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Manganese in PDB 7s9p: Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog

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

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

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp Analog, PDB code: 7s9p 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) 24.50 / 1.86
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.673, 79.621, 55.347, 90, 108.02, 90
R / Rfree (%) 17.6 / 22.8

Other elements in 7s9p:

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

Chlorine (Cl) 2 atoms
Sodium (Na) 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 Dctp Analog (pdb code 7s9p). 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 Dctp Analog, PDB code: 7s9p:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 7s9p

Go back to Manganese Binding Sites List in 7s9p
Manganese binding site 1 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp 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 Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:12.2
occ:1.00
 OD1 A:ASP190 2.0 11.1 1.0
O2B A:XC5401 2.1 12.0 1.0
OD2 A:ASP192 2.1 12.4 1.0
O1G A:XC5401 2.2 13.8 1.0
O2A A:XC5401 2.2 12.8 1.0
O A:HOH554 2.3 13.8 1.0
CG A:ASP190 3.1 10.1 1.0
CG A:ASP192 3.1 12.7 1.0
PB A:XC5401 3.1 13.3 1.0
PA A:XC5401 3.3 12.7 1.0
PG A:XC5401 3.4 16.0 1.0
OD1 A:ASP192 3.5 12.5 1.0
MN A:MN403 3.5 14.6 1.0
OD2 A:ASP190 3.6 15.2 1.0
C3A A:XC5401 3.6 14.0 1.0
O3B A:XC5401 3.7 15.5 1.0
O A:ASP190 3.9 13.7 1.0
C5' A:XC5401 4.0 14.2 1.0
O A:HOH651 4.0 17.0 1.0
O5' A:XC5401 4.2 14.2 1.0
O3G A:XC5401 4.2 15.0 1.0
C A:ASP190 4.2 13.3 1.0
CB A:ASP190 4.4 14.5 1.0
OG A:SER180 4.4 16.4 1.0
N A:ASP190 4.4 13.6 1.0
N A:SER180 4.4 15.4 1.0
CB A:ASP192 4.5 13.0 1.0
O A:HOH593 4.5 11.8 1.0
O1B A:XC5401 4.5 13.3 1.0
CA A:GLY179 4.5 12.6 1.0
O1A A:XC5401 4.5 16.1 1.0
CA A:ASP190 4.6 13.2 1.0
O2G A:XC5401 4.6 14.0 1.0
N A:ASP192 4.8 8.6 1.0
O A:HOH559 4.8 10.0 1.0
N A:MET191 4.9 10.9 1.0

Manganese binding site 2 out of 3 in 7s9p

Go back to Manganese Binding Sites List in 7s9p
Manganese binding site 2 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp 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 Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:14.6
occ:1.00
 OD2 A:ASP190 2.0 15.2 1.0
OD1 A:ASP192 2.1 12.5 1.0
O2A A:XC5401 2.2 12.8 1.0
OD2 A:ASP256 2.2 12.5 0.6
O A:HOH559 2.3 10.0 1.0
O3' P:DA10 2.3 13.7 1.0
OD2 A:ASP256 2.3 14.8 0.4
CG A:ASP190 3.0 10.1 1.0
CG A:ASP256 3.2 14.3 0.4
CG A:ASP192 3.2 12.7 1.0
PA A:XC5401 3.3 12.7 1.0
OD1 A:ASP190 3.3 11.1 1.0
OD1 A:ASP256 3.4 14.0 0.4
CG A:ASP256 3.4 13.7 0.6
C3' P:DA10 3.4 16.2 1.0
OD2 A:ASP192 3.5 12.4 1.0
MN A:MN402 3.5 12.2 1.0
O1A A:XC5401 3.6 16.1 1.0
O5' A:XC5401 3.8 14.2 1.0
C5' A:XC5401 4.0 14.2 1.0
CB A:ASP256 4.0 15.2 0.6
C4' P:DA10 4.1 15.6 1.0
C5' P:DA10 4.2 13.4 1.0
O A:HOH651 4.4 17.0 1.0
NH1 A:ARG254 4.4 11.9 0.5
CB A:ASP190 4.4 14.5 1.0
OD1 A:ASP256 4.4 16.3 0.6
CB A:ASP256 4.5 15.5 0.4
CB A:ASP192 4.5 13.0 1.0
OP1 P:DA10 4.6 14.9 1.0
C2' P:DA10 4.7 15.0 1.0
NH2 A:ARG254 4.7 16.8 0.5
O5' P:DA10 4.7 16.0 1.0
O A:MET191 4.8 14.4 1.0
O1G A:XC5401 4.9 13.8 1.0
O2B A:XC5401 4.9 12.0 1.0
C3A A:XC5401 4.9 14.0 1.0

Manganese binding site 3 out of 3 in 7s9p

Go back to Manganese Binding Sites List in 7s9p
Manganese binding site 3 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Dctp 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 Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:39.9
occ:1.00
 OD2 A:ASP145 2.1 18.1 1.0
O A:HOH657 2.3 31.9 1.0
O A:HOH775 2.6 27.3 1.0
ND1 A:HIS252 2.6 18.6 1.0
CG A:ASP145 3.2 24.8 1.0
CE1 A:HIS252 3.2 19.6 1.0
OD1 A:ASP145 3.7 27.9 1.0
CG A:HIS252 3.8 15.7 1.0
N A:HIS252 4.0 12.9 1.0
O A:HOH506 4.0 40.7 1.0
CB A:HIS252 4.2 15.1 1.0
CB A:ASP145 4.4 15.6 1.0
CD1 A:TYR142 4.4 17.9 1.0
NE2 A:HIS252 4.5 20.9 1.0
O A:HOH558 4.5 36.0 1.0
O A:HOH756 4.5 28.0 1.0
CE1 A:TYR142 4.6 17.9 1.0
O A:HOH707 4.6 26.4 1.0
CA A:HIS252 4.7 13.9 1.0
CD2 A:HIS252 4.7 19.1 1.0
CA A:PRO251 4.8 16.1 1.0
C A:PRO251 4.8 14.8 1.0
O A:TYR250 4.9 13.2 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: Sun Oct 6 10:30:30 2024

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