Magnesium in PDB 5mh1: Crystal Structure of A DM9 Domain Containing Protein From Crassostrea Gigas

The structure of Crystal Structure of A DM9 Domain Containing Protein From Crassostrea Gigas, PDB code: 5mh1 was solved by T.Weinert, E.Warkentin, G.Pang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	5.00 / 1.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	67.300, 67.300, 55.000, 90.00, 90.00, 120.00
R / Rfree (%)	10 / 11.7

The binding sites of Magnesium atom in the Crystal Structure of A DM9 Domain Containing Protein From Crassostrea Gigas (pdb code 5mh1). 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 A DM9 Domain Containing Protein From Crassostrea Gigas, PDB code: 5mh1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of A DM9 Domain Containing Protein From Crassostrea Gigas


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 A DM9 Domain Containing Protein From Crassostrea Gigas within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:13.3 occ:1.00 H A:GLY125 2.1 11.7 1.0 O A:HOH341 2.7 9.9 1.0 HA A:CYS113 2.7 8.7 1.0 HA A:MET124 2.8 10.9 1.0 O A:PRO112 2.8 7.3 1.0 N A:GLY125 2.9 9.7 1.0 HD3 A:PRO54 2.9 10.1 1.0 HG3 A:PRO54 3.0 10.9 1.0 HG22 A:ILE111 3.1 10.5 1.0 HB3 A:CYS113 3.1 9.6 1.0 HB2 A:CYS113 3.4 9.6 1.0 CA A:CYS113 3.5 7.2 1.0 CB A:CYS113 3.5 8.0 1.0 HG21 A:ILE111 3.5 10.5 1.0 HA2 A:GLY42 3.6 9.0 1.0 HA3 A:GLY125 3.6 12.3 1.0 CA A:MET124 3.6 9.1 1.0 CG A:PRO54 3.7 9.1 1.0 CD A:PRO54 3.7 8.4 1.0 HD3 A:LYS43 3.7 10.2 1.0 HB2 A:MET124 3.7 12.0 1.0 C A:MET124 3.7 10.0 1.0 CG2 A:ILE111 3.7 8.7 1.0 CA A:GLY125 3.8 10.3 1.0 C A:PRO112 3.8 6.8 1.0 HB3 A:PRO54 3.8 11.5 1.0 HG23 A:ILE111 4.1 10.5 1.0 N A:CYS113 4.1 6.8 1.0 HD2 A:PRO54 4.2 10.1 1.0 CB A:MET124 4.2 10.0 1.0 HB3 A:LYS43 4.3 9.3 1.0 O A:GLY125 4.3 10.6 1.0 O A:TYR123 4.3 7.9 1.0 CB A:PRO54 4.3 9.6 1.0 CA A:GLY42 4.3 7.5 1.0 HA3 A:GLY42 4.4 9.0 1.0 HG2 A:PRO54 4.5 10.9 1.0 HG2 A:LYS43 4.5 9.6 1.0 C A:GLY125 4.5 10.5 1.0 HB3 A:MET124 4.5 12.0 1.0 H A:LYS114 4.6 8.2 1.0 HA2 A:GLY125 4.6 12.3 1.0 CD A:LYS43 4.6 8.5 1.0 O A:HIS52 4.6 8.4 1.0 H A:LYS43 4.6 8.7 1.0 C A:CYS113 4.7 6.8 1.0 N A:MET124 4.7 8.5 1.0 C A:GLY42 4.8 6.9 1.0 N A:PRO54 4.8 8.7 1.0 N A:LYS43 4.8 7.2 1.0 HZ2 A:LYS43 4.8 11.8 1.0 CG A:LYS43 4.9 8.0 1.0 O A:MET124 4.9 11.4 1.0 OE2 A:GLU59 5.0 10.7 0.6 C A:TYR123 5.0 7.5 1.0 HB A:ILE111 5.0 9.6 1.0 N A:LYS114 5.0 6.8 1.0 HB2 A:PRO54 5.0 11.5 1.0 H A:CYS113 5.0 8.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A DM9 Domain Containing Protein From Crassostrea Gigas


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 A DM9 Domain Containing Protein From Crassostrea Gigas within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:25.6 occ:1.00 O A:LYS141 2.7 10.9 1.0 O A:HOH380 2.8 26.4 1.0 O A:HOH381 2.9 16.8 1.0 OD1 A:ASN91 3.0 17.1 1.0 HD1 A:TYR140 3.1 12.0 1.0 HB2 A:ASN91 3.1 15.2 1.0 HE1 A:TYR140 3.3 13.7 1.0 HA A:VAL142 3.3 12.9 1.0 CD1 A:TYR140 3.8 10.0 1.0 C A:LYS141 3.8 9.4 1.0 CG A:ASN91 3.8 15.4 1.0 CB A:ASN91 3.8 12.6 1.0 CE1 A:TYR140 3.9 11.4 1.0 O A:HOH448 3.9 35.5 1.0 O A:GLY90 3.9 10.8 1.0 CA A:VAL142 4.1 10.8 1.0 O A:VAL142 4.1 13.8 1.0 HB3 A:ASN91 4.2 15.2 1.0 C A:VAL142 4.4 11.4 1.0 N A:VAL142 4.4 9.6 1.0 C A:GLY90 4.7 10.2 1.0 O A:HOH419 4.8 31.1 1.0 HB3 A:LYS141 4.9 13.8 1.0

S.Jiang, L.Wang, M.Huang, Z.Jia, T.Weinert, E.Warkentin, C.Liu, X.Song, H.Zhang, J.Witt, L.Qiu, G.Peng, L.Song. DM9 Domain Containing Protein Functions As A Pattern Recognition Receptor with Broad Microbial Recognition Spectrum. Front Immunol V. 8 1607 2017.
ISSN: ESSN 1664-3224
PubMed: 29238341
DOI: 10.3389/FIMMU.2017.01607