Magnesium in PDB 6r1b: Crystal Structure of Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine

The structure of Crystal Structure of Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine, PDB code: 6r1b was solved by J.Fenn, R.Nepravishta, C.S.Guy, J.Harrison, J.Angulo, A.D.Cameron, E.Fullam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.69 / 2.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.110, 169.860, 213.310, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.6

The binding sites of Magnesium atom in the Crystal Structure of Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine (pdb code 6r1b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine, PDB code: 6r1b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine


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 Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:51.1 occ:1.00 O A:HOH602 2.0 52.1 1.0 O A:HOH605 2.1 57.1 1.0 OD2 A:ASP40 2.2 79.0 1.0 O A:HOH621 2.2 51.5 1.0 O A:HOH609 2.2 56.1 1.0 O A:HOH671 2.4 48.1 1.0 CG A:ASP40 3.1 69.8 1.0 OD1 A:ASP40 3.5 73.8 1.0 O A:SER36 3.6 64.9 1.0 OD1 A:ASP93 3.7 95.3 1.0 OD2 A:ASP93 4.3 92.9 1.0 CB A:ASP40 4.4 59.6 1.0 CG A:ASP93 4.5 92.4 1.0 O A:PRO38 4.7 64.1 1.0 C A:SER36 4.8 67.2 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine


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 Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:66.4 occ:1.00 OD1 B:ASP138 2.5 38.4 1.0 HO1 B:GOL505 3.1 53.3 1.0 CG B:ASP138 3.5 37.2 1.0 O B:HOH642 3.5 49.7 1.0 OG1 B:THR304 3.5 34.4 1.0 OD2 B:ASP138 3.7 37.2 1.0 O1 B:GOL505 3.9 44.4 1.0 OG1 B:THR380 4.1 46.8 1.0 O B:HOH649 4.2 37.8 1.0 O B:SER134 4.2 44.2 1.0 H2 B:GOL505 4.3 46.8 1.0 H11 B:GOL505 4.4 49.1 1.0 CA B:THR380 4.4 39.7 1.0 CB B:THR380 4.6 44.0 1.0 C1 B:GOL505 4.6 40.9 1.0 CB B:THR304 4.8 34.1 1.0 CB B:ASP138 4.9 36.8 1.0 CG2 B:THR304 5.0 34.9 1.0 C2 B:GOL505 5.0 39.0 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine


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 Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:72.5 occ:1.00 OD2 B:ASP40 2.4 64.6 1.0 O B:SER36 2.9 98.3 1.0 OD1 B:ASP93 3.3 93.2 1.0 OD2 B:ASP93 3.3 95.4 1.0 CG B:ASP40 3.4 59.6 1.0 OD1 B:ASP40 3.7 60.6 1.0 CG B:ASP93 3.7 93.9 1.0 C B:SER36 4.0 98.0 1.0 N B:SER36 4.1 0.2 1.0 O B:PRO38 4.7 48.7 1.0 CA B:SER36 4.8 99.1 1.0 CB B:ASP40 4.8 53.7 1.0 CA B:GLY35 5.0 96.0 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:82.3 occ:1.00 OD2 C:ASP40 2.3 75.4 1.0 CG C:ASP40 3.0 71.2 1.0 OD1 C:ASP40 3.4 72.1 1.0 O C:SER36 3.5 88.8 1.0 OD1 C:ASP93 3.8 98.2 1.0 CB C:ASP40 4.1 64.8 1.0 O C:PRO38 4.3 74.9 1.0 N C:SER36 4.3 94.9 1.0 C C:SER36 4.5 90.4 1.0 CG C:ASP93 4.7 96.8 1.0 O C:VAL94 4.8 72.2 1.0 CA C:GLY35 4.8 87.5 1.0 OD2 C:ASP93 4.8 95.8 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Ugpb From Mycobacterium Tuberculosis in Complex with Glycerophosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:40.7 occ:1.00 O D:HOH605 2.0 41.8 1.0 O D:HOH603 2.0 38.0 1.0 O D:HOH639 2.0 40.2 1.0 OD2 D:ASP40 2.1 53.7 1.0 O D:HOH609 2.1 38.3 1.0 O D:HOH612 2.2 40.2 1.0 CG D:ASP40 3.0 47.4 1.0 OD1 D:ASP40 3.2 48.7 1.0 O D:SER36 3.4 57.8 1.0 O D:HOH611 3.8 53.6 1.0 OD1 D:ASP93 4.0 55.9 1.0 O D:PRO38 4.3 43.1 1.0 OD2 D:ASP93 4.3 53.7 1.0 CB D:ASP40 4.4 43.2 1.0 O B:HOH671 4.4 36.1 1.0 CG D:ASP93 4.6 54.6 1.0 C D:SER36 4.6 62.6 1.0 CB B:PRO170 4.6 45.5 1.0

J.S.Fenn, R.Nepravishta, C.S.Guy, J.Harrison, J.Angulo, A.D.Cameron, E.Fullam. Structural Basis of Glycerophosphodiester Recognition By Themycobacterium Tuberculosissubstrate-Binding Protein Ugpb. Acs Chem.Biol. V. 14 1879 2019.
ISSN: ESSN 1554-8937
PubMed: 31433162
DOI: 10.1021/ACSCHEMBIO.9B00204