Manganese in PDB 5kfz: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 14 Degree
Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 14 Degree
All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 14 Degree:
2.7.7.7;
Protein crystallography data
The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 14 Degree, PDB code: 5kfz
was solved by
Y.Gao,
W.Yang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.73 /
1.44
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.460,
98.460,
82.250,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.5 /
21.5
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 14 Degree
(pdb code 5kfz). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the
Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 14 Degree, PDB code: 5kfz:
Jump to Manganese binding site number:
1;
2;
3;
Manganese binding site 1 out
of 3 in 5kfz
Go back to
Manganese Binding Sites List in 5kfz
Manganese binding site 1 out
of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 14 Degree
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 14 Degree within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:9.2
occ:1.00
|
OD1
|
A:ASP13
|
2.1
|
10.1
|
1.0
|
O5
|
A:DPO506
|
2.1
|
8.7
|
0.1
|
OD2
|
A:ASP115
|
2.2
|
9.9
|
1.0
|
O1B
|
A:DTP505
|
2.2
|
8.8
|
0.9
|
O1G
|
A:DTP505
|
2.2
|
8.7
|
0.9
|
O
|
A:MET14
|
2.2
|
10.2
|
1.0
|
O1A
|
A:DTP505
|
2.3
|
9.8
|
0.9
|
O1
|
A:DPO506
|
2.3
|
8.8
|
0.1
|
OP1
|
P:DA9
|
2.5
|
10.1
|
0.1
|
CG
|
A:ASP13
|
3.1
|
7.9
|
1.0
|
PB
|
A:DTP505
|
3.2
|
9.3
|
0.9
|
CG
|
A:ASP115
|
3.2
|
9.2
|
1.0
|
C
|
A:MET14
|
3.3
|
9.0
|
1.0
|
PG
|
A:DTP505
|
3.4
|
9.5
|
0.9
|
P1
|
A:DPO506
|
3.4
|
8.9
|
0.1
|
P2
|
A:DPO506
|
3.4
|
10.0
|
0.1
|
PA
|
A:DTP505
|
3.4
|
10.2
|
0.9
|
OD2
|
A:ASP13
|
3.4
|
9.7
|
1.0
|
O3A
|
A:DTP505
|
3.4
|
10.0
|
0.9
|
O3B
|
A:DTP505
|
3.6
|
9.1
|
0.9
|
MN
|
A:MN508
|
3.6
|
9.8
|
1.0
|
O2
|
A:DPO506
|
3.7
|
10.2
|
0.1
|
OD1
|
A:ASP115
|
3.7
|
9.0
|
1.0
|
NZ
|
A:LYS231
|
3.7
|
9.4
|
0.5
|
O4
|
A:DPO506
|
3.8
|
9.1
|
0.1
|
P
|
P:DA9
|
3.8
|
11.3
|
0.1
|
N
|
A:MET14
|
3.8
|
8.0
|
1.0
|
O7
|
A:DPO506
|
3.9
|
9.8
|
0.1
|
O
|
A:HOH768
|
3.9
|
12.0
|
0.9
|
O2G
|
A:DTP505
|
4.0
|
9.9
|
0.9
|
CA
|
A:MET14
|
4.0
|
9.5
|
1.0
|
C5'
|
A:DTP505
|
4.1
|
9.7
|
0.9
|
C5'
|
P:DA9
|
4.2
|
9.8
|
0.1
|
O5'
|
A:DTP505
|
4.2
|
9.1
|
0.9
|
C
|
A:ASP13
|
4.2
|
8.2
|
1.0
|
CB
|
A:ASP13
|
4.4
|
8.6
|
1.0
|
N
|
A:ASP15
|
4.4
|
7.5
|
1.0
|
O
|
P:HOH614
|
4.4
|
10.7
|
1.0
|
O
|
A:HOH768
|
4.4
|
15.0
|
0.1
|
O5'
|
P:DA9
|
4.4
|
9.9
|
0.1
|
N
|
A:CYS16
|
4.5
|
8.8
|
1.0
|
CB
|
A:ASP115
|
4.5
|
9.0
|
1.0
|
CE
|
A:LYS231
|
4.5
|
7.6
|
0.5
|
O2B
|
A:DTP505
|
4.6
|
9.5
|
0.9
|
O6
|
A:DPO506
|
4.6
|
11.3
|
0.1
|
CB
|
A:MET14
|
4.6
|
10.2
|
1.0
|
CA
|
A:ASP15
|
4.6
|
9.0
|
1.0
|
O3G
|
A:DTP505
|
4.6
|
11.1
|
0.9
|
O
|
A:ASP13
|
4.6
|
10.1
|
1.0
|
O2A
|
A:DTP505
|
4.7
|
11.4
|
0.9
|
O3
|
A:DPO506
|
4.7
|
9.4
|
0.1
|
OP2
|
P:DA9
|
4.7
|
13.1
|
0.1
|
CA
|
A:ASP13
|
4.8
|
9.7
|
1.0
|
C
|
A:ASP15
|
4.8
|
8.6
|
1.0
|
N
|
A:PHE17
|
4.8
|
8.2
|
1.0
|
O3'
|
P:DT8
|
4.8
|
9.8
|
0.1
|
CB
|
A:PHE17
|
4.9
|
8.8
|
1.0
|
O
|
A:ASP115
|
4.9
|
9.3
|
1.0
|
MN
|
P:MN101
|
5.0
|
15.4
|
0.1
|
|
Manganese binding site 2 out
of 3 in 5kfz
Go back to
Manganese Binding Sites List in 5kfz
Manganese binding site 2 out
of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 14 Degree
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 14 Degree within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn508
b:9.8
occ:1.00
|
OP1
|
P:DA9
|
1.9
|
10.1
|
0.1
|
OD2
|
A:ASP13
|
2.1
|
9.7
|
1.0
|
OD1
|
A:ASP115
|
2.1
|
9.0
|
1.0
|
O
|
P:HOH614
|
2.2
|
10.7
|
1.0
|
OE2
|
A:GLU116
|
2.2
|
10.2
|
1.0
|
O3'
|
P:DT8
|
2.2
|
9.8
|
0.1
|
O1A
|
A:DTP505
|
2.2
|
9.8
|
0.9
|
O3'
|
P:DT8
|
2.3
|
10.6
|
0.4
|
O3'
|
P:DT8
|
2.3
|
10.5
|
0.5
|
P
|
P:DA9
|
2.6
|
11.3
|
0.1
|
CG
|
A:ASP115
|
3.1
|
9.2
|
1.0
|
CD
|
A:GLU116
|
3.2
|
10.4
|
1.0
|
CG
|
A:ASP13
|
3.2
|
7.9
|
1.0
|
C3'
|
P:DT8
|
3.3
|
12.7
|
0.4
|
C3'
|
P:DT8
|
3.3
|
12.8
|
0.5
|
C3'
|
P:DT8
|
3.3
|
13.3
|
0.1
|
PA
|
A:DTP505
|
3.4
|
10.2
|
0.9
|
OD2
|
A:ASP115
|
3.4
|
9.9
|
1.0
|
OD1
|
A:ASP13
|
3.6
|
10.1
|
1.0
|
MN
|
A:MN501
|
3.6
|
9.2
|
1.0
|
OP2
|
P:DA9
|
3.6
|
13.1
|
0.1
|
OG
|
A:SER113
|
3.8
|
11.5
|
1.0
|
OE1
|
A:GLU116
|
3.8
|
12.4
|
1.0
|
O2A
|
A:DTP505
|
3.9
|
11.4
|
0.9
|
O5'
|
P:DA9
|
3.9
|
9.9
|
0.1
|
O5'
|
A:DTP505
|
3.9
|
9.1
|
0.9
|
C4'
|
P:DT8
|
4.1
|
13.8
|
0.4
|
C4'
|
P:DT8
|
4.1
|
14.0
|
0.1
|
CG
|
A:GLU116
|
4.1
|
9.6
|
1.0
|
NZ
|
A:LYS224
|
4.2
|
8.4
|
0.7
|
C5'
|
A:DTP505
|
4.2
|
9.7
|
0.9
|
C5'
|
P:DA9
|
4.2
|
9.8
|
0.1
|
O
|
A:HOH768
|
4.2
|
12.0
|
0.9
|
CB
|
A:GLU116
|
4.2
|
9.2
|
1.0
|
C4'
|
P:DT8
|
4.2
|
14.6
|
0.5
|
O
|
A:HOH768
|
4.4
|
15.0
|
0.1
|
O
|
P:HOH607
|
4.4
|
12.2
|
0.9
|
C2'
|
P:DT8
|
4.5
|
13.6
|
0.1
|
CB
|
A:ASP13
|
4.5
|
8.6
|
1.0
|
CB
|
A:ASP115
|
4.5
|
9.0
|
1.0
|
C2'
|
P:DT8
|
4.5
|
12.6
|
0.4
|
C5'
|
P:DT8
|
4.5
|
16.1
|
0.1
|
C2'
|
P:DT8
|
4.6
|
12.7
|
0.5
|
O5
|
A:DPO506
|
4.7
|
8.7
|
0.1
|
C
|
A:ASP115
|
4.7
|
9.2
|
1.0
|
O3A
|
A:DTP505
|
4.7
|
10.0
|
0.9
|
O
|
A:ASP115
|
4.7
|
9.3
|
1.0
|
CB
|
A:SER113
|
4.7
|
11.3
|
1.0
|
C5'
|
P:DT8
|
4.7
|
14.7
|
0.4
|
O1G
|
A:DTP505
|
4.8
|
8.7
|
0.9
|
O5'
|
P:DT8
|
4.9
|
16.9
|
0.5
|
N
|
A:GLU116
|
4.9
|
9.4
|
1.0
|
O1B
|
A:DTP505
|
5.0
|
8.8
|
0.9
|
C5'
|
P:DT8
|
5.0
|
21.0
|
0.5
|
|
Manganese binding site 3 out
of 3 in 5kfz
Go back to
Manganese Binding Sites List in 5kfz
Manganese binding site 3 out
of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 14 Degree
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 5 Mm MN2+ For 60S at 14 Degree within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Mn101
b:15.4
occ:0.10
|
O2A
|
A:DTP505
|
1.7
|
11.4
|
0.9
|
OP2
|
P:DA9
|
2.1
|
13.1
|
0.1
|
O
|
A:HOH601
|
2.1
|
17.1
|
0.1
|
O3A
|
A:DTP505
|
2.2
|
10.0
|
0.9
|
O2
|
A:DPO506
|
2.2
|
10.2
|
0.1
|
PA
|
A:DTP505
|
2.4
|
10.2
|
0.9
|
NH1
|
A:ARG61
|
2.5
|
21.3
|
0.9
|
O
|
A:HOH768
|
2.5
|
15.0
|
0.1
|
O
|
A:HOH652
|
2.8
|
17.1
|
1.0
|
O
|
P:HOH604
|
3.0
|
21.6
|
1.0
|
P
|
P:DA9
|
3.1
|
11.3
|
0.1
|
O
|
A:HOH919
|
3.3
|
28.9
|
1.0
|
CZ
|
A:ARG61
|
3.4
|
22.7
|
0.9
|
NE
|
A:ARG61
|
3.5
|
20.0
|
0.1
|
O1A
|
A:DTP505
|
3.5
|
9.8
|
0.9
|
O5'
|
A:DTP505
|
3.5
|
9.1
|
0.9
|
NH2
|
A:ARG61
|
3.6
|
17.6
|
0.9
|
P1
|
A:DPO506
|
3.6
|
8.9
|
0.1
|
PB
|
A:DTP505
|
3.6
|
9.3
|
0.9
|
NH2
|
A:ARG61
|
3.7
|
21.5
|
0.1
|
OP1
|
P:DA9
|
3.7
|
10.1
|
0.1
|
O5'
|
P:DA9
|
3.7
|
9.9
|
0.1
|
O
|
A:HOH712
|
3.8
|
16.4
|
0.1
|
O5
|
A:DPO506
|
3.9
|
8.7
|
0.1
|
O
|
A:HOH768
|
3.9
|
12.0
|
0.9
|
O6
|
A:DPO506
|
3.9
|
11.3
|
0.1
|
O3B
|
A:DTP505
|
4.0
|
9.1
|
0.9
|
O4
|
A:DPO506
|
4.0
|
9.1
|
0.1
|
CZ
|
A:ARG61
|
4.0
|
27.1
|
0.1
|
O3G
|
A:DTP505
|
4.0
|
11.1
|
0.9
|
O
|
A:HOH912
|
4.0
|
17.1
|
1.0
|
O
|
A:HOH748
|
4.1
|
29.6
|
0.6
|
P2
|
A:DPO506
|
4.2
|
10.0
|
0.1
|
O1G
|
A:DTP505
|
4.2
|
8.7
|
0.9
|
PG
|
A:DTP505
|
4.3
|
9.5
|
0.9
|
O2B
|
A:DTP505
|
4.4
|
9.5
|
0.9
|
O
|
P:HOH614
|
4.4
|
10.7
|
1.0
|
O3'
|
P:DT8
|
4.4
|
9.8
|
0.1
|
O3
|
A:DPO506
|
4.4
|
9.4
|
0.1
|
CD
|
A:ARG61
|
4.5
|
20.5
|
0.1
|
C3'
|
P:DT8
|
4.5
|
13.3
|
0.1
|
O
|
P:HOH621
|
4.5
|
23.5
|
1.0
|
O1
|
A:DPO506
|
4.6
|
8.8
|
0.1
|
C2'
|
P:DT8
|
4.6
|
12.7
|
0.5
|
C2'
|
P:DT8
|
4.6
|
12.6
|
0.4
|
O1B
|
A:DTP505
|
4.7
|
8.8
|
0.9
|
NE
|
A:ARG61
|
4.7
|
25.1
|
0.9
|
C3'
|
P:DT8
|
4.7
|
12.8
|
0.5
|
C5'
|
A:DTP505
|
4.8
|
9.7
|
0.9
|
C3'
|
P:DT8
|
4.8
|
12.7
|
0.4
|
C8
|
A:DTP505
|
4.8
|
11.7
|
0.9
|
C2'
|
P:DT8
|
4.8
|
13.6
|
0.1
|
C5'
|
P:DA9
|
4.8
|
9.8
|
0.1
|
C8
|
P:DA9
|
4.9
|
11.7
|
0.1
|
O3'
|
P:DT8
|
4.9
|
10.6
|
0.4
|
O3'
|
P:DT8
|
4.9
|
10.5
|
0.5
|
MN
|
A:MN501
|
5.0
|
9.2
|
1.0
|
|
Reference:
Y.Gao,
W.Yang.
Capture of A Third MG2+ Is Essential For Catalyzing Dna Synthesis. Science V. 352 1334 2016.
ISSN: ESSN 1095-9203
PubMed: 27284197
DOI: 10.1126/SCIENCE.AAD9633
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