Manganese in PDB 3dbn: Crystal Structure of the Streptoccocus Suis SEROTYPE2 D- Mannonate Dehydratase in Complex with Its Substrate

All present enzymatic activity of Crystal Structure of the Streptoccocus Suis SEROTYPE2 D- Mannonate Dehydratase in Complex with Its Substrate:
4.2.1.8;

The structure of Crystal Structure of the Streptoccocus Suis SEROTYPE2 D- Mannonate Dehydratase in Complex with Its Substrate, PDB code: 3dbn was solved by H.Peng, Q.Zhang, F.Gao, G.F.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.520, 105.520, 160.077, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 28

The binding sites of Manganese atom in the Crystal Structure of the Streptoccocus Suis SEROTYPE2 D- Mannonate Dehydratase in Complex with Its Substrate (pdb code 3dbn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the Streptoccocus Suis SEROTYPE2 D- Mannonate Dehydratase in Complex with Its Substrate, PDB code: 3dbn:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the Streptoccocus Suis SEROTYPE2 D- Mannonate Dehydratase in Complex with Its Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Streptoccocus Suis SEROTYPE2 D- Mannonate Dehydratase in Complex with Its Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn387 b:52.2 occ:1.00 OD2 B:ASP330 2.3 23.5 1.0 SG B:CYS257 2.5 18.0 1.0 CD2 B:HIS286 2.6 15.8 1.0 CE1 B:HIS219 2.9 15.1 1.0 CG B:HIS286 3.4 16.5 1.0 CG B:ASP330 3.4 22.7 1.0 NE2 B:HIS219 3.5 14.5 1.0 NH1 B:ARG288 3.6 16.3 1.0 CB B:HIS286 3.6 16.3 1.0 NE2 B:HIS286 3.7 15.6 1.0 CB B:CYS257 3.8 18.6 1.0 OD1 B:ASP330 3.9 21.4 1.0 CZ B:ARG288 4.1 16.8 1.0 OG B:SER260 4.1 22.1 1.0 ND1 B:HIS219 4.1 16.0 1.0 NH2 B:ARG288 4.3 14.8 1.0 CB B:ASP330 4.6 22.3 1.0 ND1 B:HIS286 4.6 16.9 1.0 CE1 B:HIS286 4.8 16.5 1.0 CA B:CYS257 4.8 18.7 1.0 CD2 B:HIS219 4.9 16.5 1.0 NE B:ARG288 4.9 18.1 1.0 NH1 B:ARG328 4.9 16.7 1.0 CG B:ARG288 5.0 19.9 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Streptoccocus Suis SEROTYPE2 D- Mannonate Dehydratase in Complex with Its Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Streptoccocus Suis SEROTYPE2 D- Mannonate Dehydratase in Complex with Its Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn387 b:31.4 occ:1.00 O2 A:CS2388 2.3 43.5 1.0 NE2 A:HIS219 2.4 23.6 1.0 ND1 A:HIS286 2.6 17.3 1.0 OD2 A:ASP330 2.8 25.7 1.0 SG A:CYS257 2.9 10.4 1.0 C2 A:CS2388 3.0 44.1 1.0 CE1 A:HIS219 3.2 23.0 1.0 O1B A:CS2388 3.2 43.3 1.0 CE1 A:HIS286 3.3 17.3 1.0 CD2 A:HIS219 3.6 22.0 1.0 C1 A:CS2388 3.6 43.0 1.0 CG A:HIS286 3.6 16.3 1.0 CG A:ASP330 3.9 23.8 1.0 CB A:HIS286 4.0 16.1 1.0 CB A:CYS257 4.1 10.4 1.0 OG A:SER260 4.2 10.6 1.0 C3 A:CS2388 4.4 45.2 1.0 O3 A:CS2388 4.4 46.5 1.0 NE A:ARG288 4.4 12.7 1.0 NE2 A:HIS286 4.4 17.1 1.0 ND1 A:HIS219 4.4 22.3 1.0 CD2 A:HIS286 4.6 16.9 1.0 CG A:HIS219 4.6 19.7 1.0 CB A:ASP330 4.7 22.9 1.0 NH2 A:ARG288 4.8 12.1 1.0 O1A A:CS2388 4.8 41.2 1.0 OD1 A:ASP330 4.9 24.9 1.0

Q.Zhang, F.Gao, H.Peng, H.Cheng, Y.Liu, J.Tang, J.Thompson, G.Wei, J.Zhang, Y.Du, J.Yan, G.F.Gao. Crystal Structures of Streptococcus Suis Mannonate Dehydratase (Mand) and Its Complex with Substrate: Genetic and Biochemical Evidence For A Catalytic Mechanism J.Bacteriol. V. 191 5832 2009.
ISSN: ISSN 0021-9193
PubMed: 19617363
DOI: 10.1128/JB.00599-09