Magnesium in PDB 3bjy: Catalytic Core of REV1 in Complex with Dna (Modified Template Guanine) and Incoming Nucleotide

The structure of Catalytic Core of REV1 in Complex with Dna (Modified Template Guanine) and Incoming Nucleotide, PDB code: 3bjy was solved by D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.41
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	181.062, 199.578, 55.677, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 24.1

The binding sites of Magnesium atom in the Catalytic Core of REV1 in Complex with Dna (Modified Template Guanine) and Incoming Nucleotide (pdb code 3bjy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Catalytic Core of REV1 in Complex with Dna (Modified Template Guanine) and Incoming Nucleotide, PDB code: 3bjy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Catalytic Core of REV1 in Complex with Dna (Modified Template Guanine) and Incoming Nucleotide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Catalytic Core of REV1 in Complex with Dna (Modified Template Guanine) and Incoming Nucleotide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg297 b:47.7 occ:1.00 OD2 A:ASP467 2.4 24.7 1.0 OE2 A:GLU468 2.7 41.9 1.0 OD2 A:ASP362 2.7 40.8 1.0 O1A A:DCP739 2.7 29.9 1.0 CG A:ASP467 3.2 26.6 1.0 OD1 A:ASP467 3.3 27.4 1.0 MG A:MG298 3.5 33.4 1.0 C3' P:DOC12 3.6 58.5 1.0 PA A:DCP739 3.7 27.9 1.0 O5' A:DCP739 3.7 27.2 1.0 CB A:GLU468 3.7 31.7 1.0 CG A:ASP362 3.7 34.3 1.0 CD A:GLU468 3.8 41.0 1.0 C5' A:DCP739 3.8 27.1 1.0 OD1 A:ASP362 4.1 37.1 1.0 O A:HOH753 4.2 40.1 1.0 OG A:SER465 4.3 35.5 1.0 CG A:GLU468 4.4 36.4 1.0 O2A A:DCP739 4.4 29.3 1.0 O A:ASP467 4.4 29.0 1.0 C2' P:DOC12 4.5 56.8 1.0 C A:ASP467 4.5 28.5 1.0 CB A:SER465 4.5 34.1 1.0 CB A:ASP467 4.6 27.0 1.0 O2B A:DCP739 4.7 30.2 1.0 OE1 A:GLU468 4.7 41.5 1.0 N A:GLU468 4.8 28.4 1.0 C4' P:DOC12 4.8 59.3 1.0 CA A:GLU468 4.8 30.6 1.0 CB A:ASP362 4.9 34.2 1.0

Magnesium binding site 2 out of 2 in the Catalytic Core of REV1 in Complex with Dna (Modified Template Guanine) and Incoming Nucleotide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Catalytic Core of REV1 in Complex with Dna (Modified Template Guanine) and Incoming Nucleotide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg298 b:33.4 occ:1.00 O2B A:DCP739 2.0 30.2 1.0 OD1 A:ASP362 2.1 37.1 1.0 O A:PHE363 2.3 28.3 1.0 OD1 A:ASP467 2.5 27.4 1.0 O3G A:DCP739 2.5 23.3 1.0 O1A A:DCP739 2.5 29.9 1.0 CG A:ASP362 2.9 34.3 1.0 OD2 A:ASP362 3.1 40.8 1.0 PB A:DCP739 3.3 25.6 1.0 C A:PHE363 3.5 29.8 1.0 MG A:MG297 3.5 47.7 1.0 O A:HOH753 3.6 40.1 1.0 CG A:ASP467 3.6 26.6 1.0 PA A:DCP739 3.6 27.9 1.0 PG A:DCP739 3.6 26.0 1.0 O3B A:DCP739 3.9 28.4 1.0 O3A A:DCP739 3.9 27.7 1.0 N A:PHE363 4.0 28.7 1.0 C5' A:DCP739 4.0 27.1 1.0 OD2 A:ASP467 4.1 24.7 1.0 O2G A:DCP739 4.2 28.1 1.0 NZ A:LYS525 4.2 45.0 1.0 CA A:PHE363 4.2 28.3 1.0 O5' A:DCP739 4.3 27.2 1.0 CB A:ASP362 4.3 34.2 1.0 C A:ASP362 4.4 30.1 1.0 CB A:PHE363 4.5 29.1 1.0 CE A:LYS525 4.5 42.6 1.0 CB A:PHE366 4.5 26.8 1.0 N A:ASP364 4.5 30.8 1.0 N A:CYS365 4.5 28.3 1.0 N A:PHE366 4.6 26.8 1.0 O1B A:DCP739 4.6 29.6 1.0 CA A:ASP364 4.6 30.7 1.0 O2A A:DCP739 4.7 29.3 1.0 C A:ASP364 4.7 30.1 1.0 CA A:ASP362 4.8 31.0 1.0 CB A:ASP467 4.8 27.0 1.0 O A:ASP467 4.9 29.0 1.0 O1G A:DCP739 5.0 28.6 1.0

D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. Protein-Template-Directed Synthesis Across An Acrolein-Derived Dna Adduct By Yeast REV1 Dna Polymerase Structure V. 16 239 2008.
ISSN: ISSN 0969-2126
PubMed: 18275815
DOI: 10.1016/J.STR.2007.12.009