Manganese in PDB 7kt4: Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)
Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)
All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN):
2.7.7.7;
Protein crystallography data
The structure of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN), PDB code: 7kt4
was solved by
J.A.Jamsen,
S.H.Wilson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
21.43 /
1.92
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.119,
68.819,
110.296,
90,
90,
90
|
R / Rfree (%)
|
16.6 /
20.4
|
Other elements in 7kt4:
The structure of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)
(pdb code 7kt4). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN), PDB code: 7kt4:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 7kt4
Go back to
Manganese Binding Sites List in 7kt4
Manganese binding site 1 out
of 4 in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)
![](/pictures/MN/pdb/kt/7kt4-MN-sphere_01.jpg) Mono view
![](/pictures/MN/pdb/kt/7kt4-MN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn502
b:20.4
occ:1.00
|
OD2
|
A:ASP330
|
1.7
|
15.9
|
0.5
|
OP1
|
P:8OG5
|
1.9
|
10.5
|
0.6
|
OD1
|
A:ASP332
|
2.1
|
17.1
|
1.0
|
OD2
|
A:ASP418
|
2.1
|
13.0
|
1.0
|
O
|
P:HOH202
|
2.4
|
21.4
|
1.0
|
OD1
|
A:ASP330
|
2.5
|
20.6
|
0.5
|
O
|
A:HOH705
|
2.5
|
25.1
|
0.5
|
CG
|
A:ASP330
|
2.7
|
20.2
|
0.5
|
O2A
|
A:8DG512
|
2.8
|
10.4
|
0.4
|
P
|
P:8OG5
|
3.0
|
13.8
|
0.6
|
O3'
|
P:DA4
|
3.0
|
18.9
|
0.4
|
O3'
|
P:DA4
|
3.1
|
18.6
|
0.6
|
CG
|
A:ASP418
|
3.1
|
14.7
|
1.0
|
OD1
|
A:ASP330
|
3.1
|
12.9
|
0.5
|
CG
|
A:ASP332
|
3.1
|
16.4
|
1.0
|
CG
|
A:ASP330
|
3.3
|
33.6
|
0.5
|
MN
|
A:MN503
|
3.4
|
16.3
|
1.0
|
OD2
|
A:ASP332
|
3.5
|
14.0
|
1.0
|
PA
|
A:8DG512
|
3.7
|
16.2
|
0.4
|
CB
|
A:ASP418
|
3.8
|
16.6
|
1.0
|
OD2
|
A:ASP330
|
3.8
|
28.8
|
0.5
|
OP2
|
P:8OG5
|
3.8
|
18.0
|
0.6
|
O1A
|
A:8DG512
|
3.9
|
15.6
|
0.4
|
CB
|
A:ASP330
|
4.0
|
16.2
|
0.5
|
OD1
|
A:ASP418
|
4.0
|
14.5
|
1.0
|
C3'
|
P:DA4
|
4.1
|
15.5
|
0.4
|
C5'
|
P:DA4
|
4.1
|
15.7
|
0.4
|
C5'
|
P:DA4
|
4.1
|
16.3
|
0.6
|
C3'
|
P:DA4
|
4.1
|
11.0
|
0.6
|
CB
|
A:ASP330
|
4.2
|
19.6
|
0.5
|
O5'
|
A:8DG512
|
4.2
|
10.2
|
0.4
|
C4'
|
P:DA4
|
4.2
|
14.4
|
0.4
|
O5'
|
P:8OG5
|
4.3
|
14.0
|
0.6
|
C4'
|
P:DA4
|
4.3
|
11.9
|
0.6
|
CB
|
A:ASP332
|
4.5
|
10.6
|
1.0
|
NH2
|
A:ARG416
|
4.5
|
15.2
|
1.0
|
O
|
P:HOH205
|
4.6
|
22.3
|
0.5
|
OP1
|
P:DA4
|
4.6
|
13.6
|
0.6
|
C5'
|
A:8DG512
|
4.6
|
10.0
|
0.4
|
OP1
|
P:DA4
|
4.6
|
15.5
|
0.4
|
O1G
|
A:8DG512
|
4.6
|
21.5
|
0.4
|
C5'
|
P:8OG5
|
4.7
|
15.4
|
0.6
|
O
|
A:VAL331
|
4.7
|
13.7
|
1.0
|
CZ3
|
A:TRP434
|
4.7
|
16.1
|
1.0
|
O32
|
A:PPV511
|
4.8
|
29.3
|
0.2
|
NE2
|
A:HIS329
|
4.9
|
29.5
|
0.5
|
O5'
|
P:DA4
|
4.9
|
21.0
|
0.4
|
O5'
|
P:DA4
|
4.9
|
17.7
|
0.6
|
N
|
A:ASP418
|
4.9
|
12.6
|
1.0
|
O
|
A:HOH617
|
5.0
|
13.2
|
1.0
|
C
|
A:VAL331
|
5.0
|
13.7
|
1.0
|
CA
|
A:ASP418
|
5.0
|
12.5
|
1.0
|
|
Manganese binding site 2 out
of 4 in 7kt4
Go back to
Manganese Binding Sites List in 7kt4
Manganese binding site 2 out
of 4 in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)
![](/pictures/MN/pdb/kt/7kt4-MN-sphere_02.jpg) Mono view
![](/pictures/MN/pdb/kt/7kt4-MN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn503
b:16.3
occ:1.00
|
O2A
|
A:8DG512
|
1.6
|
10.4
|
0.4
|
O
|
A:HOH617
|
1.9
|
13.2
|
1.0
|
OD1
|
A:ASP330
|
2.1
|
12.9
|
0.5
|
OD2
|
A:ASP332
|
2.1
|
14.0
|
1.0
|
O1B
|
A:8DG512
|
2.1
|
16.6
|
0.4
|
O1G
|
A:8DG512
|
2.1
|
21.5
|
0.4
|
O11
|
A:PPV511
|
2.2
|
17.2
|
0.6
|
OD1
|
A:ASP330
|
2.3
|
20.6
|
0.5
|
O32
|
A:PPV511
|
2.3
|
29.3
|
0.2
|
OP1
|
P:8OG5
|
2.4
|
10.5
|
0.6
|
PA
|
A:8DG512
|
2.9
|
16.2
|
0.4
|
CG
|
A:ASP330
|
3.1
|
33.6
|
0.5
|
CG
|
A:ASP332
|
3.1
|
16.4
|
1.0
|
P1
|
A:PPV511
|
3.1
|
27.7
|
0.6
|
CG
|
A:ASP330
|
3.1
|
20.2
|
0.5
|
PB
|
A:8DG512
|
3.1
|
23.5
|
0.4
|
O31
|
A:PPV511
|
3.2
|
29.9
|
0.6
|
OD2
|
A:ASP330
|
3.2
|
28.8
|
0.5
|
O3A
|
A:8DG512
|
3.3
|
32.9
|
0.4
|
OD1
|
A:ASP332
|
3.4
|
17.1
|
1.0
|
PG
|
A:8DG512
|
3.4
|
36.3
|
0.4
|
MN
|
A:MN502
|
3.4
|
20.4
|
1.0
|
OD2
|
A:ASP330
|
3.5
|
15.9
|
0.5
|
P2
|
A:PPV511
|
3.6
|
29.2
|
0.2
|
OPP
|
A:PPV511
|
3.7
|
28.8
|
0.2
|
O3B
|
A:8DG512
|
3.7
|
25.0
|
0.4
|
P
|
P:8OG5
|
3.7
|
13.8
|
0.6
|
O5'
|
P:8OG5
|
3.9
|
14.0
|
0.6
|
O5'
|
A:8DG512
|
3.9
|
10.2
|
0.4
|
O1A
|
A:8DG512
|
4.0
|
15.6
|
0.4
|
O
|
A:ASP330
|
4.0
|
15.5
|
0.5
|
C5'
|
A:8DG512
|
4.0
|
10.0
|
0.4
|
O2G
|
A:8DG512
|
4.0
|
25.9
|
0.4
|
O
|
A:HOH722
|
4.1
|
11.3
|
0.6
|
C5'
|
P:8OG5
|
4.3
|
15.4
|
0.6
|
O12
|
A:PPV511
|
4.3
|
33.9
|
0.2
|
O
|
A:ASP330
|
4.3
|
11.6
|
0.5
|
OP2
|
P:8OG5
|
4.3
|
18.0
|
0.6
|
N
|
A:GLY320
|
4.3
|
12.0
|
1.0
|
C
|
A:ASP330
|
4.3
|
15.5
|
0.5
|
O
|
A:HOH629
|
4.4
|
15.6
|
1.0
|
CB
|
A:ASP330
|
4.4
|
16.2
|
0.5
|
CB
|
A:ASP332
|
4.4
|
10.6
|
1.0
|
CB
|
A:ASP330
|
4.5
|
19.6
|
0.5
|
CA
|
A:GLY319
|
4.5
|
13.2
|
1.0
|
O21
|
A:PPV511
|
4.5
|
24.4
|
0.6
|
O
|
P:HOH202
|
4.5
|
21.4
|
1.0
|
C
|
A:ASP330
|
4.5
|
15.9
|
0.5
|
O2B
|
A:8DG512
|
4.5
|
17.4
|
0.4
|
O3G
|
A:8DG512
|
4.6
|
36.5
|
0.4
|
CD2
|
A:HIS329
|
4.6
|
35.9
|
0.5
|
O
|
P:HOH205
|
4.7
|
22.3
|
0.5
|
NE2
|
A:HIS329
|
4.7
|
29.5
|
0.5
|
O22
|
A:PPV511
|
4.8
|
41.8
|
0.2
|
O
|
A:HOH705
|
4.8
|
25.1
|
0.5
|
O3'
|
P:DA4
|
4.8
|
18.9
|
0.4
|
CA
|
A:ASP330
|
4.8
|
18.6
|
0.5
|
O3'
|
P:DA4
|
4.8
|
18.6
|
0.6
|
N
|
A:ASP330
|
4.9
|
14.7
|
0.5
|
N
|
A:ASP332
|
4.9
|
11.2
|
1.0
|
N
|
A:VAL331
|
4.9
|
14.1
|
1.0
|
CA
|
A:ASP330
|
5.0
|
12.2
|
0.5
|
C
|
A:GLY319
|
5.0
|
11.0
|
1.0
|
|
Manganese binding site 3 out
of 4 in 7kt4
Go back to
Manganese Binding Sites List in 7kt4
Manganese binding site 3 out
of 4 in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)
![](/pictures/MN/pdb/kt/7kt4-MN-sphere_03.jpg) Mono view
![](/pictures/MN/pdb/kt/7kt4-MN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn504
b:31.4
occ:0.65
|
O
|
A:HOH777
|
2.3
|
33.0
|
1.0
|
OE2
|
A:GLU386
|
2.3
|
33.2
|
1.0
|
O
|
T:HOH101
|
2.4
|
28.1
|
1.0
|
O
|
A:HOH826
|
2.5
|
34.8
|
1.0
|
OE1
|
A:GLU386
|
2.5
|
41.4
|
1.0
|
NE2
|
A:HIS459
|
2.7
|
37.4
|
1.0
|
CD
|
A:GLU386
|
2.8
|
32.6
|
1.0
|
CD2
|
A:HIS459
|
3.2
|
53.2
|
1.0
|
CE1
|
A:HIS459
|
3.8
|
47.9
|
1.0
|
O
|
A:HOH683
|
4.1
|
31.5
|
1.0
|
CG
|
A:GLU386
|
4.3
|
29.6
|
1.0
|
OP1
|
T:DC8
|
4.3
|
21.4
|
1.0
|
CG
|
A:HIS459
|
4.4
|
29.9
|
1.0
|
O
|
A:HOH610
|
4.5
|
21.8
|
1.0
|
OE1
|
A:GLN426
|
4.6
|
25.1
|
1.0
|
C5'
|
T:DC8
|
4.6
|
17.7
|
1.0
|
ND1
|
A:HIS459
|
4.7
|
46.2
|
1.0
|
|
Manganese binding site 4 out
of 4 in 7kt4
Go back to
Manganese Binding Sites List in 7kt4
Manganese binding site 4 out
of 4 in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)
![](/pictures/MN/pdb/kt/7kt4-MN-sphere_04.jpg) Mono view
![](/pictures/MN/pdb/kt/7kt4-MN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn505
b:81.8
occ:1.00
|
NE2
|
A:HIS219
|
2.3
|
56.1
|
1.0
|
CE1
|
A:HIS219
|
3.2
|
47.4
|
1.0
|
CD2
|
A:HIS219
|
3.4
|
54.0
|
1.0
|
CD
|
A:GLU218
|
3.7
|
52.1
|
1.0
|
ND1
|
A:HIS219
|
4.4
|
51.0
|
1.0
|
CB
|
A:GLU218
|
4.4
|
41.6
|
1.0
|
CG
|
A:HIS219
|
4.5
|
44.2
|
1.0
|
CG
|
A:GLU218
|
4.7
|
53.0
|
1.0
|
CD
|
A:GLN214
|
5.0
|
40.0
|
1.0
|
|
Reference:
J.A.Jamsen,
A.Sassa,
D.D.Shock,
W.A.Beard,
S.H.Wilson.
Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) To Be Published.
Page generated: Fri Dec 17 11:05:29 2021
|