Manganese in PDB 7omb: Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang
Enzymatic activity of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang
All present enzymatic activity of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang:
2.7.7.7;
Protein crystallography data
The structure of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang, PDB code: 7omb
was solved by
K.Betz,
H.M.Kropp,
K.Diederichs,
A.Marx,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.28 /
2.01
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
108.081,
147.153,
71.332,
90,
90,
90
|
R / Rfree (%)
|
20 /
23.6
|
Other elements in 7omb:
The structure of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang
(pdb code 7omb). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang, PDB code: 7omb:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 7omb
Go back to
Manganese Binding Sites List in 7omb
Manganese binding site 1 out
of 4 in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn804
b:34.9
occ:1.00
|
OD2
|
A:ASP542
|
2.1
|
35.6
|
1.0
|
OD2
|
A:ASP404
|
2.1
|
35.5
|
1.0
|
O
|
A:PHE405
|
2.2
|
33.3
|
1.0
|
O1B
|
A:DTP801
|
2.2
|
35.0
|
1.0
|
O1G
|
A:DTP801
|
2.2
|
28.4
|
1.0
|
O1A
|
A:DTP801
|
2.3
|
34.8
|
1.0
|
CG
|
A:ASP404
|
3.0
|
38.5
|
1.0
|
CG
|
A:ASP542
|
3.1
|
32.6
|
1.0
|
H5'2
|
A:DTP801
|
3.2
|
40.1
|
1.0
|
PB
|
A:DTP801
|
3.3
|
35.0
|
1.0
|
C
|
A:PHE405
|
3.3
|
30.2
|
1.0
|
PA
|
A:DTP801
|
3.4
|
33.2
|
1.0
|
OD1
|
A:ASP542
|
3.5
|
37.0
|
1.0
|
OD1
|
A:ASP404
|
3.5
|
39.9
|
1.0
|
MG
|
A:MG803
|
3.5
|
30.0
|
1.0
|
MN
|
A:MN806
|
3.5
|
36.6
|
0.6
|
O3A
|
A:DTP801
|
3.5
|
30.4
|
1.0
|
PG
|
A:DTP801
|
3.6
|
33.7
|
1.0
|
O3B
|
A:DTP801
|
3.7
|
33.6
|
1.0
|
H
|
A:PHE405
|
3.8
|
42.0
|
1.0
|
H
|
A:LEU408
|
3.8
|
39.5
|
1.0
|
N
|
A:PHE405
|
3.9
|
34.9
|
1.0
|
HB2
|
A:PHE405
|
4.0
|
40.2
|
1.0
|
O
|
A:HOH931
|
4.0
|
34.3
|
1.0
|
CA
|
A:PHE405
|
4.0
|
33.2
|
1.0
|
O
|
A:HOH951
|
4.1
|
36.4
|
1.0
|
H
|
A:SER407
|
4.1
|
43.1
|
1.0
|
C5'
|
A:DTP801
|
4.2
|
33.3
|
1.0
|
HB2
|
A:LEU408
|
4.2
|
36.0
|
1.0
|
HA
|
A:ARG406
|
4.3
|
44.0
|
1.0
|
O2G
|
A:DTP801
|
4.3
|
30.3
|
1.0
|
O5'
|
A:DTP801
|
4.3
|
31.6
|
1.0
|
CB
|
A:ASP404
|
4.4
|
34.3
|
1.0
|
C
|
A:ASP404
|
4.4
|
35.6
|
1.0
|
N
|
A:ARG406
|
4.4
|
36.0
|
1.0
|
CB
|
A:PHE405
|
4.4
|
33.5
|
1.0
|
N
|
A:SER407
|
4.4
|
35.9
|
1.0
|
CB
|
A:ASP542
|
4.4
|
32.2
|
1.0
|
HB2
|
A:ASP542
|
4.5
|
38.8
|
1.0
|
HB3
|
A:ASP404
|
4.5
|
41.3
|
1.0
|
O
|
A:HOH1074
|
4.5
|
43.3
|
1.0
|
HB3
|
A:PHE405
|
4.6
|
40.2
|
1.0
|
H5'1
|
A:DTP801
|
4.6
|
40.1
|
1.0
|
O2A
|
A:DTP801
|
4.6
|
30.4
|
1.0
|
N
|
A:LEU408
|
4.6
|
32.8
|
1.0
|
O2B
|
A:DTP801
|
4.6
|
32.8
|
1.0
|
CA
|
A:ARG406
|
4.7
|
36.6
|
1.0
|
C
|
A:ARG406
|
4.7
|
34.1
|
1.0
|
O
|
A:ASP542
|
4.7
|
30.6
|
1.0
|
O3G
|
A:DTP801
|
4.8
|
35.8
|
1.0
|
HA
|
A:SER407
|
4.8
|
44.1
|
1.0
|
CA
|
A:ASP404
|
4.9
|
37.2
|
1.0
|
HB3
|
A:ASP542
|
4.9
|
38.8
|
1.0
|
HA
|
A:PHE405
|
4.9
|
39.9
|
1.0
|
O
|
A:ASP404
|
4.9
|
32.3
|
1.0
|
HB3
|
A:LEU408
|
4.9
|
36.0
|
1.0
|
HA
|
A:ASP404
|
4.9
|
44.7
|
1.0
|
CB
|
A:LEU408
|
5.0
|
29.9
|
1.0
|
|
Manganese binding site 2 out
of 4 in 7omb
Go back to
Manganese Binding Sites List in 7omb
Manganese binding site 2 out
of 4 in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn805
b:74.1
occ:1.00
|
O
|
A:HOH1123
|
2.2
|
65.5
|
1.0
|
O
|
T:HOH220
|
2.4
|
61.2
|
1.0
|
O
|
T:HOH212
|
2.4
|
55.7
|
1.0
|
O
|
A:HOH1121
|
2.5
|
55.5
|
1.0
|
O
|
P:HOH202
|
2.6
|
50.0
|
1.0
|
O
|
A:HOH1030
|
2.8
|
56.4
|
1.0
|
OE2
|
A:GLU664
|
3.2
|
57.1
|
1.0
|
H5'
|
T:DT17
|
3.7
|
67.4
|
1.0
|
H21
|
P:DG7
|
3.9
|
51.1
|
1.0
|
CD
|
A:GLU664
|
4.0
|
50.7
|
1.0
|
O
|
T:HOH209
|
4.1
|
52.4
|
1.0
|
O
|
T:HOH222
|
4.2
|
56.8
|
1.0
|
OE1
|
A:GLU664
|
4.2
|
55.8
|
1.0
|
H1'
|
T:DG16
|
4.3
|
64.6
|
1.0
|
O
|
A:HOH1003
|
4.5
|
50.8
|
1.0
|
C5'
|
T:DT17
|
4.6
|
56.1
|
1.0
|
H21
|
T:DG16
|
4.6
|
62.9
|
1.0
|
O
|
A:HOH909
|
4.6
|
51.4
|
1.0
|
O4'
|
T:DG16
|
4.7
|
49.4
|
1.0
|
N3
|
T:DG16
|
4.7
|
47.8
|
1.0
|
N2
|
P:DG7
|
4.7
|
42.5
|
1.0
|
O3'
|
T:DG16
|
4.8
|
58.1
|
1.0
|
H5''
|
T:DT17
|
4.8
|
67.4
|
1.0
|
H4'
|
T:DG16
|
4.8
|
63.0
|
1.0
|
C1'
|
T:DG16
|
4.9
|
53.7
|
1.0
|
OD2
|
A:ASP614
|
5.0
|
46.0
|
1.0
|
|
Manganese binding site 3 out
of 4 in 7omb
Go back to
Manganese Binding Sites List in 7omb
Manganese binding site 3 out
of 4 in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn806
b:36.6
occ:0.60
|
O
|
A:HOH931
|
2.0
|
34.3
|
1.0
|
OD2
|
A:ASP404
|
2.2
|
35.5
|
1.0
|
O1G
|
A:DTP801
|
2.3
|
28.4
|
1.0
|
O
|
A:HOH928
|
2.3
|
43.5
|
1.0
|
O
|
A:HOH951
|
2.4
|
36.4
|
1.0
|
OE1
|
A:GLU580
|
2.4
|
68.4
|
1.0
|
HB3
|
A:ASP404
|
2.9
|
41.3
|
1.0
|
OE2
|
A:GLU580
|
2.9
|
58.3
|
1.0
|
CD
|
A:GLU580
|
3.0
|
66.6
|
1.0
|
CG
|
A:ASP404
|
3.0
|
38.5
|
1.0
|
PG
|
A:DTP801
|
3.4
|
33.7
|
1.0
|
CB
|
A:ASP404
|
3.5
|
34.3
|
1.0
|
MN
|
A:MN804
|
3.5
|
34.9
|
1.0
|
O3G
|
A:DTP801
|
3.6
|
35.8
|
1.0
|
O
|
A:PHE405
|
3.8
|
33.3
|
1.0
|
O2G
|
A:DTP801
|
3.9
|
30.3
|
1.0
|
HB2
|
A:ASP404
|
4.0
|
41.3
|
1.0
|
OD1
|
A:ASP404
|
4.0
|
39.9
|
1.0
|
OE1
|
A:GLU578
|
4.2
|
42.2
|
1.0
|
O1A
|
A:DTP801
|
4.3
|
34.8
|
1.0
|
O
|
A:HOH1041
|
4.4
|
53.4
|
1.0
|
O
|
A:ASP404
|
4.5
|
32.3
|
1.0
|
O
|
A:HOH1074
|
4.5
|
43.3
|
1.0
|
HA
|
A:ARG406
|
4.5
|
44.0
|
1.0
|
C
|
A:ASP404
|
4.5
|
35.6
|
1.0
|
HB2
|
A:GLU580
|
4.5
|
54.1
|
1.0
|
CG
|
A:GLU580
|
4.5
|
56.7
|
1.0
|
CA
|
A:ASP404
|
4.6
|
37.2
|
1.0
|
C
|
A:PHE405
|
4.7
|
30.2
|
1.0
|
O3B
|
A:DTP801
|
4.7
|
33.6
|
1.0
|
HZ2
|
A:LYS487
|
4.7
|
52.5
|
1.0
|
HB2
|
A:GLU578
|
4.8
|
46.1
|
1.0
|
O
|
A:HOH964
|
4.8
|
36.0
|
1.0
|
HH22
|
A:ARG460
|
4.9
|
46.0
|
1.0
|
HG3
|
A:GLU580
|
4.9
|
68.1
|
1.0
|
MG
|
A:MG803
|
5.0
|
30.0
|
1.0
|
HG2
|
A:GLU580
|
5.0
|
68.1
|
1.0
|
|
Manganese binding site 4 out
of 4 in 7omb
Go back to
Manganese Binding Sites List in 7omb
Manganese binding site 4 out
of 4 in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with A P/T Duplex Containing An Extended 5' Single Stranded Template Overhang within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Mn101
b:80.3
occ:1.00
|
N7
|
P:DG7
|
2.7
|
43.8
|
1.0
|
H8
|
P:DG7
|
3.5
|
48.5
|
1.0
|
C8
|
P:DG7
|
3.5
|
40.3
|
1.0
|
C5
|
P:DG7
|
3.8
|
44.9
|
1.0
|
O6
|
P:DG7
|
4.1
|
42.7
|
1.0
|
H2'
|
P:DC6
|
4.3
|
58.4
|
1.0
|
C6
|
P:DG7
|
4.4
|
42.0
|
1.0
|
H5
|
P:DC6
|
4.5
|
57.1
|
1.0
|
O6
|
P:DG8
|
4.5
|
40.0
|
1.0
|
H6
|
P:DC6
|
4.5
|
55.1
|
1.0
|
C5
|
P:DC6
|
4.6
|
47.6
|
1.0
|
C6
|
P:DC6
|
4.7
|
45.9
|
1.0
|
N9
|
P:DG7
|
4.8
|
47.7
|
1.0
|
C4
|
P:DG7
|
5.0
|
44.6
|
1.0
|
|
Reference:
H.M.Kropp,
S.Ludmann,
K.Diederichs,
K.Betz,
A.Marx.
Structural Basis For the Recognition of Deaminated Nucleobases By An Archaeal Dna Polymerase. Chembiochem 2021.
ISSN: ESSN 1439-7633
PubMed: 34486208
DOI: 10.1002/CBIC.202100306
Page generated: Sun Oct 6 10:22:58 2024
|