Magnesium in PDB 4chg: Crystal Structure of VAPBC15 Complex From Mycobacterium Tuberculosis

The structure of Crystal Structure of VAPBC15 Complex From Mycobacterium Tuberculosis, PDB code: 4chg was solved by U.Das, V.Pogenberg, U.K.Tiruttani Subhramanyam, M.Wilmanns, A.Srinivasan, S.Gourinath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.062 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.160, 131.200, 149.350, 90.00, 90.00, 90.00
R / Rfree (%)	16.74 / 19.97

The structure of Crystal Structure of VAPBC15 Complex From Mycobacterium Tuberculosis also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of VAPBC15 Complex From Mycobacterium Tuberculosis (pdb code 4chg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of VAPBC15 Complex From Mycobacterium Tuberculosis, PDB code: 4chg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of VAPBC15 Complex From Mycobacterium Tuberculosis


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 VAPBC15 Complex From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1134 b:25.9 occ:1.00 OE2 G:GLU67 2.0 27.4 1.0 OD1 A:ASP96 2.0 24.1 1.0 O A:HOH2005 2.1 27.7 1.0 O A:HOH2028 2.1 23.7 1.0 O A:HOH2004 2.1 24.4 1.0 O A:HOH2029 2.1 21.5 1.0 CD G:GLU67 3.1 30.5 1.0 CG A:ASP96 3.1 27.7 1.0 OD2 A:ASP96 3.6 28.0 1.0 CG G:GLU67 3.6 30.2 1.0 MN A:MN1133 3.8 24.5 1.0 OD2 A:ASP114 3.8 25.6 1.0 OE1 A:GLU42 3.9 23.8 1.0 OE2 A:GLU42 4.1 25.6 1.0 OE1 G:GLU67 4.1 30.8 1.0 OG A:SER93 4.1 31.4 1.0 OD1 G:ASN63 4.2 29.3 1.0 OD1 A:ASP4 4.2 25.4 1.0 CB A:SER93 4.3 25.9 1.0 ND2 G:ASN63 4.3 25.9 1.0 OD2 A:ASP4 4.4 26.9 1.0 N A:ASP96 4.4 19.0 1.0 CD A:GLU42 4.4 30.1 1.0 CB A:ASP96 4.4 23.8 1.0 CA A:ASP96 4.6 21.1 1.0 CG G:ASN63 4.7 28.6 1.0 OH A:TYR117 4.8 23.7 1.0 CG A:ASP4 4.8 27.2 1.0 CG2 A:ILE95 4.8 26.9 1.0 CB A:THR5 4.9 24.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of VAPBC15 Complex From Mycobacterium Tuberculosis


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 VAPBC15 Complex From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1134 b:26.6 occ:1.00 OE2 H:GLU67 2.0 27.7 1.0 O B:HOH2004 2.0 26.4 1.0 OD1 B:ASP96 2.1 26.8 1.0 O B:HOH2023 2.1 23.7 1.0 O B:HOH2003 2.1 22.3 1.0 O B:HOH2022 2.2 25.6 1.0 CD H:GLU67 3.1 30.4 1.0 CG B:ASP96 3.2 32.4 1.0 OD2 B:ASP96 3.6 30.3 1.0 CG H:GLU67 3.7 31.9 1.0 OE1 B:GLU42 3.8 23.9 1.0 MN B:MN1133 3.8 23.8 1.0 OD2 B:ASP114 3.8 27.8 1.0 OE2 B:GLU42 4.0 27.2 1.0 OE1 H:GLU67 4.1 30.1 1.0 OD1 B:ASP4 4.1 25.9 1.0 OG B:SER93 4.2 37.9 1.0 OD1 H:ASN63 4.3 30.5 1.0 ND2 H:ASN63 4.3 27.9 1.0 CB B:SER93 4.3 31.0 1.0 OD2 B:ASP4 4.3 30.9 1.0 CD B:GLU42 4.3 29.3 1.0 CB B:ASP96 4.5 27.6 1.0 N B:ASP96 4.5 22.1 1.0 OH B:TYR117 4.6 24.5 1.0 CA B:ASP96 4.7 24.2 1.0 CG B:ASP4 4.7 31.6 1.0 CG H:ASN63 4.7 33.2 1.0 CG2 B:ILE95 4.9 22.9 1.0 CB B:THR5 4.9 28.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of VAPBC15 Complex From Mycobacterium Tuberculosis


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 VAPBC15 Complex From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1134 b:20.8 occ:1.00 OE2 I:GLU67 2.0 23.3 1.0 O D:HOH2004 2.0 20.4 1.0 O D:HOH2033 2.1 21.8 1.0 O D:HOH2032 2.1 18.3 1.0 OD1 D:ASP96 2.1 17.9 1.0 O D:HOH2003 2.2 21.5 1.0 CD I:GLU67 3.1 22.9 1.0 CG D:ASP96 3.2 25.5 1.0 CG I:GLU67 3.6 26.5 1.0 OD2 D:ASP96 3.7 23.2 1.0 OE1 D:GLU42 3.8 26.4 1.0 OD2 D:ASP114 3.9 21.5 1.0 MN D:MN1133 3.9 20.8 1.0 OE2 D:GLU42 4.0 27.1 1.0 OD1 D:ASP4 4.1 23.5 1.0 OE1 I:GLU67 4.1 22.6 1.0 OD2 D:ASP4 4.2 25.5 1.0 OG D:SER93 4.3 28.5 1.0 OD1 I:ASN63 4.3 28.5 1.0 ND2 I:ASN63 4.3 25.6 1.0 CD D:GLU42 4.3 27.0 1.0 CB D:ASP96 4.5 23.1 1.0 OH D:TYR117 4.5 26.5 1.0 N D:ASP96 4.5 20.6 1.0 CB D:SER93 4.6 22.4 1.0 CG D:ASP4 4.6 25.7 1.0 CA D:ASP96 4.6 20.2 1.0 CG I:ASN63 4.7 28.6 1.0 CB D:THR5 4.8 22.5 1.0 CG2 D:ILE95 5.0 20.7 1.0 CE2 D:TYR117 5.0 18.9 1.0 CB I:GLU67 5.0 25.0 1.0 OG1 D:THR5 5.0 26.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of VAPBC15 Complex From Mycobacterium Tuberculosis


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 VAPBC15 Complex From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1134 b:22.8 occ:1.00 O F:HOH2004 2.0 16.8 1.0 OE2 J:GLU67 2.0 19.5 1.0 OD1 F:ASP96 2.0 20.1 1.0 O F:HOH2005 2.0 17.3 1.0 O F:HOH2028 2.0 18.1 1.0 O F:HOH2027 2.1 18.7 1.0 CD J:GLU67 3.1 23.5 1.0 CG F:ASP96 3.1 23.8 1.0 OD2 F:ASP96 3.6 26.4 1.0 CG J:GLU67 3.6 24.4 1.0 MN F:MN1133 3.8 22.1 1.0 OE1 F:GLU42 3.8 20.1 1.0 OD2 F:ASP114 3.8 27.5 1.0 OD1 F:ASP4 4.1 21.7 1.0 OE2 F:GLU42 4.1 20.9 1.0 OE1 J:GLU67 4.1 24.6 1.0 OG F:SER93 4.2 27.7 1.0 OD2 F:ASP4 4.2 24.5 1.0 ND2 J:ASN63 4.3 21.0 1.0 OD1 J:ASN63 4.3 21.8 1.0 CB F:ASP96 4.4 21.5 1.0 CD F:GLU42 4.4 24.2 1.0 N F:ASP96 4.4 18.9 1.0 OH F:TYR117 4.5 25.1 1.0 CB F:SER93 4.5 27.5 1.0 CA F:ASP96 4.5 19.2 1.0 CG F:ASP4 4.6 24.4 1.0 CG J:ASN63 4.7 25.1 1.0 CG2 F:ILE95 4.8 19.4 1.0 CB F:THR5 4.9 24.8 1.0 CE2 F:TYR117 5.0 20.8 1.0 CB J:GLU67 5.0 23.5 1.0

U.Das, V.Pogenberg, U.K.Tiruttani Subhramanyam, M.Wilmanns, S.Gourinath, A.Srinivasan. Crystal Structure of the Vapbc-15 Complex From Mycobacterium Tuberculosis Reveals A Two-Metal Ion Dependent Pin-Domain Ribonuclease and A Variable Mode of Toxin-Antitoxin Assembly J.Struct.Biol. 2014.
ISSN: ESSN 1095-8657
DOI: 10.1016/J.JSB.2014.10.002