Manganese in PDB 5kg6: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm CA2+ For 60S
Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm CA2+ For 60S
All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction First with 1 Mm MN2+ For 1800S Then with 10 Mm CA2+ For 60S:
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 10 Mm CA2+ For 60S, PDB code: 5kg6
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)
|
19.66 /
1.55
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.110,
98.110,
81.960,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19.2 /
22.9
|
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 10 Mm CA2+ For 60S
(pdb code 5kg6). 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 10 Mm CA2+ For 60S, PDB code: 5kg6:
Jump to Manganese binding site number:
1;
2;
3;
Manganese binding site 1 out
of 3 in 5kg6
Go back to
Manganese Binding Sites List in 5kg6
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 10 Mm CA2+ For 60S
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 10 Mm CA2+ For 60S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:12.3
occ:1.00
|
OP1
|
P:DA9
|
2.0
|
12.7
|
0.1
|
OD2
|
A:ASP13
|
2.1
|
13.3
|
1.0
|
O
|
A:HOH785
|
2.1
|
12.9
|
1.0
|
OE2
|
A:GLU116
|
2.2
|
14.0
|
1.0
|
OD1
|
A:ASP115
|
2.2
|
11.3
|
1.0
|
O2A
|
A:DTP506
|
2.2
|
12.9
|
0.9
|
O3'
|
P:DT8
|
2.3
|
11.6
|
0.9
|
O3'
|
P:DT8
|
2.5
|
13.1
|
0.1
|
P
|
P:DA9
|
2.7
|
14.2
|
0.1
|
CG
|
A:ASP115
|
3.1
|
13.0
|
1.0
|
CG
|
A:ASP13
|
3.2
|
11.9
|
1.0
|
CD
|
A:GLU116
|
3.2
|
11.8
|
1.0
|
C3'
|
P:DT8
|
3.3
|
14.5
|
0.9
|
PA
|
A:DTP506
|
3.4
|
11.5
|
0.9
|
OD2
|
A:ASP115
|
3.4
|
11.9
|
1.0
|
OD1
|
A:ASP13
|
3.6
|
11.8
|
1.0
|
MN
|
A:MN502
|
3.6
|
11.4
|
1.0
|
C3'
|
P:DT8
|
3.7
|
15.5
|
0.1
|
OG
|
A:SER113
|
3.7
|
14.1
|
1.0
|
OP2
|
P:DA9
|
3.8
|
14.4
|
0.1
|
OE1
|
A:GLU116
|
3.8
|
15.2
|
1.0
|
O1A
|
A:DTP506
|
3.9
|
14.0
|
0.9
|
O5'
|
P:DA9
|
3.9
|
12.2
|
0.1
|
O5'
|
A:DTP506
|
4.0
|
10.8
|
0.9
|
CG
|
A:GLU116
|
4.1
|
11.2
|
1.0
|
C4'
|
P:DT8
|
4.1
|
17.2
|
0.1
|
CB
|
A:GLU116
|
4.1
|
12.4
|
1.0
|
C4'
|
P:DT8
|
4.2
|
16.6
|
0.9
|
O
|
A:HOH806
|
4.2
|
14.3
|
0.8
|
NZ
|
A:LYS224
|
4.2
|
15.0
|
1.0
|
C5'
|
A:DTP506
|
4.2
|
13.0
|
0.9
|
C5'
|
P:DA9
|
4.2
|
12.8
|
0.1
|
C5'
|
P:DT8
|
4.4
|
22.8
|
0.1
|
CB
|
A:ASP13
|
4.4
|
11.4
|
1.0
|
O
|
P:HOH205
|
4.5
|
15.7
|
1.0
|
CB
|
A:ASP115
|
4.5
|
11.7
|
1.0
|
C2'
|
P:DT8
|
4.6
|
15.2
|
0.9
|
O7
|
A:DPO507
|
4.6
|
11.2
|
0.1
|
C
|
A:ASP115
|
4.7
|
12.7
|
1.0
|
O
|
A:ASP115
|
4.7
|
12.6
|
1.0
|
C5'
|
P:DT8
|
4.7
|
22.2
|
0.9
|
O3A
|
A:DTP506
|
4.7
|
11.9
|
0.9
|
CB
|
A:SER113
|
4.8
|
13.7
|
1.0
|
O3G
|
A:DTP506
|
4.8
|
10.4
|
0.9
|
O5'
|
P:DT8
|
4.9
|
33.6
|
0.9
|
N
|
A:GLU116
|
4.9
|
9.3
|
1.0
|
C2'
|
P:DT8
|
5.0
|
16.1
|
0.1
|
O1B
|
A:DTP506
|
5.0
|
10.1
|
0.9
|
|
Manganese binding site 2 out
of 3 in 5kg6
Go back to
Manganese Binding Sites List in 5kg6
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 10 Mm CA2+ For 60S
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 10 Mm CA2+ For 60S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn502
b:11.4
occ:1.00
|
O7
|
A:DPO507
|
2.1
|
11.2
|
0.1
|
OD1
|
A:ASP13
|
2.1
|
11.8
|
1.0
|
O3G
|
A:DTP506
|
2.1
|
10.4
|
0.9
|
O1B
|
A:DTP506
|
2.2
|
10.1
|
0.9
|
OD2
|
A:ASP115
|
2.2
|
11.9
|
1.0
|
O
|
A:MET14
|
2.3
|
13.2
|
1.0
|
O2A
|
A:DTP506
|
2.3
|
12.9
|
0.9
|
O2
|
A:DPO507
|
2.4
|
10.7
|
0.1
|
OP1
|
P:DA9
|
2.6
|
12.7
|
0.1
|
CG
|
A:ASP13
|
3.1
|
11.9
|
1.0
|
PB
|
A:DTP506
|
3.2
|
10.9
|
0.9
|
CG
|
A:ASP115
|
3.2
|
13.0
|
1.0
|
PA
|
A:DTP506
|
3.4
|
11.5
|
0.9
|
P2
|
A:DPO507
|
3.4
|
12.3
|
0.1
|
OD2
|
A:ASP13
|
3.4
|
13.3
|
1.0
|
C
|
A:MET14
|
3.4
|
11.8
|
1.0
|
PG
|
A:DTP506
|
3.4
|
11.9
|
0.9
|
P1
|
A:DPO507
|
3.4
|
11.6
|
0.1
|
O3A
|
A:DTP506
|
3.4
|
11.9
|
0.9
|
MN
|
A:MN501
|
3.6
|
12.3
|
1.0
|
O3B
|
A:DTP506
|
3.7
|
11.5
|
0.9
|
OD1
|
A:ASP115
|
3.7
|
11.3
|
1.0
|
O1
|
A:DPO507
|
3.7
|
12.7
|
0.1
|
NZ
|
A:LYS231
|
3.8
|
17.4
|
1.0
|
O4
|
A:DPO507
|
3.8
|
11.7
|
0.1
|
N
|
A:MET14
|
3.9
|
9.9
|
1.0
|
O5
|
A:DPO507
|
3.9
|
12.2
|
0.1
|
P
|
P:DA9
|
3.9
|
14.2
|
0.1
|
O
|
A:HOH806
|
3.9
|
14.3
|
0.8
|
O2G
|
A:DTP506
|
4.0
|
12.0
|
0.9
|
C5'
|
A:DTP506
|
4.0
|
13.0
|
0.9
|
CA
|
A:MET14
|
4.1
|
11.0
|
1.0
|
O5'
|
A:DTP506
|
4.2
|
10.8
|
0.9
|
C5'
|
P:DA9
|
4.2
|
12.8
|
0.1
|
C
|
A:ASP13
|
4.2
|
9.4
|
1.0
|
CB
|
A:ASP13
|
4.3
|
11.4
|
1.0
|
N
|
A:ASP15
|
4.4
|
9.5
|
1.0
|
O
|
A:HOH785
|
4.4
|
12.9
|
1.0
|
N
|
A:CYS16
|
4.4
|
10.1
|
1.0
|
O5'
|
P:DA9
|
4.5
|
12.2
|
0.1
|
CE
|
A:LYS231
|
4.5
|
18.6
|
1.0
|
CB
|
A:ASP115
|
4.5
|
11.7
|
1.0
|
O2B
|
A:DTP506
|
4.5
|
12.3
|
0.9
|
O6
|
A:DPO507
|
4.5
|
12.7
|
0.1
|
CA
|
A:ASP15
|
4.6
|
9.9
|
1.0
|
O1A
|
A:DTP506
|
4.6
|
14.0
|
0.9
|
O1G
|
A:DTP506
|
4.6
|
12.6
|
0.9
|
CB
|
A:MET14
|
4.6
|
13.2
|
1.0
|
OP2
|
P:DA9
|
4.7
|
14.4
|
0.1
|
O
|
A:ASP13
|
4.7
|
11.6
|
1.0
|
C
|
A:ASP15
|
4.7
|
12.5
|
1.0
|
O3
|
A:DPO507
|
4.7
|
12.2
|
0.1
|
N
|
A:PHE17
|
4.7
|
10.4
|
1.0
|
CA
|
A:ASP13
|
4.8
|
11.4
|
1.0
|
CB
|
A:PHE17
|
4.9
|
10.0
|
1.0
|
O
|
A:ASP115
|
4.9
|
12.6
|
1.0
|
|
Manganese binding site 3 out
of 3 in 5kg6
Go back to
Manganese Binding Sites List in 5kg6
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 10 Mm CA2+ For 60S
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 10 Mm CA2+ For 60S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Mn101
b:16.6
occ:0.10
|
O1A
|
A:DTP506
|
1.7
|
14.0
|
0.9
|
OP2
|
P:DA9
|
1.9
|
14.4
|
0.1
|
O
|
P:HOH218
|
2.1
|
18.7
|
0.1
|
O3A
|
A:DTP506
|
2.2
|
11.9
|
0.9
|
O1
|
A:DPO507
|
2.2
|
12.7
|
0.1
|
PA
|
A:DTP506
|
2.4
|
11.5
|
0.9
|
O
|
A:HOH806
|
2.5
|
18.2
|
0.2
|
NH1
|
A:ARG61
|
2.5
|
23.2
|
0.9
|
O
|
A:HOH688
|
2.7
|
29.0
|
1.0
|
O
|
A:HOH631
|
2.8
|
18.7
|
1.0
|
P
|
P:DA9
|
3.1
|
14.2
|
0.1
|
CZ
|
A:ARG61
|
3.5
|
23.3
|
0.9
|
O2A
|
A:DTP506
|
3.5
|
12.9
|
0.9
|
O5'
|
A:DTP506
|
3.6
|
10.8
|
0.9
|
NH2
|
A:ARG61
|
3.6
|
19.4
|
0.9
|
P1
|
A:DPO507
|
3.7
|
11.6
|
0.1
|
PB
|
A:DTP506
|
3.7
|
10.9
|
0.9
|
OP1
|
P:DA9
|
3.7
|
12.7
|
0.1
|
O5'
|
P:DA9
|
3.8
|
12.2
|
0.1
|
O
|
A:HOH724
|
3.8
|
18.4
|
0.1
|
O
|
A:HOH654
|
3.9
|
30.2
|
0.6
|
O
|
A:HOH806
|
3.9
|
14.3
|
0.8
|
O6
|
A:DPO507
|
3.9
|
12.7
|
0.1
|
O7
|
A:DPO507
|
4.0
|
11.2
|
0.1
|
O
|
A:HOH911
|
4.0
|
20.6
|
1.0
|
O3B
|
A:DTP506
|
4.0
|
11.5
|
0.9
|
O1G
|
A:DTP506
|
4.1
|
12.6
|
0.9
|
O4
|
A:DPO507
|
4.1
|
11.7
|
0.1
|
O3G
|
A:DTP506
|
4.2
|
10.4
|
0.9
|
P2
|
A:DPO507
|
4.2
|
12.3
|
0.1
|
O3'
|
P:DT8
|
4.3
|
13.1
|
0.1
|
O
|
A:HOH785
|
4.4
|
12.9
|
1.0
|
PG
|
A:DTP506
|
4.4
|
11.9
|
0.9
|
O2B
|
A:DTP506
|
4.4
|
12.3
|
0.9
|
O
|
P:HOH223
|
4.5
|
29.2
|
1.0
|
C3'
|
P:DT8
|
4.5
|
15.5
|
0.1
|
O3
|
A:DPO507
|
4.5
|
12.2
|
0.1
|
C2'
|
P:DT8
|
4.5
|
15.2
|
0.9
|
O2
|
A:DPO507
|
4.6
|
10.7
|
0.1
|
NE
|
A:ARG61
|
4.7
|
24.1
|
0.9
|
O1B
|
A:DTP506
|
4.8
|
10.1
|
0.9
|
C3'
|
P:DT8
|
4.8
|
14.5
|
0.9
|
C8
|
A:DTP506
|
4.8
|
14.1
|
0.9
|
C5'
|
A:DTP506
|
4.8
|
13.0
|
0.9
|
C2'
|
P:DT8
|
4.8
|
16.1
|
0.1
|
C8
|
P:DA9
|
4.9
|
14.3
|
0.1
|
O3'
|
P:DT8
|
4.9
|
11.6
|
0.9
|
C5'
|
P:DA9
|
4.9
|
12.8
|
0.1
|
NE
|
A:ARG61
|
5.0
|
26.4
|
0.1
|
|
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
Page generated: Sun Oct 6 01:44:45 2024
|