Magnesium in PDB 2z2p: Crystal Structure of Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus with Quinupristin

The structure of Crystal Structure of Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus with Quinupristin, PDB code: 2z2p was solved by M.Korczynska, A.M.Berghuis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.18 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.999, 93.700, 95.301, 90.00, 90.00, 90.00
R / Rfree (%)	26.2 / 31.8

The binding sites of Magnesium atom in the Crystal Structure of Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus with Quinupristin (pdb code 2z2p). 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 Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus with Quinupristin, PDB code: 2z2p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus with Quinupristin


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 Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus with Quinupristin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:2.0 occ:1.00 OG1 C:MHW1 1.7 20.7 1.0 OE1 A:GLU284 1.9 21.0 1.0 O C:MHW1 1.9 20.0 1.0 OE1 A:GLU268 2.1 21.3 1.0 CB C:MHW1 2.8 20.7 1.0 C C:MHW1 2.9 20.7 1.0 CD A:GLU284 3.0 21.3 1.0 CD A:GLU268 3.1 21.9 1.0 CA C:MHW1 3.3 20.8 1.0 OE2 A:GLU284 3.4 21.8 1.0 OE2 A:GLU268 3.6 21.4 1.0 CG2 C:MHW1 4.0 20.5 1.0 N C:THR2 4.1 20.9 1.0 NE1 A:TRP243 4.2 12.3 1.0 CG A:GLU284 4.3 20.9 1.0 CG A:GLU268 4.3 23.6 1.0 CB A:GLU268 4.6 24.8 1.0 CB A:GLU284 4.6 20.8 1.0 N C:MHW1 4.7 20.6 1.0 CA C:THR2 4.7 21.2 1.0 CZ2 A:TRP243 4.8 12.3 1.0 CE2 A:TRP243 4.8 12.4 1.0 O40 A:DOL2002 5.0 34.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus with Quinupristin


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 Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus with Quinupristin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:18.5 occ:1.00 OE2 A:GLU69 2.0 15.6 1.0 OD2 A:ASP127 2.1 24.9 1.0 OD1 A:ASP127 2.4 25.4 1.0 OD2 A:ASP67 2.5 17.7 1.0 CG A:ASP127 2.6 24.7 1.0 OD1 A:ASP67 3.0 18.1 1.0 CG A:ASP67 3.1 17.3 1.0 CD A:GLU69 3.2 16.1 1.0 NE1 A:TRP71 3.7 13.0 1.0 CZ2 A:TRP71 4.0 12.9 1.0 OG A:SER65 4.0 16.2 1.0 OE1 A:GLU69 4.0 17.0 1.0 CB A:ASP127 4.1 24.3 1.0 NH2 A:ARG82 4.1 20.4 1.0 CG A:GLU69 4.2 15.4 1.0 CE2 A:TRP71 4.2 12.9 1.0 CB A:GLU69 4.4 15.2 1.0 CB A:ASP67 4.6 16.9 1.0 NE A:ARG82 4.7 19.7 1.0 CZ A:ARG82 4.7 19.9 1.0 CB A:SER65 4.7 16.1 1.0 CA A:ASP127 4.8 24.4 1.0 CD1 A:TRP71 4.9 13.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus with Quinupristin


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 Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus with Quinupristin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:2.0 occ:1.00 OG1 D:MHW1 1.7 17.3 1.0 OE1 B:GLU284 1.9 20.8 1.0 O D:MHW1 2.1 17.4 1.0 OE1 B:GLU268 2.1 21.5 1.0 CB D:MHW1 2.8 17.5 1.0 CD B:GLU268 3.0 22.3 1.0 CD B:GLU284 3.0 21.0 1.0 C D:MHW1 3.1 17.8 1.0 OE2 B:GLU268 3.3 21.7 1.0 CA D:MHW1 3.4 17.6 1.0 OE2 B:GLU284 3.4 21.6 1.0 CG2 D:MHW1 4.0 17.4 1.0 N D:THR2 4.3 17.7 1.0 NE1 B:TRP243 4.3 12.6 1.0 CG B:GLU284 4.3 20.8 1.0 CG B:GLU268 4.3 23.8 1.0 O41 B:DOL2003 4.6 35.8 1.0 CB B:GLU284 4.7 20.6 1.0 CB B:GLU268 4.7 24.8 1.0 N D:MHW1 4.8 17.4 1.0 CZ2 B:TRP243 4.8 12.2 1.0 CA D:THR2 4.9 17.8 1.0 CE2 B:TRP243 4.9 12.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus with Quinupristin


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 Catalytically Inactive H270A Virginiamycin B Lyase From Staphylococcus Aureus with Quinupristin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1004 b:15.4 occ:1.00 OE2 B:GLU69 1.9 15.3 1.0 OD2 B:ASP127 2.1 24.7 1.0 OD1 B:ASP127 2.4 25.6 1.0 OD2 B:ASP67 2.5 18.0 1.0 CG B:ASP127 2.5 24.9 1.0 CD B:GLU69 3.1 15.6 1.0 CG B:ASP67 3.1 17.6 1.0 OD1 B:ASP67 3.1 18.4 1.0 OE1 B:GLU69 3.8 16.7 1.0 NE1 B:TRP71 3.8 13.2 1.0 CB B:ASP127 4.0 24.4 1.0 OG B:SER65 4.1 15.9 1.0 CZ2 B:TRP71 4.2 13.2 1.0 CG B:GLU69 4.2 15.3 1.0 CE2 B:TRP71 4.4 13.0 1.0 CB B:ASP67 4.5 16.9 1.0 CB B:GLU69 4.6 15.2 1.0 CA B:ASP127 4.7 24.4 1.0 CB B:SER65 4.8 16.1 1.0

M.Korczynska, T.A.Mukhtar, G.D.Wright, A.M.Berghuis. Structural Basis For Streptogramin B Resistance in Staphylococcus Aureus By Virginiamycin B Lyase Proc.Natl.Acad.Sci.Usa V. 104 10388 2007.
ISSN: ISSN 0027-8424
PubMed: 17563376
DOI: 10.1073/PNAS.0701809104