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:
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: Fri Apr 7 12:22:11 2023
|