Magnesium in PDB 2r72: Crystal Structure of Infectious Bursal Disease Virus VP1 Polymerase, Incubated with MG2+ Ion.

The structure of Crystal Structure of Infectious Bursal Disease Virus VP1 Polymerase, Incubated with MG2+ Ion., PDB code: 2r72 was solved by D.Garriga, A.Navarro, J.Querol-Audi, F.Abaitua, J.F.Rodriguez, N.Verdaguer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.15
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	122.838, 122.838, 354.255, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 23.5

The binding sites of Magnesium atom in the Crystal Structure of Infectious Bursal Disease Virus VP1 Polymerase, Incubated with MG2+ Ion. (pdb code 2r72). 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 Infectious Bursal Disease Virus VP1 Polymerase, Incubated with MG2+ Ion., PDB code: 2r72:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Infectious Bursal Disease Virus VP1 Polymerase, Incubated with MG2+ Ion.


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 Infectious Bursal Disease Virus VP1 Polymerase, Incubated with MG2+ Ion. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg846 b:71.6 occ:1.00 OD2 A:ASP402 2.7 60.4 1.0 O A:LEU417 2.7 67.4 1.0 N A:GLY420 3.3 68.2 1.0 C A:LYS419 3.4 68.5 1.0 CG A:ASP402 3.5 59.7 1.0 CA A:GLY420 3.6 67.8 1.0 CB A:ASP402 3.6 59.1 1.0 O A:LYS419 3.7 68.7 1.0 C A:LEU417 3.8 67.4 1.0 CA A:LYS419 4.0 68.5 1.0 O A:GLU418 4.1 68.8 1.0 C A:GLU418 4.3 68.5 1.0 OE2 A:GLU421 4.3 69.5 1.0 CB A:LEU417 4.3 66.9 1.0 N A:LYS419 4.3 68.4 1.0 CA A:LEU417 4.4 67.0 1.0 N A:LEU417 4.5 66.7 1.0 OD1 A:ASP402 4.5 60.3 1.0 N A:GLU418 4.8 67.8 1.0 C A:GLY420 4.9 67.5 1.0 O A:ASP402 4.9 58.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Infectious Bursal Disease Virus VP1 Polymerase, Incubated with MG2+ Ion.


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 Infectious Bursal Disease Virus VP1 Polymerase, Incubated with MG2+ Ion. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg847 b:0.7 occ:1.00 ND2 A:ASN493 3.0 63.4 1.0 OD1 A:ASP402 3.1 60.3 1.0 CB A:ALA401 3.6 58.5 1.0 OG1 A:THR489 3.8 69.9 1.0 CG A:ASN493 4.0 62.8 1.0 CG A:ASP402 4.0 59.7 1.0 OD1 A:ASN486 4.2 74.5 1.0 CB A:ASN493 4.2 62.2 1.0 O A:ASN486 4.3 73.9 1.0 CA A:PHE490 4.5 67.2 1.0 O A:THR489 4.6 69.1 1.0 N A:ASP402 4.6 58.8 1.0 OE2 A:GLU421 4.6 69.5 1.0 C A:THR489 4.7 69.1 1.0 N A:PHE490 4.7 68.1 1.0 CB A:ASP402 4.8 59.1 1.0 OD2 A:ASP402 4.8 60.4 1.0 CB A:THR489 4.9 69.8 1.0 CG A:ASN486 4.9 74.4 1.0 CA A:ALA401 4.9 58.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Infectious Bursal Disease Virus VP1 Polymerase, Incubated with MG2+ Ion.


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 Infectious Bursal Disease Virus VP1 Polymerase, Incubated with MG2+ Ion. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg848 b:86.8 occ:1.00 O A:ILE415 2.7 64.7 1.0 OG A:SER414 3.3 62.7 1.0 OD1 A:ASN403 3.4 59.1 1.0 CB A:ASN403 3.4 58.4 1.0 N A:ILE415 3.4 63.5 1.0 OD1 A:ASP416 3.4 68.0 1.0 CE2 A:TYR405 3.5 57.7 1.0 C A:ILE415 3.5 64.6 1.0 CZ A:TYR405 3.5 57.8 1.0 O A:ILE404 3.7 57.7 1.0 CA A:ASN403 3.8 58.4 1.0 N A:ILE404 3.8 58.0 1.0 OH A:TYR405 3.8 58.2 1.0 CG A:ASN403 3.9 58.6 1.0 CD2 A:TYR405 4.0 57.7 1.0 C A:SER414 4.0 62.9 1.0 CA A:ILE415 4.1 64.1 1.0 CE1 A:TYR405 4.1 57.3 1.0 C A:ASN403 4.1 58.3 1.0 CA A:SER414 4.2 62.5 1.0 CG A:ASP416 4.2 66.9 1.0 C A:ILE404 4.2 57.8 1.0 CB A:SER414 4.3 62.5 1.0 N A:ASP416 4.4 65.2 1.0 CG A:TYR405 4.5 57.7 1.0 CD1 A:TYR405 4.5 57.6 1.0 OD2 A:ASP416 4.7 67.6 1.0 CA A:ILE404 4.7 57.8 1.0 O A:SER414 4.8 62.9 1.0 CA A:ASP416 4.8 66.0 1.0 N A:TYR405 5.0 57.7 1.0

D.Garriga, A.Navarro, J.Querol-Audi, F.Abaitua, J.F.Rodriguez, N.Verdaguer. Activation Mechanism of A Noncanonical Rna-Dependent Rna Polymerase. Proc.Natl.Acad.Sci.Usa V. 104 20540 2007.
ISSN: ISSN 0027-8424
PubMed: 18077388
DOI: 10.1073/PNAS.0704447104