Manganese in PDB 1zql: 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) and MGCL2 (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) and MGCL2 (15 Millimolar), PDB code: 1zql 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 / 3.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.509, 57.730, 48.028, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 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) and MGCL2 (15 Millimolar) (pdb code 1zql). 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) and MGCL2 (15 Millimolar), PDB code: 1zql:
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) and MGCL2 (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) and MGCL2 (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:83.3 occ:1.00 O3' P:DG7 2.4 74.0 1.0 C3' P:DG7 2.7 71.7 1.0 OD2 A:ASP190 3.0 38.9 1.0 C4' P:DG7 3.3 68.6 1.0 O A:HOH642 3.4 42.2 1.0 O A:HOH639 3.4 36.7 1.0 OD2 A:ASP192 3.5 51.9 1.0 OD2 A:ASP256 3.7 30.6 1.0 O5' P:DG7 3.7 59.6 1.0 OD1 A:ASP192 3.7 50.7 1.0 C5' P:DG7 3.8 63.2 1.0 CG A:ASP190 3.9 29.7 1.0 CG A:ASP192 4.0 49.1 1.0 OD1 A:ASP190 4.0 25.9 1.0 C2' P:DG7 4.1 71.3 1.0 O4' P:DG7 4.6 70.2 1.0 CG A:ASP256 4.6 25.8 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) and MGCL2 (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) and MGCL2 (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn341 b:68.0 occ:1.00 O A:THR101 2.0 22.6 1.0 OP1 P:DT6 2.6 23.1 1.0 O A:ILE106 2.8 14.5 1.0 O A:VAL103 2.9 3.7 1.0 O A:HOH588 3.0 97.3 1.0 C A:THR101 3.1 17.8 1.0 C A:VAL103 3.2 1.9 1.0 N A:VAL103 3.5 20.0 1.0 C A:ARG102 3.5 20.9 1.0 N A:SER104 3.6 1.0 1.0 CA A:SER104 3.7 10.4 1.0 C A:ILE106 3.8 5.7 1.0 P P:DT6 3.8 12.1 1.0 O A:ARG102 3.9 21.2 1.0 CA A:VAL103 3.9 11.6 1.0 CA A:ARG102 3.9 18.5 1.0 N A:ARG102 4.0 18.9 1.0 N A:ILE106 4.1 4.1 1.0 CA A:ILE106 4.1 4.8 1.0 CB A:ILE106 4.2 1.0 1.0 OP2 P:DT6 4.2 10.6 1.0 CA A:THR101 4.2 4.5 1.0 N A:GLY105 4.2 7.1 1.0 C A:SER104 4.4 11.2 1.0 O A:LEU100 4.6 12.8 1.0 CG2 A:ILE106 4.8 1.0 1.0 O5' P:DT6 4.8 2.9 1.0 O3' P:DA5 4.9 1.0 1.0 CB A:VAL103 4.9 7.4 1.0 N A:GLY107 4.9 1.6 1.0 CB A:THR101 4.9 2.2 1.0 CG2 A:THR101 4.9 9.6 1.0 OG1 A:THR101 5.0 1.3 1.0 C A:GLY105 5.0 1.0 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) and MGCL2 (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) and MGCL2 (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn342 b:0.0 occ:1.00 O A:LEU62 2.5 38.2 1.0 O A:LYS60 3.1 32.1 1.0 C A:LEU62 3.6 35.2 1.0 O A:LYS61 3.6 47.4 1.0 O A:VAL65 3.9 24.2 1.0 C A:LYS61 4.0 44.2 1.0 C A:LYS60 4.3 33.5 1.0 N A:LEU62 4.4 35.1 1.0 N A:PRO63 4.5 34.0 1.0 CA A:LEU62 4.5 32.2 1.0 CA A:PRO63 4.6 34.8 1.0 CA A:LYS61 4.7 48.6 1.0 N A:VAL65 4.8 19.8 1.0 C A:VAL65 4.8 19.9 1.0 CD A:PRO63 5.0 33.5 1.0 N A:LYS61 5.0 42.0 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