Manganese in PDB 6vfb: Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)
Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)
All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min):
2.7.7.7;
Protein crystallography data
The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min), PDB code: 6vfb
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)
|
34.99 /
1.55
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.198,
62.334,
118.756,
90,
90,
90
|
R / Rfree (%)
|
16.7 /
18.2
|
Other elements in 6vfb:
The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)
(pdb code 6vfb). 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-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min), PDB code: 6vfb:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
Manganese binding site 1 out
of 7 in 6vfb
Go back to
Manganese Binding Sites List in 6vfb
Manganese binding site 1 out
of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn505
b:19.3
occ:1.00
|
O2G
|
A:8GT510
|
1.9
|
18.9
|
0.5
|
OD1
|
A:ASP330
|
2.1
|
19.6
|
1.0
|
O21
|
A:PPV512
|
2.1
|
19.2
|
0.5
|
O2B
|
A:8GT510
|
2.1
|
19.1
|
0.5
|
OD2
|
A:ASP332
|
2.2
|
18.4
|
1.0
|
O2A
|
A:8GT510
|
2.2
|
32.7
|
0.5
|
O
|
A:HOH692
|
2.3
|
20.8
|
1.0
|
O32
|
A:PPV512
|
2.4
|
29.7
|
0.5
|
OP1
|
P:8GM5
|
2.6
|
23.1
|
0.5
|
CG
|
A:ASP332
|
3.1
|
18.2
|
1.0
|
CG
|
A:ASP330
|
3.1
|
21.6
|
1.0
|
P1
|
A:PPV512
|
3.1
|
21.0
|
0.5
|
PG
|
A:8GT510
|
3.2
|
20.8
|
0.5
|
O31
|
A:PPV512
|
3.2
|
21.2
|
0.5
|
PB
|
A:8GT510
|
3.3
|
25.1
|
0.5
|
OD1
|
A:ASP332
|
3.5
|
19.0
|
1.0
|
PA
|
A:8GT510
|
3.5
|
37.4
|
0.5
|
OD2
|
A:ASP330
|
3.5
|
24.1
|
1.0
|
MN
|
P:MN101
|
3.5
|
22.9
|
1.0
|
O3B
|
A:8GT510
|
3.6
|
24.6
|
0.5
|
P2
|
A:PPV512
|
3.7
|
25.6
|
0.5
|
O3A
|
A:8GT510
|
3.7
|
28.3
|
0.5
|
P
|
P:8GM5
|
3.8
|
24.5
|
0.5
|
OPP
|
A:PPV512
|
3.8
|
23.6
|
0.5
|
O5'
|
P:8GM5
|
3.9
|
32.8
|
0.5
|
O1G
|
A:8GT510
|
4.0
|
25.7
|
0.5
|
O
|
A:ASP330
|
4.0
|
19.8
|
1.0
|
ND1
|
A:HIS329
|
4.2
|
40.5
|
1.0
|
C5'
|
P:8GM5
|
4.2
|
30.6
|
0.5
|
N
|
A:GLY320
|
4.3
|
17.3
|
1.0
|
O
|
A:HOH618
|
4.3
|
19.6
|
1.0
|
CE1
|
A:HIS329
|
4.3
|
43.1
|
1.0
|
C
|
A:ASP330
|
4.3
|
17.9
|
1.0
|
O3G
|
A:8GT510
|
4.3
|
21.0
|
0.5
|
O
|
A:HOH612
|
4.4
|
29.8
|
1.0
|
O11
|
A:PPV512
|
4.5
|
23.0
|
0.5
|
CB
|
A:ASP330
|
4.5
|
21.4
|
1.0
|
O1A
|
A:8GT510
|
4.5
|
40.5
|
0.5
|
O12
|
A:PPV512
|
4.5
|
35.9
|
0.5
|
CB
|
A:ASP332
|
4.5
|
16.6
|
1.0
|
CA
|
A:GLY319
|
4.5
|
17.9
|
1.0
|
O5'
|
A:8GT510
|
4.6
|
38.4
|
0.5
|
O1B
|
A:8GT510
|
4.7
|
25.3
|
0.5
|
OP2
|
P:8GM5
|
4.7
|
28.8
|
0.5
|
N
|
A:ASP330
|
4.7
|
21.0
|
1.0
|
O
|
P:HOH201
|
4.7
|
29.0
|
1.0
|
O
|
A:HOH775
|
4.7
|
20.9
|
0.5
|
CA
|
A:ASP330
|
4.7
|
18.1
|
1.0
|
O22
|
A:PPV512
|
4.7
|
33.7
|
0.5
|
N
|
A:ASP332
|
4.8
|
16.8
|
1.0
|
N
|
A:VAL331
|
4.9
|
18.7
|
1.0
|
O3'
|
P:DA4
|
4.9
|
27.7
|
0.5
|
C
|
A:GLY319
|
5.0
|
19.6
|
1.0
|
|
Manganese binding site 2 out
of 7 in 6vfb
Go back to
Manganese Binding Sites List in 6vfb
Manganese binding site 2 out
of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn506
b:84.7
occ:0.96
|
NE2
|
A:HIS219
|
2.2
|
55.9
|
1.0
|
CD2
|
A:HIS219
|
3.2
|
52.6
|
1.0
|
CE1
|
A:HIS219
|
3.2
|
52.7
|
1.0
|
CD
|
A:GLU218
|
3.7
|
50.7
|
1.0
|
ND1
|
A:HIS219
|
4.3
|
52.1
|
1.0
|
CG
|
A:HIS219
|
4.3
|
51.2
|
1.0
|
CB
|
A:GLU218
|
4.5
|
42.4
|
1.0
|
CG
|
A:GLU218
|
4.7
|
50.3
|
1.0
|
|
Manganese binding site 3 out
of 7 in 6vfb
Go back to
Manganese Binding Sites List in 6vfb
Manganese binding site 3 out
of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn507
b:58.5
occ:0.55
|
O
|
T:HOH201
|
2.1
|
47.4
|
0.6
|
OE2
|
A:GLU386
|
2.3
|
57.0
|
1.0
|
NE2
|
A:HIS459
|
2.6
|
34.5
|
0.6
|
O
|
A:HOH771
|
2.7
|
33.7
|
0.6
|
CD
|
A:GLU386
|
3.1
|
56.7
|
1.0
|
OE1
|
A:GLU386
|
3.1
|
57.7
|
1.0
|
CD2
|
A:HIS459
|
3.2
|
35.7
|
0.6
|
NE2
|
A:HIS459
|
3.5
|
35.9
|
0.5
|
CE1
|
A:HIS459
|
3.5
|
33.0
|
0.5
|
CE1
|
A:HIS459
|
3.7
|
36.2
|
0.6
|
OP1
|
T:DC8
|
3.8
|
42.6
|
1.0
|
CD2
|
A:HIS459
|
4.2
|
31.7
|
0.5
|
ND1
|
A:HIS459
|
4.2
|
31.1
|
0.5
|
C5'
|
T:DC8
|
4.3
|
35.5
|
1.0
|
O
|
A:HOH667
|
4.4
|
30.8
|
1.0
|
CG
|
A:HIS459
|
4.5
|
27.8
|
0.6
|
CG
|
A:GLU386
|
4.5
|
44.8
|
1.0
|
CG
|
A:HIS459
|
4.7
|
28.7
|
0.5
|
ND1
|
A:HIS459
|
4.7
|
36.8
|
0.6
|
O
|
A:HOH663
|
4.8
|
48.2
|
1.0
|
O5'
|
T:DC8
|
4.9
|
42.0
|
1.0
|
P
|
T:DC8
|
5.0
|
33.4
|
1.0
|
|
Manganese binding site 4 out
of 7 in 6vfb
Go back to
Manganese Binding Sites List in 6vfb
Manganese binding site 4 out
of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Mn101
b:56.3
occ:0.62
|
N7
|
T:DG2
|
2.3
|
30.4
|
0.7
|
O
|
T:HOH210
|
2.4
|
43.6
|
1.0
|
N7
|
T:DG2
|
2.5
|
29.5
|
0.3
|
O
|
T:HOH204
|
2.6
|
47.6
|
1.0
|
C8
|
T:DG2
|
3.1
|
26.9
|
0.7
|
C5
|
T:DG2
|
3.4
|
25.2
|
0.7
|
C8
|
T:DG2
|
3.4
|
26.0
|
0.3
|
C5
|
T:DG2
|
3.5
|
25.2
|
0.3
|
O6
|
T:DG2
|
3.6
|
26.8
|
0.3
|
O6
|
T:DG2
|
3.8
|
26.5
|
0.7
|
C6
|
T:DG2
|
3.9
|
23.8
|
0.3
|
C6
|
T:DG2
|
3.9
|
22.9
|
0.7
|
O
|
T:HOH211
|
4.0
|
39.2
|
1.0
|
N9
|
T:DG2
|
4.3
|
23.0
|
0.7
|
C4
|
T:DG2
|
4.4
|
24.1
|
0.7
|
O6
|
T:DG3
|
4.4
|
23.9
|
1.0
|
OP2
|
T:DG2
|
4.5
|
31.2
|
0.7
|
N9
|
T:DG2
|
4.6
|
25.9
|
0.3
|
C4
|
T:DG2
|
4.6
|
24.6
|
0.3
|
C6
|
T:DC1
|
4.9
|
25.6
|
0.5
|
C2'
|
T:DC1
|
4.9
|
31.5
|
0.5
|
C5
|
T:DC1
|
5.0
|
25.4
|
0.5
|
|
Manganese binding site 5 out
of 7 in 6vfb
Go back to
Manganese Binding Sites List in 6vfb
Manganese binding site 5 out
of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Mn101
b:22.9
occ:1.00
|
OP1
|
P:8GM5
|
1.6
|
23.1
|
0.5
|
OD2
|
A:ASP330
|
1.9
|
24.1
|
1.0
|
OD1
|
A:ASP332
|
2.2
|
19.0
|
1.0
|
OD2
|
A:ASP418
|
2.2
|
21.4
|
1.0
|
O
|
P:HOH201
|
2.2
|
29.0
|
1.0
|
O
|
A:HOH775
|
2.3
|
20.9
|
0.5
|
O2G
|
A:8GT510
|
2.4
|
18.9
|
0.5
|
O3'
|
P:DA4
|
2.4
|
27.7
|
0.5
|
P
|
P:8GM5
|
2.5
|
24.5
|
0.5
|
CG
|
A:ASP330
|
3.0
|
21.6
|
1.0
|
CG
|
A:ASP332
|
3.2
|
18.2
|
1.0
|
CG
|
A:ASP418
|
3.2
|
20.5
|
1.0
|
OD1
|
A:ASP330
|
3.3
|
19.6
|
1.0
|
PG
|
A:8GT510
|
3.5
|
20.8
|
0.5
|
MN
|
A:MN505
|
3.5
|
19.3
|
1.0
|
OD2
|
A:ASP332
|
3.6
|
18.4
|
1.0
|
OP2
|
P:8GM5
|
3.6
|
28.8
|
0.5
|
O5'
|
P:8GM5
|
3.6
|
32.8
|
0.5
|
C3'
|
P:DA4
|
3.6
|
25.2
|
0.5
|
O3G
|
A:8GT510
|
3.8
|
21.0
|
0.5
|
C5'
|
P:8GM5
|
3.9
|
30.6
|
0.5
|
C4'
|
P:DA4
|
3.9
|
20.9
|
0.5
|
CB
|
A:ASP418
|
3.9
|
18.1
|
1.0
|
C5'
|
P:DA4
|
3.9
|
17.4
|
0.5
|
O1G
|
A:8GT510
|
4.0
|
25.7
|
0.5
|
OD1
|
A:ASP418
|
4.2
|
21.7
|
1.0
|
CE1
|
A:HIS329
|
4.2
|
43.1
|
1.0
|
CB
|
A:ASP330
|
4.4
|
21.4
|
1.0
|
CB
|
A:ASP332
|
4.4
|
16.6
|
1.0
|
O5'
|
P:DA4
|
4.5
|
19.1
|
0.5
|
NH2
|
A:ARG416
|
4.5
|
21.3
|
1.0
|
OP1
|
P:DA4
|
4.6
|
22.2
|
0.5
|
OP1
|
P:DA4
|
4.6
|
24.1
|
0.5
|
O2A
|
A:8GT510
|
4.7
|
32.7
|
0.5
|
C2'
|
P:DA4
|
4.8
|
21.5
|
0.5
|
O2B
|
A:8GT510
|
4.8
|
19.1
|
0.5
|
CZ3
|
A:TRP434
|
4.9
|
36.0
|
1.0
|
O31
|
A:PPV512
|
4.9
|
21.2
|
0.5
|
O3B
|
A:8GT510
|
4.9
|
24.6
|
0.5
|
NE2
|
A:HIS329
|
5.0
|
41.4
|
1.0
|
|
Manganese binding site 6 out
of 7 in 6vfb
Go back to
Manganese Binding Sites List in 6vfb
Manganese binding site 6 out
of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Mn102
b:35.2
occ:0.26
|
O3G
|
A:8GT510
|
1.9
|
21.0
|
0.5
|
O3B
|
A:8GT510
|
2.0
|
24.6
|
0.5
|
O31
|
A:PPV512
|
2.4
|
21.2
|
0.5
|
PG
|
A:8GT510
|
2.5
|
20.8
|
0.5
|
OP2
|
P:8GM5
|
2.5
|
28.8
|
0.5
|
O8
|
P:8GM5
|
2.5
|
39.3
|
0.5
|
O1G
|
A:8GT510
|
3.1
|
25.7
|
0.5
|
O5'
|
P:8GM5
|
3.3
|
32.8
|
0.5
|
C4'
|
A:8GT510
|
3.3
|
35.4
|
0.5
|
C5'
|
A:8GT510
|
3.3
|
32.9
|
0.5
|
P
|
P:8GM5
|
3.4
|
24.5
|
0.5
|
O
|
A:HOH605
|
3.5
|
26.1
|
1.0
|
PB
|
A:8GT510
|
3.5
|
25.1
|
0.5
|
C8
|
P:8GM5
|
3.6
|
36.3
|
0.5
|
O3'
|
A:8GT510
|
3.7
|
43.6
|
0.5
|
P1
|
A:PPV512
|
3.7
|
21.0
|
0.5
|
O1B
|
A:8GT510
|
3.9
|
25.3
|
0.5
|
O2G
|
A:8GT510
|
3.9
|
18.9
|
0.5
|
O3A
|
A:8GT510
|
3.9
|
28.3
|
0.5
|
C3'
|
A:8GT510
|
3.9
|
38.8
|
0.5
|
O5'
|
A:8GT510
|
4.1
|
38.4
|
0.5
|
N7
|
P:8GM5
|
4.1
|
36.5
|
0.5
|
O11
|
A:PPV512
|
4.1
|
23.0
|
0.5
|
OP1
|
P:8GM5
|
4.2
|
23.1
|
0.5
|
OPP
|
A:PPV512
|
4.3
|
23.6
|
0.5
|
C3'
|
P:8GM5
|
4.5
|
25.5
|
0.5
|
O2B
|
A:8GT510
|
4.5
|
19.1
|
0.5
|
O4'
|
A:8GT510
|
4.6
|
40.9
|
0.5
|
PA
|
A:8GT510
|
4.6
|
37.4
|
0.5
|
O
|
P:HOH201
|
4.6
|
29.0
|
1.0
|
C5'
|
P:8GM5
|
4.6
|
30.6
|
0.5
|
O22
|
A:PPV512
|
4.6
|
33.7
|
0.5
|
CB
|
A:LYS438
|
4.7
|
33.4
|
1.0
|
O2A
|
A:8GT510
|
4.7
|
32.7
|
0.5
|
O3'
|
P:DA4
|
4.8
|
27.7
|
0.5
|
N9
|
P:8GM5
|
4.8
|
32.2
|
0.5
|
O21
|
A:PPV512
|
4.9
|
19.2
|
0.5
|
P2
|
A:PPV512
|
4.9
|
25.6
|
0.5
|
CE1
|
A:HIS329
|
5.0
|
43.1
|
1.0
|
O4'
|
P:DA4
|
5.0
|
23.7
|
0.5
|
|
Manganese binding site 7 out
of 7 in 6vfb
Go back to
Manganese Binding Sites List in 6vfb
Manganese binding site 7 out
of 7 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn101
b:80.9
occ:0.61
|
N7
|
D:DG1
|
2.5
|
23.1
|
1.0
|
C8
|
D:DG1
|
3.5
|
24.0
|
1.0
|
C5
|
D:DG1
|
3.5
|
20.6
|
1.0
|
O6
|
D:DG1
|
3.5
|
24.1
|
1.0
|
C6
|
D:DG1
|
3.8
|
22.4
|
1.0
|
N4
|
D:DC2
|
4.1
|
26.6
|
1.0
|
O
|
T:HOH210
|
4.1
|
43.6
|
1.0
|
NE
|
A:ARG175
|
4.4
|
28.2
|
0.5
|
C4
|
D:DG1
|
4.6
|
20.4
|
1.0
|
N9
|
D:DG1
|
4.7
|
21.0
|
1.0
|
O
|
A:HOH757
|
4.9
|
33.4
|
0.4
|
C4
|
D:DC2
|
4.9
|
23.5
|
1.0
|
O
|
D:HOH211
|
4.9
|
43.1
|
1.0
|
|
Reference:
J.A.Jamsen,
A.Sassa,
D.D.Shock,
W.A.Beard,
S.H.Wilson.
Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) To Be Published.
Page generated: Sun Oct 6 07:32:12 2024
|