Manganese in PDB 7kt5: Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)
Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)
All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN):
2.7.7.7;
Protein crystallography data
The structure of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN), PDB code: 7kt5
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)
|
34.93 /
1.46
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.996,
68.701,
110.125,
90,
90,
90
|
R / Rfree (%)
|
16.2 /
18.3
|
Other elements in 7kt5:
The structure of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)
(pdb code 7kt5). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the
Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN), PDB code: 7kt5:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
Manganese binding site 1 out
of 7 in 7kt5
Go back to
Manganese Binding Sites List in 7kt5
Manganese binding site 1 out
of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)
![](/pictures/MN/pdb/kt/7kt5-MN-sphere_01.jpg) Mono view
![](/pictures/MN/pdb/kt/7kt5-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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:13.8
occ:1.00
|
O
|
A:HOH621
|
2.0
|
15.4
|
1.0
|
OD2
|
A:ASP330
|
2.1
|
13.7
|
0.5
|
OD2
|
A:ASP332
|
2.1
|
13.5
|
1.0
|
O12
|
A:GOA514
|
2.1
|
14.0
|
1.0
|
O2
|
A:GOA514
|
2.2
|
15.3
|
0.9
|
OP1
|
P:8OG5
|
2.3
|
16.6
|
1.0
|
OD1
|
A:ASP330
|
2.3
|
14.7
|
0.5
|
CG
|
A:ASP330
|
3.0
|
15.3
|
0.5
|
C1
|
A:GOA514
|
3.0
|
12.1
|
1.0
|
CG
|
A:ASP332
|
3.1
|
13.3
|
1.0
|
C2
|
A:GOA514
|
3.1
|
15.4
|
0.9
|
OD1
|
A:ASP330
|
3.3
|
13.8
|
0.5
|
MN
|
A:MN502
|
3.3
|
14.9
|
0.9
|
CG
|
A:ASP330
|
3.4
|
17.6
|
0.5
|
OD1
|
A:ASP332
|
3.4
|
15.0
|
1.0
|
P
|
P:8OG5
|
3.5
|
16.0
|
1.0
|
O5'
|
P:8OG5
|
3.8
|
12.1
|
1.0
|
OD2
|
A:ASP330
|
3.9
|
22.0
|
0.5
|
O
|
A:ASP330
|
3.9
|
14.4
|
0.5
|
C5'
|
P:8OG5
|
4.1
|
14.2
|
1.0
|
O
|
A:HOH851
|
4.1
|
19.2
|
1.0
|
O
|
P:HOH101
|
4.2
|
25.0
|
1.0
|
OP2
|
P:8OG5
|
4.2
|
16.6
|
1.0
|
O
|
A:HOH669
|
4.3
|
17.6
|
1.0
|
O11
|
A:GOA514
|
4.3
|
15.1
|
1.0
|
CB
|
A:ASP330
|
4.3
|
16.2
|
0.5
|
O
|
A:HOH632
|
4.4
|
15.1
|
1.0
|
N
|
A:GLY320
|
4.4
|
11.8
|
1.0
|
C
|
A:ASP330
|
4.4
|
14.3
|
0.5
|
O
|
A:ASP330
|
4.5
|
13.7
|
0.5
|
CB
|
A:ASP332
|
4.5
|
12.5
|
1.0
|
CA
|
A:GLY319
|
4.5
|
12.0
|
1.0
|
O
|
A:HOH660
|
4.5
|
26.2
|
1.0
|
CB
|
A:ASP330
|
4.6
|
16.6
|
0.5
|
C
|
A:ASP330
|
4.6
|
14.4
|
0.5
|
O3'
|
P:DA4
|
4.7
|
13.5
|
1.0
|
N
|
A:ASP332
|
5.0
|
13.2
|
1.0
|
O
|
A:HOH773
|
5.0
|
12.1
|
0.5
|
CA
|
A:ASP330
|
5.0
|
15.7
|
0.5
|
|
Manganese binding site 2 out
of 7 in 7kt5
Go back to
Manganese Binding Sites List in 7kt5
Manganese binding site 2 out
of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)
![](/pictures/MN/pdb/kt/7kt5-MN-sphere_02.jpg) Mono view
![](/pictures/MN/pdb/kt/7kt5-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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn502
b:14.9
occ:0.92
|
OD2
|
A:ASP330
|
1.8
|
22.0
|
0.5
|
OP1
|
P:8OG5
|
2.1
|
16.6
|
1.0
|
OD2
|
A:ASP418
|
2.1
|
13.9
|
1.0
|
OD1
|
A:ASP332
|
2.1
|
15.0
|
1.0
|
O
|
A:HOH669
|
2.2
|
17.6
|
1.0
|
OD2
|
A:ASP330
|
2.3
|
13.7
|
0.5
|
O
|
A:HOH773
|
2.5
|
12.1
|
0.5
|
CG
|
A:ASP330
|
2.5
|
17.6
|
0.5
|
OD1
|
A:ASP330
|
2.7
|
14.7
|
0.5
|
CG
|
A:ASP418
|
3.1
|
14.7
|
1.0
|
CG
|
A:ASP332
|
3.1
|
13.3
|
1.0
|
P
|
P:8OG5
|
3.2
|
16.0
|
1.0
|
O3'
|
P:DA4
|
3.3
|
13.5
|
1.0
|
CG
|
A:ASP330
|
3.3
|
15.3
|
0.5
|
MN
|
A:MN501
|
3.3
|
13.8
|
1.0
|
OD2
|
A:ASP332
|
3.5
|
13.5
|
1.0
|
CB
|
A:ASP418
|
3.9
|
13.8
|
1.0
|
CB
|
A:ASP330
|
3.9
|
16.2
|
0.5
|
OD1
|
A:ASP418
|
3.9
|
15.8
|
1.0
|
CB
|
A:ASP330
|
3.9
|
16.6
|
0.5
|
OP2
|
P:8OG5
|
3.9
|
16.6
|
1.0
|
O
|
P:HOH101
|
4.2
|
25.0
|
1.0
|
OD1
|
A:ASP330
|
4.3
|
13.8
|
0.5
|
C5'
|
P:DA4
|
4.3
|
14.9
|
1.0
|
C3'
|
P:DA4
|
4.4
|
14.2
|
1.0
|
O
|
A:VAL331
|
4.4
|
14.3
|
1.0
|
NH2
|
A:ARG416
|
4.4
|
16.9
|
1.0
|
CB
|
A:ASP332
|
4.5
|
12.5
|
1.0
|
O5'
|
P:8OG5
|
4.5
|
12.1
|
1.0
|
C4'
|
P:DA4
|
4.5
|
13.0
|
1.0
|
O2
|
A:GOA514
|
4.5
|
15.3
|
0.9
|
OP1
|
P:DA4
|
4.6
|
16.7
|
1.0
|
C
|
A:VAL331
|
4.8
|
14.0
|
1.0
|
N
|
A:ASP418
|
4.8
|
13.4
|
1.0
|
O
|
A:HOH621
|
4.9
|
15.4
|
1.0
|
C5'
|
P:8OG5
|
4.9
|
14.2
|
1.0
|
CA
|
A:ASP418
|
4.9
|
14.1
|
1.0
|
CA
|
A:ASP332
|
4.9
|
11.9
|
1.0
|
N
|
A:VAL331
|
5.0
|
14.6
|
1.0
|
C
|
A:ASP330
|
5.0
|
14.3
|
0.5
|
CZ3
|
A:TRP434
|
5.0
|
14.5
|
1.0
|
|
Manganese binding site 3 out
of 7 in 7kt5
Go back to
Manganese Binding Sites List in 7kt5
Manganese binding site 3 out
of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)
![](/pictures/MN/pdb/kt/7kt5-MN-sphere_03.jpg) Mono view
![](/pictures/MN/pdb/kt/7kt5-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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn503
b:19.9
occ:0.81
|
OE2
|
A:GLU386
|
2.1
|
26.2
|
1.0
|
O
|
T:HOH205
|
2.2
|
24.0
|
1.0
|
O
|
A:HOH734
|
2.2
|
24.5
|
1.0
|
O
|
A:HOH841
|
2.2
|
26.7
|
1.0
|
NE2
|
A:HIS459
|
2.3
|
21.9
|
1.0
|
OE1
|
A:GLU386
|
2.3
|
23.3
|
1.0
|
CD
|
A:GLU386
|
2.5
|
26.5
|
1.0
|
CD2
|
A:HIS459
|
3.2
|
20.7
|
1.0
|
CE1
|
A:HIS459
|
3.3
|
20.4
|
1.0
|
CG
|
A:GLU386
|
4.0
|
32.1
|
1.0
|
O
|
A:HOH706
|
4.2
|
26.5
|
1.0
|
O
|
A:HOH830
|
4.2
|
42.2
|
1.0
|
OP1
|
T:DC8
|
4.3
|
23.4
|
1.0
|
CG
|
A:HIS459
|
4.3
|
19.6
|
1.0
|
O
|
A:HOH848
|
4.4
|
39.8
|
1.0
|
ND1
|
A:HIS459
|
4.4
|
20.7
|
1.0
|
O
|
A:HOH646
|
4.4
|
21.1
|
1.0
|
OE1
|
A:GLN426
|
4.5
|
23.2
|
1.0
|
C5'
|
T:DC8
|
4.6
|
20.4
|
1.0
|
CB
|
A:GLU386
|
4.9
|
24.6
|
1.0
|
|
Manganese binding site 4 out
of 7 in 7kt5
Go back to
Manganese Binding Sites List in 7kt5
Manganese binding site 4 out
of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)
![](/pictures/MN/pdb/kt/7kt5-MN-sphere_04.jpg) Mono view
![](/pictures/MN/pdb/kt/7kt5-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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn504
b:52.1
occ:0.81
|
O
|
A:HOH843
|
2.2
|
55.7
|
0.7
|
O
|
A:HOH782
|
2.2
|
49.5
|
1.0
|
O
|
A:HOH774
|
2.2
|
59.6
|
1.0
|
NE2
|
A:HIS219
|
2.2
|
45.9
|
1.0
|
CE1
|
A:HIS219
|
3.2
|
47.4
|
1.0
|
CD2
|
A:HIS219
|
3.2
|
43.1
|
1.0
|
ND1
|
A:HIS219
|
4.3
|
44.0
|
1.0
|
CG
|
A:HIS219
|
4.4
|
40.6
|
1.0
|
CB
|
A:GLU218
|
4.7
|
34.9
|
1.0
|
|
Manganese binding site 5 out
of 7 in 7kt5
Go back to
Manganese Binding Sites List in 7kt5
Manganese binding site 5 out
of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)
![](/pictures/MN/pdb/kt/7kt5-MN-sphere_05.jpg) Mono view
![](/pictures/MN/pdb/kt/7kt5-MN-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn505
b:30.1
occ:0.67
|
O
|
D:HOH216
|
1.9
|
36.1
|
0.8
|
O
|
D:HOH217
|
2.1
|
35.0
|
0.8
|
OP3
|
D:DG1
|
2.2
|
29.5
|
1.0
|
O
|
D:HOH207
|
2.2
|
32.1
|
0.8
|
O
|
A:HOH832
|
2.2
|
42.8
|
0.8
|
ND1
|
A:HIS208
|
2.3
|
31.8
|
1.0
|
CE1
|
A:HIS208
|
3.1
|
30.7
|
1.0
|
CG
|
A:HIS208
|
3.4
|
28.3
|
1.0
|
P
|
D:DG1
|
3.4
|
28.5
|
1.0
|
OP1
|
D:DG1
|
3.6
|
30.2
|
1.0
|
O
|
D:HOH213
|
3.7
|
44.4
|
1.0
|
CB
|
A:HIS208
|
3.7
|
25.0
|
1.0
|
O
|
A:HOH866
|
4.1
|
45.4
|
1.0
|
OP2
|
D:DG1
|
4.1
|
30.4
|
1.0
|
O
|
D:HOH206
|
4.2
|
46.2
|
1.0
|
NE2
|
A:HIS208
|
4.3
|
30.2
|
1.0
|
CD2
|
A:HIS208
|
4.4
|
30.4
|
1.0
|
O5'
|
D:DG1
|
4.5
|
24.2
|
1.0
|
CA
|
A:HIS208
|
4.6
|
24.8
|
1.0
|
C5'
|
D:DG1
|
4.8
|
23.3
|
1.0
|
|
Manganese binding site 6 out
of 7 in 7kt5
Go back to
Manganese Binding Sites List in 7kt5
Manganese binding site 6 out
of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)
![](/pictures/MN/pdb/kt/7kt5-MN-sphere_06.jpg) Mono view
![](/pictures/MN/pdb/kt/7kt5-MN-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Mn101
b:38.7
occ:0.58
|
O
|
T:HOH201
|
2.2
|
40.4
|
1.0
|
O
|
T:HOH204
|
2.3
|
49.7
|
0.8
|
O
|
T:HOH202
|
2.4
|
44.5
|
0.9
|
N7
|
T:DG2
|
2.6
|
30.7
|
1.0
|
C8
|
T:DG2
|
3.4
|
29.1
|
1.0
|
O
|
T:HOH203
|
3.6
|
37.6
|
1.0
|
C5
|
T:DG2
|
3.7
|
27.4
|
1.0
|
O6
|
T:DG2
|
4.1
|
27.9
|
1.0
|
OP2
|
T:DG2
|
4.1
|
44.8
|
1.0
|
C6
|
T:DG2
|
4.3
|
26.3
|
1.0
|
O6
|
T:DG3
|
4.4
|
23.7
|
1.0
|
O
|
D:HOH208
|
4.5
|
52.2
|
1.0
|
N9
|
T:DG2
|
4.7
|
28.8
|
1.0
|
C4
|
T:DG2
|
4.8
|
26.6
|
1.0
|
O5'
|
T:DC1
|
4.9
|
42.4
|
1.0
|
C6
|
T:DC1
|
4.9
|
35.5
|
1.0
|
C2'
|
T:DC1
|
4.9
|
42.4
|
1.0
|
C3'
|
T:DC1
|
5.0
|
43.1
|
1.0
|
|
Manganese binding site 7 out
of 7 in 7kt5
Go back to
Manganese Binding Sites List in 7kt5
Manganese binding site 7 out
of 7 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)
![](/pictures/MN/pdb/kt/7kt5-MN-sphere_07.jpg) Mono view
![](/pictures/MN/pdb/kt/7kt5-MN-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn101
b:53.1
occ:0.53
|
N7
|
D:DG1
|
2.3
|
23.2
|
1.0
|
O
|
D:HOH208
|
2.8
|
52.2
|
1.0
|
C8
|
D:DG1
|
3.1
|
23.2
|
1.0
|
C5
|
D:DG1
|
3.5
|
21.5
|
1.0
|
O6
|
D:DG1
|
3.8
|
23.8
|
1.0
|
C6
|
D:DG1
|
4.0
|
21.4
|
1.0
|
N9
|
D:DG1
|
4.4
|
22.2
|
1.0
|
OP2
|
D:DG1
|
4.5
|
30.4
|
1.0
|
N4
|
D:DC2
|
4.5
|
25.4
|
1.0
|
C4
|
D:DG1
|
4.6
|
20.6
|
1.0
|
CG
|
A:ARG175
|
4.8
|
24.7
|
1.0
|
|
Reference:
J.A.Jamsen,
A.Sassa,
D.D.Shock,
W.A.Beard,
S.H.Wilson.
Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) To Be Published.
Page generated: Fri Dec 17 11:05:29 2021
|