Magnesium in PDB 8g6p: Crystal Structure of Mycobacterium Thermoresistibile Mure in Complex with Adp and 2,6-Diaminopimelic Acid

The structure of Crystal Structure of Mycobacterium Thermoresistibile Mure in Complex with Adp and 2,6-Diaminopimelic Acid, PDB code: 8g6p was solved by N.O.Rossini, C.S.Silva, M.V.B.Dias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.40 / 1.45
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.792, 62.792, 238.267, 90, 90, 90
R / Rfree (%)	17 / 19

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Thermoresistibile Mure in Complex with Adp and 2,6-Diaminopimelic Acid (pdb code 8g6p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Thermoresistibile Mure in Complex with Adp and 2,6-Diaminopimelic Acid, PDB code: 8g6p:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Thermoresistibile Mure in Complex with Adp and 2,6-Diaminopimelic Acid


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 Mycobacterium Thermoresistibile Mure in Complex with Adp and 2,6-Diaminopimelic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:24.4 occ:1.00 O A:HOH953 2.0 25.3 1.0 O A:HOH1027 2.1 28.2 1.0 O A:HOH1480 2.1 30.5 1.0 O A:HOH1056 2.1 27.5 1.0 O A:HOH1482 2.1 30.2 1.0 O A:HOH1109 2.1 25.4 1.0 HO1 A:GOL806 3.8 20.0 0.7 O1 A:GOL806 4.0 20.0 0.7 OD1 A:ASP162 4.1 26.1 1.0 O A:HOH1005 4.1 29.7 1.0 OD2 A:ASP162 4.1 29.3 1.0 O A:HOH1087 4.2 20.7 1.0 O A:VAL154 4.3 18.8 1.0 O A:HOH1068 4.4 28.4 1.0 CG A:ASP162 4.5 26.3 1.0 O A:HOH1414 4.5 42.1 1.0 CA A:PRO164 4.9 23.0 1.0 CB A:PRO164 4.9 24.3 1.0 H31 A:GOL806 5.0 20.0 0.7

Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Thermoresistibile Mure in Complex with Adp and 2,6-Diaminopimelic Acid


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 Mycobacterium Thermoresistibile Mure in Complex with Adp and 2,6-Diaminopimelic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg810 b:14.5 occ:1.00 O A:HOH945 2.0 15.7 1.0 O A:HOH1181 2.1 17.9 1.0 O A:HOH1260 2.1 16.8 1.0 O A:HOH970 2.1 15.7 1.0 O A:HOH1002 2.1 18.3 1.0 NE2 A:HIS221 2.2 15.3 1.0 CE1 A:HIS221 3.1 16.6 1.0 CD2 A:HIS221 3.3 14.9 1.0 O A:HOH1460 3.8 21.2 1.0 NZ A:LYS130 4.0 14.5 1.0 OQ1 A:KCX235 4.0 12.8 1.0 OD2 A:ASP220 4.0 19.6 1.0 O A:HOH1364 4.1 34.9 1.0 ND1 A:HIS221 4.2 16.6 1.0 O A:HOH1385 4.2 45.5 1.0 OQ2 A:KCX235 4.3 12.5 1.0 O A:HOH1081 4.3 15.2 1.0 CG A:HIS221 4.4 14.9 1.0 O A:THR127 4.4 14.0 1.0 CX A:KCX235 4.6 11.5 1.0 O A:HOH1411 4.7 43.7 1.0 CG A:ASP220 4.8 19.1 1.0 O3B A:ADP804 4.8 25.4 0.5 CE A:LYS130 4.9 14.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Thermoresistibile Mure in Complex with Adp and 2,6-Diaminopimelic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Mycobacterium Thermoresistibile Mure in Complex with Adp and 2,6-Diaminopimelic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg811 b:29.9 occ:0.98 O2B A:ADP804 2.2 21.2 0.4 O A:HOH1364 2.6 34.9 1.0 OG1 A:THR153 2.6 23.3 0.8 CG2 A:THR153 2.7 23.0 0.2 OE1 A:GLU193 2.7 19.3 1.0 OG1 A:THR131 2.9 14.2 1.0 O3B A:ADP804 2.9 25.4 0.5 PB A:ADP804 3.1 10.8 0.7 CD A:GLU193 3.6 15.3 1.0 CB A:THR153 3.7 19.6 0.8 CB A:THR153 3.8 20.7 0.2 OG1 A:THR153 3.8 21.9 0.2 O A:HOH1181 3.8 17.9 1.0 O2A A:ADP804 3.9 32.2 0.6 OE2 A:GLU193 3.9 16.5 1.0 O A:HOH1107 4.0 21.1 1.0 CE A:LYS130 4.1 14.5 1.0 O A:HOH1460 4.1 21.2 1.0 O1B A:ADP804 4.2 22.2 0.4 NZ A:LYS130 4.2 14.5 1.0 CB A:THR131 4.2 12.4 1.0 CG2 A:THR153 4.3 22.1 0.8 O3A A:ADP804 4.3 30.3 0.4 N A:THR131 4.5 11.3 1.0 CB A:LYS130 4.7 10.9 1.0 NH2 A:ARG350 4.8 23.4 0.9 PA A:ADP804 4.8 27.5 0.3 CA A:THR131 4.9 11.5 1.0 CG A:GLU193 4.9 14.4 1.0 CA A:THR153 5.0 18.1 0.8

N.O.Rossini, C.Silva, M.V.B.Dias. The Crystal Structure of Mycobacterium Thermoresistibile Mure Ligase Reveals the Binding Mode of the Substrate M-Diaminopimelate. J.Struct.Biol. V. 215 07957 2023.
ISSN: ESSN 1095-8657
PubMed: 36944394
DOI: 10.1016/J.JSB.2023.107957