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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)

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 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

Manganese Binding Sites:

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 1zql

Go back to Manganese Binding Sites List in 1zql
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 1zql

Go back to Manganese Binding Sites List in 1zql
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 1zql

Go back to Manganese Binding Sites List in 1zql
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

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 03:58:52 2020

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