Manganese in PDB 6vf7: Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)
Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)
All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min):
2.7.7.7;
Protein crystallography data
The structure of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vf7
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)
|
35.04 /
1.87
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.159,
68.927,
110.446,
90,
90,
90
|
R / Rfree (%)
|
16.6 /
19.7
|
Other elements in 6vf7:
The structure of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)
(pdb code 6vf7). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the
Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vf7:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 6vf7
Go back to
Manganese Binding Sites List in 6vf7
Manganese binding site 1 out
of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:29.9
occ:0.52
|
O2G
|
A:8DG508
|
2.2
|
27.1
|
1.0
|
O
|
A:HOH674
|
2.2
|
25.1
|
0.7
|
O
|
A:HOH820
|
2.3
|
44.0
|
0.8
|
ND1
|
A:HIS329
|
2.5
|
43.4
|
1.0
|
O
|
A:HOH646
|
2.8
|
25.9
|
0.7
|
CG
|
A:HIS329
|
3.5
|
36.1
|
1.0
|
CE1
|
A:HIS329
|
3.5
|
45.3
|
1.0
|
PG
|
A:8DG508
|
3.5
|
25.5
|
1.0
|
CB
|
A:HIS329
|
3.7
|
26.6
|
1.0
|
O1G
|
A:8DG508
|
3.8
|
27.0
|
1.0
|
O1A
|
A:8DG508
|
4.2
|
25.4
|
1.0
|
O3B
|
A:8DG508
|
4.4
|
22.5
|
1.0
|
O3G
|
A:8DG508
|
4.5
|
26.4
|
1.0
|
NE2
|
A:HIS329
|
4.6
|
39.7
|
1.0
|
CD2
|
A:HIS329
|
4.6
|
37.7
|
1.0
|
O3A
|
A:8DG508
|
4.7
|
23.5
|
1.0
|
PA
|
A:8DG508
|
4.9
|
23.2
|
1.0
|
O
|
A:HOH826
|
5.0
|
41.3
|
1.0
|
|
Manganese binding site 2 out
of 8 in 6vf7
Go back to
Manganese Binding Sites List in 6vf7
Manganese binding site 2 out
of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn502
b:26.9
occ:1.00
|
OD2
|
A:ASP330
|
2.1
|
26.0
|
1.0
|
OD2
|
A:ASP418
|
2.3
|
17.4
|
1.0
|
OD1
|
A:ASP332
|
2.3
|
17.4
|
1.0
|
O
|
P:HOH101
|
2.5
|
21.4
|
1.0
|
O2A
|
A:8DG508
|
2.6
|
17.8
|
1.0
|
O3'
|
P:DA4
|
2.7
|
17.6
|
1.0
|
CG
|
A:ASP330
|
3.1
|
22.0
|
1.0
|
CG
|
A:ASP332
|
3.3
|
18.6
|
1.0
|
CG
|
A:ASP418
|
3.3
|
19.2
|
1.0
|
OD1
|
A:ASP330
|
3.4
|
21.1
|
1.0
|
PA
|
A:8DG508
|
3.5
|
23.2
|
1.0
|
OD2
|
A:ASP332
|
3.7
|
17.4
|
1.0
|
MN
|
A:MN503
|
3.7
|
18.7
|
1.0
|
C3'
|
P:DA4
|
3.8
|
17.1
|
1.0
|
O5'
|
A:8DG508
|
3.8
|
18.9
|
1.0
|
O1A
|
A:8DG508
|
3.9
|
25.4
|
1.0
|
CB
|
A:ASP418
|
4.0
|
20.6
|
1.0
|
C5'
|
P:DA4
|
4.0
|
23.4
|
1.0
|
C4'
|
P:DA4
|
4.0
|
17.4
|
1.0
|
OD1
|
A:ASP418
|
4.3
|
18.7
|
1.0
|
O
|
A:HOH646
|
4.4
|
25.9
|
0.7
|
C5'
|
A:8DG508
|
4.4
|
16.8
|
1.0
|
CB
|
A:ASP330
|
4.5
|
17.0
|
1.0
|
CZ3
|
A:TRP434
|
4.5
|
19.4
|
1.0
|
OP1
|
P:DA4
|
4.5
|
19.5
|
1.0
|
NH2
|
A:ARG416
|
4.5
|
18.6
|
1.0
|
CB
|
A:ASP332
|
4.6
|
15.7
|
1.0
|
O5'
|
P:DA4
|
4.7
|
21.6
|
1.0
|
O1G
|
A:8DG508
|
4.8
|
27.0
|
1.0
|
O3A
|
A:8DG508
|
5.0
|
23.5
|
1.0
|
|
Manganese binding site 3 out
of 8 in 6vf7
Go back to
Manganese Binding Sites List in 6vf7
Manganese binding site 3 out
of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn503
b:18.7
occ:1.00
|
O2A
|
A:8DG508
|
2.0
|
17.8
|
1.0
|
OD1
|
A:ASP330
|
2.1
|
21.1
|
1.0
|
O2B
|
A:8DG508
|
2.1
|
18.2
|
1.0
|
OD2
|
A:ASP332
|
2.1
|
17.4
|
1.0
|
O
|
A:HOH635
|
2.2
|
21.7
|
1.0
|
O1G
|
A:8DG508
|
2.2
|
27.0
|
1.0
|
CG
|
A:ASP332
|
3.2
|
18.6
|
1.0
|
CG
|
A:ASP330
|
3.2
|
22.0
|
1.0
|
PB
|
A:8DG508
|
3.2
|
22.0
|
1.0
|
PA
|
A:8DG508
|
3.3
|
23.2
|
1.0
|
PG
|
A:8DG508
|
3.5
|
25.5
|
1.0
|
OD1
|
A:ASP332
|
3.5
|
17.4
|
1.0
|
O3A
|
A:8DG508
|
3.6
|
23.5
|
1.0
|
OD2
|
A:ASP330
|
3.6
|
26.0
|
1.0
|
O3B
|
A:8DG508
|
3.7
|
22.5
|
1.0
|
MN
|
A:MN502
|
3.7
|
26.9
|
1.0
|
O
|
A:ASP330
|
3.9
|
20.7
|
1.0
|
O3G
|
A:8DG508
|
4.1
|
26.4
|
1.0
|
O
|
A:HOH646
|
4.1
|
25.9
|
0.7
|
O
|
A:HOH689
|
4.2
|
19.6
|
1.0
|
C
|
A:ASP330
|
4.2
|
22.6
|
1.0
|
O
|
A:HOH686
|
4.3
|
24.6
|
1.0
|
N
|
A:GLY320
|
4.3
|
18.4
|
1.0
|
O5'
|
A:8DG508
|
4.3
|
18.9
|
1.0
|
C5'
|
A:8DG508
|
4.4
|
16.8
|
1.0
|
O1A
|
A:8DG508
|
4.4
|
25.4
|
1.0
|
CB
|
A:ASP330
|
4.5
|
17.0
|
1.0
|
CB
|
A:ASP332
|
4.5
|
15.7
|
1.0
|
CA
|
A:GLY319
|
4.5
|
21.4
|
1.0
|
O1B
|
A:8DG508
|
4.6
|
21.8
|
1.0
|
N
|
A:ASP330
|
4.6
|
19.5
|
1.0
|
O2G
|
A:8DG508
|
4.7
|
27.1
|
1.0
|
CA
|
A:ASP330
|
4.7
|
18.1
|
1.0
|
N
|
A:ASP332
|
4.8
|
18.9
|
1.0
|
N
|
A:VAL331
|
4.8
|
17.8
|
1.0
|
O
|
P:HOH101
|
4.9
|
21.4
|
1.0
|
C
|
A:VAL331
|
5.0
|
19.6
|
1.0
|
|
Manganese binding site 4 out
of 8 in 6vf7
Go back to
Manganese Binding Sites List in 6vf7
Manganese binding site 4 out
of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn504
b:16.6
occ:0.57
|
OE2
|
A:GLU386
|
2.1
|
31.5
|
1.0
|
O
|
A:HOH734
|
2.1
|
23.2
|
0.9
|
O
|
A:HOH810
|
2.2
|
24.9
|
0.9
|
O
|
T:HOH202
|
2.2
|
23.7
|
1.0
|
OE1
|
A:GLU386
|
2.3
|
27.5
|
1.0
|
NE2
|
A:HIS459
|
2.4
|
30.4
|
1.0
|
CD
|
A:GLU386
|
2.5
|
29.4
|
1.0
|
CD2
|
A:HIS459
|
3.1
|
35.2
|
1.0
|
CE1
|
A:HIS459
|
3.5
|
28.9
|
1.0
|
CG
|
A:GLU386
|
4.0
|
36.9
|
1.0
|
O
|
A:HOH655
|
4.1
|
29.2
|
1.0
|
OP1
|
T:DC8
|
4.2
|
29.6
|
1.0
|
O
|
A:HOH812
|
4.2
|
41.9
|
1.0
|
CG
|
A:HIS459
|
4.4
|
30.5
|
1.0
|
O
|
A:HOH712
|
4.4
|
22.2
|
1.0
|
OE1
|
A:GLN426
|
4.5
|
23.9
|
1.0
|
ND1
|
A:HIS459
|
4.5
|
29.8
|
1.0
|
C5'
|
T:DC8
|
4.5
|
19.3
|
1.0
|
CB
|
A:GLU386
|
4.9
|
25.9
|
1.0
|
|
Manganese binding site 5 out
of 8 in 6vf7
Go back to
Manganese Binding Sites List in 6vf7
Manganese binding site 5 out
of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn505
b:33.4
occ:0.60
|
O
|
A:HOH790
|
1.9
|
43.9
|
1.0
|
O
|
D:HOH208
|
2.0
|
39.2
|
1.0
|
O
|
A:HOH805
|
2.1
|
46.1
|
0.7
|
OP3
|
D:DG1
|
2.2
|
35.1
|
1.0
|
ND1
|
A:HIS208
|
2.2
|
35.1
|
1.0
|
O
|
D:HOH202
|
2.4
|
31.6
|
0.4
|
CE1
|
A:HIS208
|
3.0
|
30.3
|
1.0
|
CG
|
A:HIS208
|
3.3
|
30.8
|
1.0
|
P
|
D:DG1
|
3.4
|
34.1
|
1.0
|
OP1
|
D:DG1
|
3.5
|
28.2
|
1.0
|
CB
|
A:HIS208
|
3.7
|
28.0
|
1.0
|
O
|
D:HOH209
|
4.0
|
42.5
|
1.0
|
OP2
|
D:DG1
|
4.1
|
31.4
|
1.0
|
NE2
|
A:HIS208
|
4.2
|
31.6
|
1.0
|
O
|
D:HOH202
|
4.2
|
35.4
|
0.6
|
CD2
|
A:HIS208
|
4.3
|
33.6
|
1.0
|
O
|
A:HOH837
|
4.4
|
48.1
|
1.0
|
O5'
|
D:DG1
|
4.6
|
30.4
|
1.0
|
CA
|
A:HIS208
|
4.6
|
26.2
|
1.0
|
C5'
|
D:DG1
|
4.8
|
27.6
|
1.0
|
|
Manganese binding site 6 out
of 8 in 6vf7
Go back to
Manganese Binding Sites List in 6vf7
Manganese binding site 6 out
of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn506
b:47.6
occ:0.69
|
O
|
A:HOH641
|
2.1
|
54.4
|
1.0
|
NE2
|
A:HIS219
|
2.3
|
58.6
|
1.0
|
CE1
|
A:HIS219
|
3.2
|
55.6
|
1.0
|
CD2
|
A:HIS219
|
3.3
|
43.1
|
1.0
|
ND1
|
A:HIS219
|
4.3
|
48.1
|
1.0
|
CG
|
A:HIS219
|
4.4
|
45.9
|
1.0
|
CB
|
A:GLU218
|
4.7
|
46.1
|
1.0
|
|
Manganese binding site 7 out
of 8 in 6vf7
Go back to
Manganese Binding Sites List in 6vf7
Manganese binding site 7 out
of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 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-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Mn101
b:54.3
occ:0.71
|
O
|
T:HOH212
|
2.3
|
48.9
|
1.0
|
O
|
T:HOH203
|
2.4
|
59.0
|
1.0
|
N7
|
T:DG2
|
2.6
|
38.8
|
1.0
|
C8
|
T:DG2
|
3.5
|
36.6
|
1.0
|
C5
|
T:DG2
|
3.7
|
32.5
|
1.0
|
O6
|
T:DG2
|
3.9
|
31.8
|
1.0
|
O
|
T:HOH201
|
3.9
|
43.5
|
1.0
|
C6
|
T:DG2
|
4.2
|
31.2
|
1.0
|
OP2
|
T:DG2
|
4.2
|
55.5
|
1.0
|
O6
|
T:DG3
|
4.3
|
29.5
|
1.0
|
N9
|
T:DG2
|
4.8
|
35.2
|
1.0
|
O5'
|
T:DC1
|
4.8
|
52.3
|
1.0
|
C4
|
T:DG2
|
4.9
|
30.7
|
1.0
|
C3'
|
T:DC1
|
4.9
|
57.2
|
1.0
|
C6
|
T:DC1
|
5.0
|
56.5
|
1.0
|
|
Manganese binding site 8 out
of 8 in 6vf7
Go back to
Manganese Binding Sites List in 6vf7
Manganese binding site 8 out
of 8 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn101
b:89.8
occ:0.94
|
O
|
D:HOH212
|
2.4
|
55.7
|
1.0
|
N7
|
D:DG1
|
2.5
|
30.3
|
1.0
|
O
|
D:HOH211
|
2.5
|
51.3
|
1.0
|
C8
|
D:DG1
|
3.3
|
28.9
|
1.0
|
C5
|
D:DG1
|
3.6
|
26.0
|
1.0
|
O6
|
D:DG1
|
3.9
|
28.2
|
1.0
|
C6
|
D:DG1
|
4.2
|
27.2
|
1.0
|
OP2
|
D:DG1
|
4.5
|
31.4
|
1.0
|
CG
|
A:ARG175
|
4.5
|
30.2
|
1.0
|
N9
|
D:DG1
|
4.6
|
31.1
|
1.0
|
CD
|
A:ARG175
|
4.7
|
43.4
|
1.0
|
C4
|
D:DG1
|
4.7
|
27.4
|
1.0
|
O
|
A:HOH809
|
4.8
|
29.1
|
1.0
|
N4
|
D:DC2
|
4.9
|
29.5
|
1.0
|
|
Reference:
J.A.Jamsen,
A.Sassa,
W.A.Beard,
S.H.Wilson.
Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) To Be Published.
Page generated: Sun Oct 6 07:32:12 2024
|