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Magnesium in PDB 5v1r: Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp

Enzymatic activity of Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp

All present enzymatic activity of Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp, PDB code: 5v1r was solved by B.D.Freudenthal, M.R.Smith, A.M.Whitaker, M.A.Schaich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.98 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.596, 79.730, 55.647, 90.00, 107.53, 90.00
R / Rfree (%) 18 / 23.7

Other elements in 5v1r:

The structure of Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp (pdb code 5v1r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp, PDB code: 5v1r:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5v1r

Go back to Magnesium Binding Sites List in 5v1r
Magnesium binding site 1 out of 3 in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp


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 Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:47.6
occ:0.85
 O A:HOH642 2.0 58.7 1.0
O1A A:DCP409 2.3 32.8 0.8
O A:HOH648 2.5 57.6 1.0
O3A A:DCP409 2.5 37.6 0.8
O A:HOH611 2.6 36.0 1.0
OP2 P:DC11 2.7 35.3 0.2
O A:HOH632 2.8 41.5 1.0
O32 A:PPV410 2.9 36.1 0.2
PA A:DCP409 3.0 31.0 0.8
O3G A:DCP409 3.3 43.1 0.8
O21 A:PPV410 3.3 43.0 0.2
O11 A:PPV410 3.7 34.8 0.2
OPP A:PPV410 3.8 38.8 0.2
P P:DC11 3.8 29.4 0.2
PB A:DCP409 3.8 46.8 0.8
P1 A:PPV410 3.8 35.7 0.2
O3B A:DCP409 3.9 39.0 0.8
PG A:DCP409 3.9 36.0 0.8
P2 A:PPV410 3.9 38.6 0.2
O2A A:DCP409 4.0 29.0 0.8
O2G A:DCP409 4.0 34.7 0.8
O A:HOH507 4.1 59.0 1.0
OP1 P:DC11 4.2 30.1 0.2
O A:HOH671 4.2 46.5 1.0
O5' A:DCP409 4.3 31.0 0.8
O5' P:DC11 4.4 31.1 0.2
O A:HOH546 4.5 27.8 1.0
O A:HOH503 4.7 41.3 1.0
O2B A:DCP409 4.8 30.5 0.8
O12 A:PPV410 4.9 30.2 0.2
O1B A:DCP409 4.9 33.1 0.8
O22 A:PPV410 5.0 32.2 0.2

Magnesium binding site 2 out of 3 in 5v1r

Go back to Magnesium Binding Sites List in 5v1r
Magnesium binding site 2 out of 3 in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:21.5
occ:1.00
 O2A A:DCP409 1.9 29.0 0.8
OD2 A:ASP192 2.0 21.7 1.0
OD1 A:ASP190 2.0 28.1 1.0
O2B A:DCP409 2.1 30.5 0.8
O2G A:DCP409 2.1 34.7 0.8
O A:HOH551 2.2 24.1 1.0
O12 A:PPV410 2.3 30.2 0.2
O11 A:PPV410 2.3 34.8 0.2
OP1 P:DC11 2.5 30.1 0.2
CG A:ASP192 3.1 23.9 1.0
CG A:ASP190 3.1 29.5 1.0
PB A:DCP409 3.2 46.8 0.8
PA A:DCP409 3.2 31.0 0.8
P2 A:PPV410 3.4 38.6 0.2
PG A:DCP409 3.5 36.0 0.8
P1 A:PPV410 3.5 35.7 0.2
OD1 A:ASP192 3.6 23.3 1.0
O3A A:DCP409 3.6 37.6 0.8
OD2 A:ASP190 3.6 33.1 1.0
O32 A:PPV410 3.7 36.1 0.2
MG A:MG402 3.7 21.5 1.0
OPP A:PPV410 3.8 38.8 0.2
O3B A:DCP409 3.9 39.0 0.8
P P:DC11 3.9 29.4 0.2
O A:ASP190 3.9 26.2 1.0
C5' A:DCP409 4.1 28.1 0.8
O31 A:PPV410 4.1 32.1 0.2
O A:HOH607 4.1 26.2 1.0
C A:ASP190 4.3 26.1 1.0
O5' A:DCP409 4.3 31.0 0.8
O1A A:DCP409 4.3 32.8 0.8
O A:HOH632 4.3 41.5 1.0
C5' P:DC11 4.3 28.9 0.2
N A:ASP190 4.3 26.6 1.0
O1G A:DCP409 4.4 31.5 0.8
CA A:GLY179 4.4 18.8 1.0
CB A:ASP190 4.4 22.7 1.0
CB A:ASP192 4.4 25.6 1.0
O5' P:DC11 4.4 31.1 0.2
N A:SER180 4.4 25.9 1.0
O1B A:DCP409 4.5 33.1 0.8
O3G A:DCP409 4.5 43.1 0.8
CA A:ASP190 4.6 28.9 1.0
OG A:SER180 4.6 28.2 1.0
OP2 P:DC11 4.7 35.3 0.2
O22 A:PPV410 4.7 32.2 0.2
O21 A:PPV410 4.7 43.0 0.2
O A:HOH503 4.8 41.3 1.0
N A:MET191 4.9 19.1 1.0
N A:ASP192 4.9 25.5 1.0
O3' P:8OG10 4.9 35.9 0.5
O3' P:8OG10 4.9 35.8 0.5

Magnesium binding site 3 out of 3 in 5v1r

Go back to Magnesium Binding Sites List in 5v1r
Magnesium binding site 3 out of 3 in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:21.5
occ:1.00
 OD1 A:ASP192 2.1 23.3 1.0
OP1 P:DC11 2.2 30.1 0.2
OD2 A:ASP190 2.2 33.1 1.0
O A:HOH503 2.3 41.3 1.0
O3' P:8OG10 2.4 35.8 0.5
O3' P:8OG10 2.4 35.9 0.5
OD2 A:ASP256 2.4 32.2 1.0
O2A A:DCP409 2.6 29.0 0.8
P P:DC11 2.8 29.4 0.2
CG A:ASP190 3.1 29.5 1.0
CG A:ASP192 3.2 23.9 1.0
OD1 A:ASP190 3.2 28.1 1.0
CG A:ASP256 3.4 27.6 1.0
OD2 A:ASP192 3.5 21.7 1.0
PA A:DCP409 3.6 31.0 0.8
MG A:MG401 3.7 21.5 1.0
C3' P:8OG10 3.7 34.1 0.5
C3' P:8OG10 3.7 34.1 0.5
OP2 P:DC11 3.8 35.3 0.2
O1A A:DCP409 3.9 32.8 0.8
O5' P:DC11 4.0 31.1 0.2
CB A:ASP256 4.0 23.5 1.0
O5' A:DCP409 4.0 31.0 0.8
C5' A:DCP409 4.0 28.1 0.8
C4' P:8OG10 4.1 35.3 0.5
C5' P:DC11 4.1 28.9 0.2
C4' P:8OG10 4.1 35.3 0.5
C5' P:8OG10 4.3 36.5 0.5
OD1 A:ASP256 4.3 29.0 1.0
O5' P:8OG10 4.4 37.8 0.5
C5' P:8OG10 4.4 36.5 0.5
CB A:ASP190 4.4 22.7 1.0
O5' P:8OG10 4.4 37.8 0.5
CB A:ASP192 4.5 25.6 1.0
O A:HOH632 4.6 41.5 1.0
C2' P:8OG10 4.6 33.6 0.5
O P:HOH204 4.6 40.4 1.0
C2' P:8OG10 4.6 33.6 0.5
O A:MET191 4.8 24.8 1.0
NH2 A:ARG254 4.9 30.1 1.0
OP1 P:8OG10 5.0 38.9 0.5
OP1 P:8OG10 5.0 38.8 0.5
CA A:ASP192 5.0 22.8 1.0
O11 A:PPV410 5.0 34.8 0.2
O2G A:DCP409 5.0 34.7 0.8

Reference:

A.M.Whitaker, M.R.Smith, M.A.Schaich, B.D.Freudenthal. Capturing A Mammalian Dna Polymerase Extending From An Oxidized Nucleotide. Nucleic Acids Res. V. 45 6934 2017.
ISSN: ESSN 1362-4962
PubMed: 28449123
DOI: 10.1093/NAR/GKX293
Page generated: Mon Sep 30 05:56:41 2024

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