Magnesium in PDB 8ici: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dgtp (1 Millimolar) and MGCL2 (5 Millimolar)

Protein crystallography data

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 Dgtp (1 Millimolar) and MGCL2 (5 Millimolar), PDB code: 8ici 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 / 2.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 179.222, 57.694, 48.229, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / n/a

Other elements in 8ici:

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 Dgtp (1 Millimolar) and MGCL2 (5 Millimolar) also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Dgtp (1 Millimolar) and MGCL2 (5 Millimolar) (pdb code 8ici). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was 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 Dgtp (1 Millimolar) and MGCL2 (5 Millimolar), PDB code: 8ici:

Magnesium binding site 1 out of 1 in 8ici

Go back to Magnesium Binding Sites List in 8ici
Magnesium binding site 1 out of 1 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 Dgtp (1 Millimolar) and MGCL2 (5 Millimolar)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 Dgtp (1 Millimolar) and MGCL2 (5 Millimolar) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg343

b:30.0
occ:0.86
OP1 P:DG7 2.2 20.6 1.0
OG A:SER104 2.8 18.3 1.0
O P:HOH575 2.8 43.9 1.0
P P:DG7 3.2 27.8 1.0
NE A:ARG254 3.3 13.5 1.0
O P:HOH534 3.3 74.1 1.0
O3' P:DT6 3.5 22.6 1.0
CB A:SER104 3.8 11.9 1.0
OP2 P:DG7 3.8 26.1 1.0
CD A:ARG254 4.1 7.2 1.0
NH2 A:ARG254 4.3 12.4 1.0
CZ A:ARG254 4.3 17.6 1.0
C3' P:DT6 4.3 13.2 1.0
CG A:ARG254 4.5 3.7 1.0
O5' P:DG7 4.5 41.4 1.0
CA A:SER104 4.7 5.1 1.0
C4' P:DT6 4.9 1.9 1.0
NE2 A:HIS135 5.0 1.0 1.0

Reference:

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
Page generated: Tue Dec 15 03:45:41 2020

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