER799 4.2 8.0 1.0 CD A:ARG802 4.3 13.3 1.0 CA A:ARG766 4.4 6.6 1.0 OG A:SER799 4.4 8.1 1.0 N A:GLY765 4.4 6.7 1.0 CZ A:TYR875 4.6 9.4 1.0 O A:GLY761 4.8 8.5 1.0 N A:GLY761 4.8 7.0 1.0 CG A:ARG766 4.9 7.5 1.0 CG A:ARG802 4.9 10.3 1.0 N A:ILE800 4.9 7.0 1.0

J.H.Hehemann, C.Marsters, A.B.Boraston. Ab Initio Phasing of A Nucleoside Hydrolase-Related Hypothetical Protein From Saccharophagus Degradans That Is Associated with Carbohydrate Metabolism. Proteins V. 79 2992 2011.
ISSN: ESSN 1097-0134
PubMed: 21905122
DOI: 10.1002/PROT.23126