Manganese in PDB 1zqq: 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 Nacl (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 Nacl (15 Millimolar), PDB code: 1zqq 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 (°)	180.065, 57.369, 47.788, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 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 MNCL2 (15 Millimolar) and Nacl (15 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 MNCL2 (15 Millimolar) and Nacl (15 Millimolar) (pdb code 1zqq). 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 MNCL2 (15 Millimolar) and Nacl (15 Millimolar), PDB code: 1zqq:
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 MNCL2 (15 Millimolar) and Nacl (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 Nacl (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:48.1 occ:1.00 O3' P:DG7 2.7 71.7 1.0 OD2 A:ASP192 2.7 41.7 1.0 OD2 A:ASP190 2.8 48.5 1.0 OD1 A:ASP192 2.9 44.2 1.0 C3' P:DG7 3.1 66.4 1.0 CG A:ASP192 3.2 42.5 1.0 OD1 A:ASP190 3.3 41.8 1.0 CG A:ASP190 3.3 43.3 1.0 O A:HOH639 3.6 7.1 1.0 C4' P:DG7 3.6 61.9 1.0 O A:HOH642 3.8 58.7 1.0 O5' P:DG7 3.8 42.9 1.0 OD2 A:ASP256 4.0 15.0 1.0 C5' P:DG7 4.2 52.8 1.0 C2' P:DG7 4.5 67.6 1.0 CG A:ASP256 4.6 6.6 1.0 O A:HOH637 4.7 38.6 1.0 CB A:ASP192 4.7 38.9 1.0 CB A:ASP190 4.7 38.5 1.0 CB A:ASP256 4.8 7.9 1.0 O4' P:DG7 5.0 66.5 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 MNCL2 (15 Millimolar) and Nacl (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 Nacl (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn343 b:82.9 occ:1.00 OD1 A:ASN133 2.8 19.5 1.0 O P:HOH583 3.1 24.7 1.0 O A:GLY105 3.1 14.1 1.0 O P:HOH559 3.5 29.5 1.0 O T:HOH558 3.7 1.0 1.0 OE1 A:GLN136 3.8 8.7 1.0 CG A:ASN133 3.9 14.9 1.0 C A:GLY105 4.0 9.0 1.0 CG A:GLN136 4.1 7.9 1.0 CA A:GLY105 4.2 10.2 1.0 C4' P:DA5 4.2 3.0 1.0 CD A:GLN136 4.2 10.7 1.0 ND2 A:ASN133 4.2 19.9 1.0 O T:HOH512 4.3 5.8 1.0 CB A:HIS135 4.3 10.0 1.0 C5' P:DA5 4.3 1.0 1.0 ND1 A:HIS135 4.5 4.9 1.0 O P:HOH562 4.6 14.7 1.0 O4' P:DA5 4.7 3.9 1.0 CG A:HIS135 4.7 7.7 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