Manganese in PDB 1zqm: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of MNCL2 (15 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 MNCL2 (15 Millimolar), PDB code: 1zqm 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 / 3.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.881, 57.634, 48.080, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / n/a

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 MNCL2 (15 Millimolar) (pdb code 1zqm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 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 MNCL2 (15 Millimolar), PDB code: 1zqm:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 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 MNCL2 (15 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 MNCL2 (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:89.7 occ:1.00 O3' P:DG7 2.5 77.0 1.0 C3' P:DG7 2.8 78.2 1.0 OD2 A:ASP190 3.0 53.1 1.0 OD2 A:ASP192 3.2 64.5 1.0 OD1 A:ASP192 3.3 53.7 1.0 O A:HOH639 3.5 26.6 1.0 OD1 A:ASP190 3.5 41.5 1.0 CG A:ASP192 3.6 51.5 1.0 CG A:ASP190 3.7 44.7 1.0 C4' P:DG7 3.7 77.7 1.0 OD2 A:ASP256 3.9 24.7 1.0 C2' P:DG7 4.2 76.7 1.0 O5' P:DG7 4.2 71.5 1.0 C5' P:DG7 4.3 74.6 1.0 O A:HOH642 4.8 70.4 1.0 CG A:ASP256 4.9 29.2 1.0 O4' P:DG7 4.9 76.3 1.0

Manganese binding site 2 out of 3 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 MNCL2 (15 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 MNCL2 (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn341 b:26.4 occ:1.00 O A:THR101 2.3 32.5 1.0 O A:ILE106 2.5 10.6 1.0 OP1 P:DT6 2.6 27.0 1.0 O A:HOH588 2.7 76.8 1.0 O A:VAL103 2.9 1.0 1.0 C A:VAL103 3.3 4.5 1.0 C A:THR101 3.4 24.5 1.0 C A:ILE106 3.5 3.0 1.0 P P:DT6 3.6 14.7 1.0 N A:SER104 3.6 10.3 1.0 N A:VAL103 3.6 20.3 1.0 CA A:SER104 3.7 13.0 1.0 OP2 P:DT6 3.7 10.2 1.0 C A:ARG102 3.7 30.0 1.0 N A:ILE106 3.9 4.5 1.0 N A:GLY105 4.0 3.7 1.0 CA A:ILE106 4.0 1.0 1.0 CA A:VAL103 4.1 11.4 1.0 CA A:ARG102 4.1 36.1 1.0 N A:ARG102 4.2 34.5 1.0 O A:ARG102 4.2 30.8 1.0 CB A:ILE106 4.2 1.0 1.0 CA A:THR101 4.3 3.6 1.0 C A:SER104 4.4 7.9 1.0 O5' P:DT6 4.6 4.3 1.0 N A:GLY107 4.7 1.8 1.0 O3' P:DA5 4.8 2.2 1.0 CG2 A:ILE106 4.8 1.0 1.0 O A:LEU100 4.8 11.1 1.0 C A:GLY105 4.9 1.1 1.0 CG2 A:THR101 4.9 15.1 1.0 CB A:SER104 5.0 25.5 1.0

Manganese binding site 3 out of 3 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 MNCL2 (15 Millimolar)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of MNCL2 (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn342 b:99.8 occ:1.00 O A:LEU62 2.6 29.8 1.0 O A:LYS60 3.4 37.5 1.0 C A:LEU62 3.7 27.5 1.0 O A:VAL65 3.9 21.8 1.0 O A:LYS61 4.1 34.2 1.0 C A:LYS61 4.3 34.8 1.0 CA A:PRO63 4.4 24.4 1.0 N A:PRO63 4.5 27.1 1.0 N A:LEU62 4.5 25.4 1.0 C A:LYS60 4.6 33.9 1.0 N A:VAL65 4.6 14.5 1.0 CA A:LEU62 4.7 21.1 1.0 N A:GLY64 4.7 34.4 1.0 C A:VAL65 4.8 15.5 1.0 CA A:LYS61 4.9 42.1 1.0

H.Pelletier, M.R.Sawaya. Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human Dna Polymerase Beta By X-Ray Structural Analysis. Biochemistry V. 35 12778 1996.
ISSN: ISSN 0006-2960
PubMed: 8841120
DOI: 10.1021/BI960790I