Manganese in PDB 7s9q: Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog, PDB code: 7s9q was solved by B.D.Freudenthal, B.J.Ryan, M.R.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.15 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.624, 78.583, 54.916, 90, 112.44, 90
R / Rfree (%) 19.3 / 24.7

Other elements in 7s9q:

The structure of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog also contains other interesting chemical elements:

Sodium (Na) 3 atoms
Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog (pdb code 7s9q). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog, PDB code: 7s9q:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 7s9q

Go back to Manganese Binding Sites List in 7s9q
Manganese binding site 1 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:19.6
occ:1.00
 OD1 A:ASP192 2.0 13.8 1.0
OD2 A:ASP190 2.2 13.3 1.0
O A:HOH520 2.2 18.2 1.0
O P:HOH102 2.3 17.4 1.0
OD2 A:ASP256 2.3 24.1 1.0
O1A A:F2A406 2.5 17.3 1.0
CG A:ASP192 3.1 14.1 1.0
CG A:ASP190 3.2 11.8 1.0
CG A:ASP256 3.4 15.9 1.0
OD1 A:ASP190 3.5 16.2 1.0
OD2 A:ASP192 3.5 15.8 1.0
PA A:F2A406 3.6 18.5 1.0
O2A A:F2A406 3.6 23.4 1.0
MN A:MN404 3.6 19.2 1.0
O3' P:DA10 3.9 33.5 1.0
CB A:ASP256 4.0 17.9 1.0
C5' A:F2A406 4.1 13.6 1.0
O A:HOH710 4.2 25.0 1.0
O5' A:F2A406 4.2 19.5 1.0
O P:HOH101 4.3 27.5 1.0
CB A:ASP192 4.4 18.9 1.0
OD1 A:ASP256 4.4 22.7 1.0
O A:HOH684 4.4 26.1 1.0
C5' P:DA10 4.5 33.9 1.0
CB A:ASP190 4.5 19.2 1.0
C3' P:DA10 4.6 31.6 1.0
OP1 P:DA10 4.6 32.2 1.0
C4' P:DA10 4.8 37.6 1.0
O5' P:DA10 4.9 37.2 1.0
O2B A:F2A406 4.9 19.1 1.0
NH2 A:ARG254 5.0 16.8 1.0
O A:MET191 5.0 13.8 1.0
CA A:ASP192 5.0 17.8 1.0

Manganese binding site 2 out of 3 in 7s9q

Go back to Manganese Binding Sites List in 7s9q
Manganese binding site 2 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:19.2
occ:1.00
 OD1 A:ASP190 2.0 16.2 1.0
OD2 A:ASP192 2.0 15.8 1.0
O2B A:F2A406 2.0 19.1 1.0
O1A A:F2A406 2.1 17.3 1.0
O A:HOH556 2.3 19.6 1.0
O3G A:F2A406 2.4 21.1 1.0
CG A:ASP192 3.0 14.1 1.0
CG A:ASP190 3.1 11.8 1.0
PB A:F2A406 3.2 20.2 1.0
PA A:F2A406 3.4 18.5 1.0
OD1 A:ASP192 3.4 13.8 1.0
OD2 A:ASP190 3.5 13.3 1.0
PG A:F2A406 3.5 22.0 1.0
O3B A:F2A406 3.6 23.5 1.0
C3A A:F2A406 3.6 15.4 1.0
MN A:MN403 3.6 19.6 1.0
C5' A:F2A406 3.9 13.6 1.0
O A:HOH684 4.1 26.1 1.0
O A:ASP190 4.1 18.2 1.0
O5' A:F2A406 4.3 19.5 1.0
O2A A:F2A406 4.3 23.4 1.0
N A:ASP190 4.3 16.6 1.0
CB A:ASP192 4.3 18.9 1.0
C A:ASP190 4.4 14.9 1.0
O2G A:F2A406 4.4 24.4 1.0
OG A:SER180 4.4 20.6 1.0
CB A:ASP190 4.4 19.2 1.0
N A:SER180 4.5 26.3 1.0
O1B A:F2A406 4.5 15.9 1.0
O A:HOH608 4.5 15.3 1.0
CA A:GLY179 4.5 18.6 1.0
O A:HOH520 4.6 18.2 1.0
CA A:ASP190 4.6 18.2 1.0
O1G A:F2A406 4.7 22.6 1.0
N A:ASP192 4.8 17.2 1.0
N A:MET191 5.0 14.4 1.0

Manganese binding site 3 out of 3 in 7s9q

Go back to Manganese Binding Sites List in 7s9q
Manganese binding site 3 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn407

b:31.3
occ:1.00
 O A:HOH637 1.9 31.7 1.0
O A:HOH641 2.2 21.4 1.0
OD1 A:ASP124 2.3 29.4 1.0
O A:HOH660 2.4 31.1 1.0
O A:HOH597 2.5 27.0 1.0
CG A:ASP124 3.2 28.5 1.0
OD2 A:ASP124 3.4 21.7 1.0
OG1 A:THR121 3.9 22.9 1.0
O A:HOH570 4.1 28.7 1.0
CB A:ASP124 4.6 24.8 1.0
N A:ASP124 4.8 21.0 1.0
CG2 A:THR121 4.9 17.6 1.0
CA A:ASP124 4.9 23.0 1.0

Reference:

B.J.Ryan, H.Yang, J.H.T.Bacurio, M.R.Smith, A.K.Basu, M.M.Greenberg, B.D.Freudenthal. Structural Dynamics of A Common Mutagenic Oxidative Dna Lesion in Duplex Dna and During Dna Replication. J.Am.Chem.Soc. V. 144 8054 2022.
ISSN: ESSN 1520-5126
PubMed: 35499923
DOI: 10.1021/JACS.2C00193
Page generated: Fri Apr 7 12:22:10 2023

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