Manganese in PDB 1lv5: Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp

All present enzymatic activity of Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp:
2.7.7.7;

The structure of Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp, PDB code: 1lv5 was solved by S.J.Johnson, J.S.Taylor, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.70 / 1.95
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	91.681, 91.681, 190.116, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 26.1

The structure of Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp (pdb code 1lv5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp, PDB code: 1lv5:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1 b:40.6 occ:1.00 O2G A:DCP201 2.0 33.2 1.0 O2A A:DCP201 2.0 30.1 1.0 O2B A:DCP201 2.0 33.0 1.0 OD1 A:ASP653 2.1 36.4 1.0 OD2 A:ASP830 2.5 23.9 1.0 O A:TYR654 2.7 36.7 1.0 CG A:ASP653 2.7 36.1 1.0 OD2 A:ASP653 2.8 36.3 1.0 OD1 A:ASP830 3.1 22.2 1.0 CG A:ASP830 3.1 23.2 1.0 PB A:DCP201 3.3 31.4 1.0 PG A:DCP201 3.3 32.3 1.0 PA A:DCP201 3.3 28.8 1.0 MG A:MG205 3.5 34.5 1.0 O3A A:DCP201 3.7 29.9 1.0 O3B A:DCP201 3.7 32.7 1.0 C A:TYR654 3.8 35.1 1.0 N A:TYR654 4.0 35.5 1.0 C5' A:DCP201 4.1 27.1 1.0 O5' A:DCP201 4.2 29.3 1.0 CB A:ASP653 4.2 35.9 1.0 O1G A:DCP201 4.3 33.6 1.0 O3G A:DCP201 4.4 32.5 1.0 CA A:TYR654 4.4 35.1 1.0 O1A A:DCP201 4.5 29.0 1.0 O A:ASP830 4.5 25.2 1.0 CB A:TYR654 4.5 34.4 1.0 O1B A:DCP201 4.6 30.9 1.0 CB A:ASP830 4.6 24.2 1.0 N A:GLN656 4.6 32.0 1.0 C A:ASP653 4.7 35.3 1.0 N A:SER655 4.8 34.4 1.0 CA A:ASP653 4.9 35.1 1.0 CA A:SER655 5.0 33.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2 b:27.3 occ:1.00 O B:TYR654 1.9 30.5 1.0 O2B B:DCP202 2.0 22.5 1.0 O2A B:DCP202 2.1 27.9 1.0 O2G B:DCP202 2.1 27.6 1.0 OD1 B:ASP830 2.2 31.7 1.0 OD2 B:ASP653 2.5 33.2 1.0 C B:TYR654 3.1 30.6 1.0 PB B:DCP202 3.3 26.5 1.0 CG B:ASP830 3.3 30.9 1.0 PA B:DCP202 3.4 28.3 1.0 PG B:DCP202 3.4 28.8 1.0 CG B:ASP653 3.7 34.5 1.0 O3A B:DCP202 3.7 24.4 1.0 O3B B:DCP202 3.8 26.1 1.0 CA B:SER655 3.9 31.6 1.0 N B:TYR654 3.9 30.8 1.0 N B:SER655 3.9 30.7 1.0 C5' B:DCP202 4.0 30.7 1.0 OD2 B:ASP830 4.1 31.8 1.0 CA B:TYR654 4.1 30.0 1.0 O5' B:DCP202 4.2 28.9 1.0 N B:GLN656 4.3 30.7 1.0 O3G B:DCP202 4.3 29.7 1.0 CB B:ASP830 4.3 32.2 1.0 C B:SER655 4.4 31.1 1.0 CG2 B:ILE657 4.5 26.8 1.0 C B:ASP653 4.5 31.8 1.0 O1G B:DCP202 4.5 27.9 1.0 CB B:TYR654 4.5 30.2 1.0 OD1 B:ASP653 4.6 36.5 1.0 O1A B:DCP202 4.6 27.3 1.0 O1B B:DCP202 4.6 22.7 1.0 CB B:ASP653 4.6 33.7 1.0 N B:ILE657 4.7 27.4 1.0 CB B:ILE657 4.7 26.4 1.0 CA B:ASP653 4.9 32.0 1.0

S.J.Johnson, J.S.Taylor, L.S.Beese. Processive Dna Synthesis Observed in A Polymerase Crystal Suggests A Mechanism For the Prevention of Frameshift Mutations Proc.Natl.Acad.Sci.Usa V. 100 3895 2003.
ISSN: ISSN 0027-8424
PubMed: 12649320
DOI: 10.1073/PNAS.0630532100