Manganese in PDB 8icu: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Ddatp (1 Millimolar) and MNCL2 (5 Millimolar)

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Ddatp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8icu was solved by H.Pelletier, M.R.Sawaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.670, 57.593, 48.139, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / n/a

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Ddatp (1 Millimolar) and MNCL2 (5 Millimolar) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Manganese atom in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Ddatp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb code 8icu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Ddatp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8icu:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Ddatp (1 Millimolar) and MNCL2 (5 Millimolar)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Ddatp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn339 b:30.0 occ:0.53 O1A A:DAD338 1.1 67.7 0.5 OD1 A:ASP190 2.4 50.7 1.0 PA A:DAD338 2.6 62.3 0.5 O1G A:DAD338 2.6 30.4 0.5 O3G A:DAD338 3.1 43.7 0.5 O2B A:DAD338 3.2 57.5 0.5 PG A:DAD338 3.3 39.4 0.5 O A:HOH655 3.3 39.2 1.0 O3A A:DAD338 3.3 63.5 0.5 MN A:MN340 3.3 30.0 0.4 O A:ASP190 3.4 27.4 1.0 O5' A:DAD338 3.4 60.4 0.5 O3B A:DAD338 3.4 49.9 0.5 CG A:ASP190 3.5 52.9 1.0 OD2 A:ASP192 3.5 56.5 1.0 OP2 P:DA8 3.6 0.0 1.0 PB A:DAD338 3.6 59.4 0.5 O2A A:DAD338 3.7 61.5 0.5 OD1 A:ASP192 3.9 58.8 1.0 CG A:ASP192 3.9 51.0 1.0 OD2 A:ASP190 4.1 67.8 1.0 O A:HOH502 4.1 6.9 1.0 C A:ASP190 4.3 20.4 1.0 N A:ASP190 4.3 22.6 1.0 P P:DA8 4.5 0.0 1.0 O A:HOH522 4.7 62.8 1.0 CA A:ASP190 4.7 27.1 1.0 CB A:ASP190 4.7 37.5 1.0 O2G A:DAD338 4.7 42.6 0.5 OP1 P:DA8 4.8 0.0 1.0 O5' P:DA8 4.9 0.0 1.0 CB A:ASP192 5.0 34.9 1.0

Manganese binding site 2 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Ddatp (1 Millimolar) and MNCL2 (5 Millimolar)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Ddatp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:30.0 occ:0.43 OP2 P:DA8 2.0 0.0 1.0 OD2 A:ASP190 2.3 67.8 1.0 OD1 A:ASP192 2.6 58.8 1.0 CG A:ASP190 2.8 52.9 1.0 P P:DA8 2.9 0.0 1.0 OD1 A:ASP190 2.9 50.7 1.0 OP1 P:DA8 3.1 0.0 1.0 MN A:MN339 3.3 30.0 0.5 O1A A:DAD338 3.4 67.7 0.5 OD2 A:ASP256 3.4 35.6 1.0 CG A:ASP192 3.6 51.0 1.0 O3' P:DG7 3.9 98.0 1.0 OD2 A:ASP192 4.0 56.5 1.0 CB A:ASP190 4.0 37.5 1.0 O A:HOH655 4.2 39.2 1.0 CG A:ASP256 4.2 38.4 1.0 O5' P:DA8 4.3 0.0 1.0 C3' P:DG7 4.3 84.0 1.0 PA A:DAD338 4.3 62.3 0.5 O A:ASP190 4.4 27.4 1.0 O2A A:DAD338 4.5 61.5 0.5 O A:MET191 4.5 9.1 1.0 C A:ASP190 4.7 20.4 1.0 O5' A:DAD338 4.7 60.4 0.5 CB A:ASP256 4.8 28.0 1.0 O5' P:DG7 4.8 57.2 1.0 C A:MET191 4.9 4.6 1.0 OD1 A:ASP256 4.9 43.2 1.0 CB A:ASP192 4.9 34.9 1.0 CA A:ASP190 4.9 27.1 1.0 C4' P:DG7 5.0 75.3 1.0

H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut. A Structural Basis For Metal Ion Mutagenicity and Nucleotide Selectivity in Human Dna Polymerase Beta Biochemistry V. 35 12762 1996.
ISSN: ISSN 0006-2960
PubMed: 8841119
DOI: 10.1021/BI9529566