Magnesium in PDB 5jip: Crystal Structure of the Clostridium Perfringens Spore Cortex Lytic Enzyme Slem

The structure of Crystal Structure of the Clostridium Perfringens Spore Cortex Lytic Enzyme Slem, PDB code: 5jip was solved by D.Y.Chirgadze, G.Christie, F.I.Ustok, B.Al-Riyami, K.Stott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.40 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.599, 85.852, 87.205, 90.00, 105.51, 90.00
R / Rfree (%)	15.1 / 18.2

The binding sites of Magnesium atom in the Crystal Structure of the Clostridium Perfringens Spore Cortex Lytic Enzyme Slem (pdb code 5jip). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Clostridium Perfringens Spore Cortex Lytic Enzyme Slem, PDB code: 5jip:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Clostridium Perfringens Spore Cortex Lytic Enzyme Slem


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Clostridium Perfringens Spore Cortex Lytic Enzyme Slem within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:7.2 occ:0.99 O A:MET230 2.0 9.2 1.0 OD2 A:ASP258 2.0 7.0 1.0 OD2 A:ASP304 2.1 6.2 1.0 O A:HOH604 2.1 6.0 1.0 O A:HOH552 2.1 4.7 1.0 O A:ASP227 2.2 7.2 1.0 CG A:ASP258 3.0 6.2 1.0 CG A:ASP304 3.1 5.6 1.0 C A:MET230 3.2 8.3 1.0 HA A:SER228 3.3 6.7 1.0 C A:ASP227 3.3 6.9 1.0 H A:MET230 3.3 6.5 1.0 OD1 A:ASP258 3.4 7.9 1.0 HB2 A:ASP304 3.4 6.0 1.0 HB3 A:ASP304 3.5 6.0 1.0 CB A:ASP304 3.5 5.0 1.0 N A:MET230 3.8 5.4 1.0 HA A:PRO231 3.9 7.2 1.0 CA A:SER228 3.9 5.6 1.0 O A:HOH671 4.0 5.6 1.0 HD3 A:PRO232 4.0 9.7 1.0 N A:SER228 4.1 5.5 1.0 O A:HOH544 4.1 6.3 1.0 CA A:MET230 4.1 4.6 1.0 C A:SER228 4.1 5.3 1.0 HB3 A:ASP227 4.1 8.7 1.0 OD1 A:ASP304 4.1 7.1 1.0 O A:HOH593 4.1 9.1 1.0 N A:PRO231 4.2 7.0 1.0 CA A:PRO231 4.3 6.0 1.0 HA A:ASP227 4.3 9.2 1.0 C A:PRO231 4.3 7.5 1.0 CA A:ASP227 4.4 7.7 1.0 CB A:ASP258 4.4 6.3 1.0 HB2 A:MET230 4.4 9.2 1.0 O A:SER228 4.5 6.3 1.0 N A:PRO232 4.5 6.9 1.0 HB2 A:ASP258 4.5 7.6 1.0 N A:LEU229 4.5 6.8 1.0 HB2 A:ASP308 4.7 7.2 1.0 CB A:ASP227 4.7 7.2 1.0 HB3 A:ASP258 4.7 7.6 1.0 CD A:PRO232 4.7 8.1 1.0 C A:LEU229 4.7 6.5 1.0 H A:LEU229 4.7 8.2 1.0 O A:PRO231 4.8 6.8 1.0 CB A:MET230 4.9 7.6 1.0 HA A:MET230 4.9 5.5 1.0 H A:SER228 4.9 6.6 1.0 HG1 A:THR306 4.9 9.5 1.0 HG2 A:GLU256 4.9 12.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Clostridium Perfringens Spore Cortex Lytic Enzyme Slem


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Clostridium Perfringens Spore Cortex Lytic Enzyme Slem within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:6.8 occ:0.97 O B:MET230 2.0 7.0 1.0 OD2 B:ASP304 2.1 7.9 1.0 O B:ASP227 2.1 9.1 1.0 OD2 B:ASP258 2.1 7.9 1.0 O B:HOH582 2.2 6.4 1.0 O B:HOH705 2.2 5.6 1.0 CG B:ASP258 3.1 7.1 1.0 CG B:ASP304 3.1 5.2 1.0 H B:MET230 3.2 7.8 1.0 C B:MET230 3.2 5.1 1.0 C B:ASP227 3.3 7.5 1.0 HA B:SER228 3.3 6.4 1.0 OD1 B:ASP258 3.4 7.4 1.0 HB3 B:ASP304 3.4 7.9 1.0 HB2 B:ASP304 3.5 7.9 1.0 CB B:ASP304 3.6 6.6 1.0 N B:MET230 3.8 6.5 1.0 HA B:PRO231 3.8 6.6 1.0 HD3 B:PRO232 3.9 7.5 1.0 CA B:SER228 4.0 5.3 1.0 O B:HOH643 4.0 7.0 1.0 O B:HOH532 4.0 8.7 1.0 O B:HOH560 4.0 8.4 1.0 N B:SER228 4.0 8.2 1.0 CA B:MET230 4.1 4.7 1.0 HB3 B:ASP227 4.1 6.6 1.0 C B:SER228 4.1 4.9 1.0 N B:PRO231 4.1 5.8 1.0 OD1 B:ASP304 4.2 7.5 1.0 CA B:PRO231 4.2 5.5 1.0 C B:PRO231 4.3 6.4 1.0 HA B:ASP227 4.3 6.2 1.0 CA B:ASP227 4.4 5.2 1.0 HB2 B:MET230 4.4 7.6 1.0 N B:PRO232 4.5 6.5 1.0 O B:SER228 4.5 9.7 1.0 N B:LEU229 4.5 7.8 1.0 CB B:ASP258 4.5 9.9 1.0 HB2 B:ASP308 4.6 6.9 1.0 HB2 B:ASP258 4.6 11.9 1.0 CD B:PRO232 4.6 6.3 1.0 H B:LEU229 4.6 9.3 1.0 CB B:ASP227 4.7 5.5 1.0 C B:LEU229 4.7 6.9 1.0 O B:PRO231 4.7 7.8 1.0 HB3 B:ASP258 4.8 11.9 1.0 CB B:MET230 4.8 6.3 1.0 HA B:MET230 4.8 5.6 1.0 H B:SER228 4.9 9.8 1.0 HG2 B:GLU256 5.0 9.8 1.0 HA B:PRO232 5.0 9.3 1.0 HB2 B:ASP227 5.0 6.6 1.0 HG1 B:THR306 5.0 11.0 1.0

B.Al-Riyami, F.I.Ustok, K.Stott, D.Y.Chirgadze, G.Christie. The Crystal Structure of Clostridium Perfringens Slem, A Muramidase Involved in Cortical Hydrolysis During Spore Germination. Proteins V. 84 1681 2016.
ISSN: ESSN 1097-0134
PubMed: 27488615
DOI: 10.1002/PROT.25112