Manganese in PDB 4klq: Observing A Dna Polymerase Choose Right From Wrong.
Enzymatic activity of Observing A Dna Polymerase Choose Right From Wrong.
All present enzymatic activity of Observing A Dna Polymerase Choose Right From Wrong.:
2.7.7.7;
Protein crystallography data
The structure of Observing A Dna Polymerase Choose Right From Wrong., PDB code: 4klq
was solved by
B.D.Freudenthal,
W.A.Beard,
D.D.Shock,
S.H.Wilson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.04 /
2.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.822,
78.412,
54.962,
90.00,
113.24,
90.00
|
R / Rfree (%)
|
21.4 /
26.7
|
Other elements in 4klq:
The structure of Observing A Dna Polymerase Choose Right From Wrong. also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Observing A Dna Polymerase Choose Right From Wrong.
(pdb code 4klq). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the
Observing A Dna Polymerase Choose Right From Wrong., PDB code: 4klq:
Jump to Manganese binding site number:
1;
2;
3;
Manganese binding site 1 out
of 3 in 4klq
Go back to
Manganese Binding Sites List in 4klq
Manganese binding site 1 out
of 3 in the Observing A Dna Polymerase Choose Right From Wrong.
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Observing A Dna Polymerase Choose Right From Wrong. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn403
b:25.6
occ:0.70
|
OD1
|
A:ASP192
|
2.1
|
30.8
|
1.0
|
O
|
P:HOH120
|
2.2
|
31.8
|
0.7
|
OD2
|
A:ASP190
|
2.2
|
29.3
|
1.0
|
OD2
|
A:ASP256
|
2.2
|
37.1
|
1.0
|
O
|
A:HOH631
|
2.3
|
30.0
|
0.7
|
O2A
|
A:DTP401
|
2.3
|
14.7
|
0.7
|
OP2
|
P:DA11
|
2.6
|
43.2
|
0.3
|
CG
|
A:ASP190
|
3.2
|
27.8
|
1.0
|
CG
|
A:ASP192
|
3.3
|
30.3
|
1.0
|
PA
|
A:DTP401
|
3.4
|
33.4
|
0.7
|
CG
|
A:ASP256
|
3.4
|
32.8
|
1.0
|
O1A
|
A:DTP401
|
3.6
|
32.1
|
0.7
|
OD1
|
A:ASP190
|
3.7
|
25.8
|
1.0
|
MN
|
A:MN404
|
3.7
|
37.0
|
1.0
|
OD2
|
A:ASP192
|
3.8
|
24.3
|
1.0
|
P
|
P:DA11
|
3.9
|
43.5
|
0.3
|
O
|
A:HOH576
|
3.9
|
36.4
|
1.0
|
O5'
|
A:DTP401
|
3.9
|
39.3
|
0.7
|
CB
|
A:ASP256
|
4.1
|
24.9
|
1.0
|
O5'
|
P:DA11
|
4.2
|
35.5
|
0.3
|
C5'
|
P:DA11
|
4.2
|
39.7
|
0.3
|
C3'
|
P:DC10
|
4.2
|
43.5
|
0.3
|
C3'
|
P:DC10
|
4.3
|
41.9
|
0.7
|
O3'
|
P:DC10
|
4.3
|
46.3
|
0.7
|
C5'
|
A:DTP401
|
4.4
|
37.9
|
0.7
|
O3'
|
P:DC10
|
4.4
|
44.4
|
0.3
|
OD1
|
A:ASP256
|
4.4
|
28.9
|
1.0
|
CB
|
A:ASP192
|
4.5
|
26.9
|
1.0
|
C5'
|
P:DC10
|
4.6
|
36.8
|
0.3
|
CB
|
A:ASP190
|
4.6
|
23.3
|
1.0
|
C5'
|
P:DC10
|
4.6
|
38.1
|
0.7
|
C4'
|
P:DC10
|
4.7
|
41.2
|
0.3
|
OP1
|
P:DC10
|
4.8
|
33.0
|
0.7
|
OP1
|
P:DC10
|
4.8
|
32.0
|
0.3
|
C4'
|
P:DC10
|
4.8
|
43.4
|
0.7
|
O5'
|
P:DC10
|
4.8
|
36.8
|
0.7
|
O5'
|
P:DC10
|
4.8
|
37.7
|
0.3
|
O3A
|
A:DTP401
|
4.9
|
33.4
|
0.7
|
O
|
A:MET191
|
4.9
|
22.8
|
1.0
|
O3G
|
A:DTP401
|
5.0
|
38.0
|
0.7
|
|
Manganese binding site 2 out
of 3 in 4klq
Go back to
Manganese Binding Sites List in 4klq
Manganese binding site 2 out
of 3 in the Observing A Dna Polymerase Choose Right From Wrong.
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Observing A Dna Polymerase Choose Right From Wrong. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn404
b:37.0
occ:1.00
|
O2B
|
A:DTP401
|
2.0
|
33.7
|
0.7
|
OD1
|
A:ASP190
|
2.0
|
25.8
|
1.0
|
OD2
|
A:ASP192
|
2.2
|
24.3
|
1.0
|
O2A
|
A:DTP401
|
2.2
|
14.7
|
0.7
|
O3G
|
A:DTP401
|
2.2
|
38.0
|
0.7
|
O32
|
A:PPV402
|
2.3
|
36.0
|
0.3
|
O11
|
A:PPV402
|
2.4
|
35.5
|
0.3
|
O
|
A:HOH521
|
2.4
|
36.9
|
1.0
|
CG
|
A:ASP190
|
3.0
|
27.8
|
1.0
|
PB
|
A:DTP401
|
3.0
|
39.0
|
0.7
|
CG
|
A:ASP192
|
3.1
|
30.3
|
1.0
|
PA
|
A:DTP401
|
3.3
|
33.4
|
0.7
|
OD2
|
A:ASP190
|
3.4
|
29.3
|
1.0
|
PG
|
A:DTP401
|
3.4
|
34.6
|
0.7
|
OD1
|
A:ASP192
|
3.4
|
30.8
|
1.0
|
P2
|
A:PPV402
|
3.5
|
34.2
|
0.3
|
O3A
|
A:DTP401
|
3.5
|
33.4
|
0.7
|
P1
|
A:PPV402
|
3.7
|
36.8
|
0.3
|
O3B
|
A:DTP401
|
3.7
|
44.6
|
0.7
|
MN
|
A:MN403
|
3.7
|
25.6
|
0.7
|
O12
|
A:PPV402
|
3.8
|
32.5
|
0.3
|
O1G
|
A:DTP401
|
3.9
|
35.9
|
0.7
|
OPP
|
A:PPV402
|
4.0
|
40.8
|
0.3
|
O
|
A:ASP190
|
4.1
|
24.3
|
1.0
|
C5'
|
A:DTP401
|
4.1
|
37.9
|
0.7
|
N
|
A:ASP190
|
4.2
|
27.5
|
1.0
|
CB
|
A:ASP190
|
4.3
|
23.3
|
1.0
|
O31
|
A:PPV402
|
4.3
|
36.1
|
0.3
|
C
|
A:ASP190
|
4.3
|
28.4
|
1.0
|
O5'
|
A:DTP401
|
4.3
|
39.3
|
0.7
|
C5'
|
P:DA11
|
4.3
|
39.7
|
0.3
|
O1A
|
A:DTP401
|
4.3
|
32.1
|
0.7
|
O1B
|
A:DTP401
|
4.4
|
35.4
|
0.7
|
OG
|
A:SER180
|
4.4
|
32.0
|
1.0
|
CB
|
A:ASP192
|
4.5
|
26.9
|
1.0
|
CA
|
A:ASP190
|
4.5
|
20.8
|
1.0
|
O
|
A:HOH509
|
4.6
|
25.9
|
1.0
|
N
|
A:SER180
|
4.6
|
36.3
|
1.0
|
O22
|
A:PPV402
|
4.7
|
33.3
|
0.3
|
O2G
|
A:DTP401
|
4.7
|
37.8
|
0.7
|
CA
|
A:GLY179
|
4.8
|
35.9
|
1.0
|
O21
|
A:PPV402
|
4.8
|
37.4
|
0.3
|
N
|
A:ASP192
|
4.8
|
19.7
|
1.0
|
O
|
A:HOH631
|
4.9
|
30.0
|
0.7
|
N
|
A:MET191
|
4.9
|
27.4
|
1.0
|
|
Manganese binding site 3 out
of 3 in 4klq
Go back to
Manganese Binding Sites List in 4klq
Manganese binding site 3 out
of 3 in the Observing A Dna Polymerase Choose Right From Wrong.
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Observing A Dna Polymerase Choose Right From Wrong. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn405
b:30.0
occ:1.00
|
NE2
|
A:HIS51
|
2.2
|
42.5
|
1.0
|
CD2
|
A:HIS51
|
3.1
|
44.8
|
1.0
|
CE1
|
A:HIS51
|
3.2
|
43.8
|
1.0
|
ND1
|
A:HIS51
|
4.2
|
34.8
|
1.0
|
CG
|
A:HIS51
|
4.2
|
43.1
|
1.0
|
|
Reference:
B.D.Freudenthal,
W.A.Beard,
D.D.Shock,
S.H.Wilson.
Observing A Dna Polymerase Choose Right From Wrong. Cell(Cambridge,Mass.) V. 154 157 2013.
ISSN: ISSN 0092-8674
PubMed: 23827680
DOI: 10.1016/J.CELL.2013.05.048
Page generated: Sat Oct 5 20:03:39 2024
|