Manganese in PDB 6fbc: Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer.
Enzymatic activity of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer.
All present enzymatic activity of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer.:
2.7.7.7;
Protein crystallography data
The structure of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer., PDB code: 6fbc
was solved by
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)
|
47.30 /
1.54
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
109.230,
109.230,
90.700,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.6 /
20.9
|
Other elements in 6fbc:
The structure of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer. also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer.
(pdb code 6fbc). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the
Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer., PDB code: 6fbc:
Jump to Manganese binding site number:
1;
2;
Manganese binding site 1 out
of 2 in 6fbc
Go back to
Manganese Binding Sites List in 6fbc
Manganese binding site 1 out
of 2 in the Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer.
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn903
b:22.2
occ:1.00
|
H3
|
B:D4B112
|
2.0
|
25.5
|
1.0
|
OD2
|
A:ASP610
|
2.1
|
25.8
|
1.0
|
OD1
|
A:ASP785
|
2.1
|
21.6
|
1.0
|
O
|
A:HOH1003
|
2.2
|
23.3
|
1.0
|
O1A
|
A:XG4901
|
2.2
|
19.6
|
1.0
|
O3'
|
B:D4B112
|
2.3
|
21.2
|
1.0
|
O
|
A:HOH1129
|
2.4
|
27.7
|
1.0
|
CG
|
A:ASP785
|
3.1
|
20.6
|
1.0
|
CG
|
A:ASP610
|
3.1
|
26.1
|
1.0
|
H5'B
|
B:D4B112
|
3.3
|
22.1
|
1.0
|
H3'
|
B:D4B112
|
3.4
|
26.8
|
1.0
|
PA
|
A:XG4901
|
3.4
|
22.6
|
1.0
|
C3'
|
B:D4B112
|
3.4
|
22.4
|
1.0
|
HB2
|
A:GLU786
|
3.4
|
32.0
|
1.0
|
OD2
|
A:ASP785
|
3.4
|
22.2
|
1.0
|
OD1
|
A:ASP610
|
3.5
|
26.6
|
1.0
|
MN
|
A:MN904
|
3.6
|
20.4
|
0.9
|
O2A
|
A:XG4901
|
3.7
|
24.0
|
1.0
|
H5'A
|
A:XG4901
|
3.8
|
19.2
|
1.0
|
O
|
A:HOH1118
|
3.9
|
28.8
|
1.0
|
HZ1
|
A:LYS831
|
3.9
|
45.0
|
1.0
|
O5'
|
A:XG4901
|
3.9
|
18.7
|
1.0
|
HZ2
|
A:LYS831
|
4.0
|
45.0
|
1.0
|
H
|
A:ASP785
|
4.0
|
22.8
|
1.0
|
HB3
|
A:GLU786
|
4.1
|
32.0
|
1.0
|
H5'
|
A:XG4901
|
4.1
|
19.2
|
1.0
|
C5'
|
B:D4B112
|
4.2
|
18.4
|
1.0
|
OE1
|
A:GLU786
|
4.2
|
28.8
|
1.0
|
CB
|
A:GLU786
|
4.2
|
26.6
|
1.0
|
C5'
|
A:XG4901
|
4.2
|
16.0
|
1.0
|
C4'
|
B:D4B112
|
4.2
|
21.8
|
1.0
|
O
|
A:VAL783
|
4.2
|
21.8
|
1.0
|
NZ
|
A:LYS831
|
4.3
|
37.5
|
1.0
|
HH22
|
A:ARG660
|
4.4
|
59.6
|
0.5
|
CB
|
A:ASP610
|
4.4
|
25.7
|
1.0
|
H4'
|
B:D4B112
|
4.4
|
26.2
|
1.0
|
HB2
|
A:ASP610
|
4.5
|
30.9
|
1.0
|
CB
|
A:ASP785
|
4.5
|
22.2
|
1.0
|
C
|
A:ASP785
|
4.6
|
21.0
|
1.0
|
HZ3
|
A:LYS831
|
4.6
|
45.0
|
1.0
|
O1
|
B:D4B112
|
4.7
|
21.8
|
1.0
|
C2'
|
B:D4B112
|
4.7
|
23.4
|
1.0
|
O
|
A:ASP785
|
4.7
|
20.6
|
1.0
|
O3G
|
A:XG4901
|
4.7
|
21.9
|
1.0
|
N
|
A:ASP785
|
4.8
|
19.0
|
1.0
|
N
|
A:GLU786
|
4.8
|
20.4
|
1.0
|
N3A
|
A:XG4901
|
4.8
|
21.3
|
1.0
|
H2'B
|
B:D4B112
|
4.8
|
28.1
|
1.0
|
HB3
|
A:ASP785
|
4.8
|
26.7
|
1.0
|
CA
|
A:ASP785
|
4.8
|
19.4
|
1.0
|
O
|
A:HOH1010
|
4.9
|
42.1
|
1.0
|
HA
|
A:ASP610
|
4.9
|
27.3
|
1.0
|
HB
|
A:VAL783
|
4.9
|
26.1
|
1.0
|
H2'A
|
B:D4B112
|
5.0
|
28.1
|
1.0
|
|
Manganese binding site 2 out
of 2 in 6fbc
Go back to
Manganese Binding Sites List in 6fbc
Manganese binding site 2 out
of 2 in the Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer.
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn904
b:20.4
occ:0.92
|
OD2
|
A:ASP785
|
2.0
|
22.2
|
1.0
|
O3G
|
A:XG4901
|
2.1
|
21.9
|
1.0
|
OD1
|
A:ASP610
|
2.1
|
26.6
|
1.0
|
O
|
A:TYR611
|
2.1
|
26.0
|
1.0
|
O1A
|
A:XG4901
|
2.3
|
19.6
|
1.0
|
O1B
|
A:XG4901
|
2.3
|
22.3
|
1.0
|
CG
|
A:ASP785
|
3.1
|
20.6
|
1.0
|
CG
|
A:ASP610
|
3.1
|
26.1
|
1.0
|
PB
|
A:XG4901
|
3.2
|
24.0
|
1.0
|
H5'
|
A:XG4901
|
3.2
|
19.2
|
1.0
|
C
|
A:TYR611
|
3.3
|
29.2
|
1.0
|
PG
|
A:XG4901
|
3.5
|
24.9
|
1.0
|
PA
|
A:XG4901
|
3.5
|
22.6
|
1.0
|
OD2
|
A:ASP610
|
3.5
|
25.8
|
1.0
|
OD1
|
A:ASP785
|
3.5
|
21.6
|
1.0
|
MN
|
A:MN903
|
3.6
|
22.2
|
1.0
|
N3A
|
A:XG4901
|
3.6
|
21.3
|
1.0
|
O3B
|
A:XG4901
|
3.7
|
22.8
|
1.0
|
O
|
A:HOH1118
|
3.8
|
28.8
|
1.0
|
H
|
A:GLN613
|
3.9
|
32.4
|
1.0
|
N
|
A:TYR611
|
4.0
|
22.9
|
1.0
|
H
|
A:TYR611
|
4.0
|
27.5
|
1.0
|
O
|
A:HOH1209
|
4.0
|
26.1
|
1.0
|
H
|
A:ILE614
|
4.0
|
33.0
|
1.0
|
HG22
|
A:ILE614
|
4.0
|
31.9
|
1.0
|
HA
|
A:SER612
|
4.0
|
34.6
|
1.0
|
HB2
|
A:TYR611
|
4.1
|
27.6
|
1.0
|
C5'
|
A:XG4901
|
4.1
|
16.0
|
1.0
|
H3
|
B:D4B112
|
4.1
|
25.5
|
1.0
|
CA
|
A:TYR611
|
4.2
|
26.7
|
1.0
|
O5'
|
A:XG4901
|
4.2
|
18.7
|
1.0
|
HB
|
A:ILE614
|
4.3
|
32.2
|
1.0
|
C
|
A:ASP610
|
4.3
|
23.6
|
1.0
|
N
|
A:SER612
|
4.4
|
27.0
|
1.0
|
N
|
A:GLN613
|
4.4
|
27.0
|
1.0
|
O1G
|
A:XG4901
|
4.4
|
28.5
|
1.0
|
CB
|
A:ASP610
|
4.4
|
25.7
|
1.0
|
CB
|
A:ASP785
|
4.4
|
22.2
|
1.0
|
HB2
|
A:ASP785
|
4.4
|
26.7
|
1.0
|
H5'A
|
A:XG4901
|
4.5
|
19.2
|
1.0
|
O2G
|
A:XG4901
|
4.5
|
24.6
|
1.0
|
CA
|
A:SER612
|
4.5
|
28.9
|
1.0
|
HN3A
|
A:XG4901
|
4.5
|
25.6
|
1.0
|
CB
|
A:TYR611
|
4.6
|
23.0
|
1.0
|
O2A
|
A:XG4901
|
4.6
|
24.0
|
1.0
|
HG21
|
A:ILE614
|
4.6
|
31.9
|
1.0
|
O2B
|
A:XG4901
|
4.6
|
24.2
|
1.0
|
HB3
|
A:ASP610
|
4.6
|
30.9
|
1.0
|
C
|
A:SER612
|
4.7
|
27.6
|
1.0
|
CG2
|
A:ILE614
|
4.7
|
26.6
|
1.0
|
HB3
|
A:TYR611
|
4.8
|
27.6
|
1.0
|
N
|
A:ILE614
|
4.8
|
27.5
|
1.0
|
O
|
A:ASP610
|
4.8
|
30.8
|
1.0
|
HB3
|
A:ASP785
|
4.8
|
26.7
|
1.0
|
CA
|
A:ASP610
|
4.9
|
22.8
|
1.0
|
O
|
A:ASP785
|
4.9
|
20.6
|
1.0
|
O
|
A:HOH1129
|
4.9
|
27.7
|
1.0
|
HA
|
A:ASP610
|
4.9
|
27.3
|
1.0
|
CB
|
A:ILE614
|
4.9
|
26.9
|
1.0
|
|
Reference:
H.M.Kropp,
S.L.Durr,
C.Peter,
K.Diederichs,
A.Marx.
Snapshots of A Modified Nucleotide Moving Through the Confines of A Dna Polymerase. Proc. Natl. Acad. Sci. V. 115 9992 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30224478
DOI: 10.1073/PNAS.1811518115
Page generated: Sun Oct 6 04:35:23 2024
|