Manganese in PDB 6vfa: Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min)
Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min)
All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min):
2.7.7.7;
Protein crystallography data
The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vfa
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)
|
34.96 /
1.76
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.079,
62.215,
118.925,
90,
90,
90
|
R / Rfree (%)
|
17.5 /
20.3
|
Other elements in 6vfa:
The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct 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-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min)
(pdb code 6vfa). 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-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vfa:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 6vfa
Go back to
Manganese Binding Sites List in 6vfa
Manganese binding site 1 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct 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-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:19.4
occ:1.00
|
OD2
|
A:ASP330
|
2.1
|
21.4
|
1.0
|
OD1
|
A:ASP332
|
2.1
|
17.9
|
1.0
|
OD2
|
A:ASP418
|
2.2
|
19.5
|
1.0
|
O
|
P:HOH106
|
2.3
|
19.9
|
1.0
|
O
|
A:HOH785
|
2.3
|
21.5
|
1.0
|
O1G
|
A:8GT508
|
2.3
|
17.8
|
1.0
|
CG
|
A:ASP330
|
3.1
|
18.4
|
1.0
|
CG
|
A:ASP332
|
3.2
|
20.5
|
1.0
|
CG
|
A:ASP418
|
3.3
|
20.6
|
1.0
|
PG
|
A:8GT508
|
3.4
|
21.6
|
1.0
|
OD1
|
A:ASP330
|
3.4
|
19.0
|
1.0
|
MN
|
A:MN502
|
3.6
|
18.4
|
1.0
|
OD2
|
A:ASP332
|
3.6
|
18.8
|
1.0
|
O2G
|
A:8GT508
|
3.7
|
24.1
|
1.0
|
CB
|
A:ASP418
|
3.9
|
16.6
|
1.0
|
O3G
|
A:8GT508
|
4.0
|
23.6
|
1.0
|
OD1
|
A:ASP418
|
4.2
|
18.6
|
1.0
|
CE1
|
A:HIS329
|
4.2
|
25.4
|
1.0
|
CB
|
A:ASP332
|
4.4
|
15.6
|
1.0
|
CB
|
A:ASP330
|
4.4
|
15.8
|
1.0
|
OP1
|
P:DA4
|
4.5
|
21.4
|
1.0
|
NH2
|
A:ARG416
|
4.6
|
18.1
|
1.0
|
O3B
|
A:8GT508
|
4.8
|
21.5
|
1.0
|
NE2
|
A:HIS329
|
4.8
|
27.3
|
1.0
|
CZ3
|
A:TRP434
|
4.9
|
30.7
|
1.0
|
|
Manganese binding site 2 out
of 8 in 6vfa
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Manganese Binding Sites List in 6vfa
Manganese binding site 2 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct 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-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn502
b:18.4
occ:1.00
|
O1G
|
A:8GT508
|
2.1
|
17.8
|
1.0
|
O2B
|
A:8GT508
|
2.1
|
17.4
|
1.0
|
OD1
|
A:ASP330
|
2.1
|
19.0
|
1.0
|
OD2
|
A:ASP332
|
2.1
|
18.8
|
1.0
|
O
|
A:HOH669
|
2.3
|
17.7
|
1.0
|
O2A
|
A:8GT508
|
2.4
|
28.2
|
1.0
|
CG
|
A:ASP332
|
3.1
|
20.5
|
1.0
|
CG
|
A:ASP330
|
3.1
|
18.4
|
1.0
|
PB
|
A:8GT508
|
3.2
|
20.7
|
1.0
|
PG
|
A:8GT508
|
3.2
|
21.6
|
1.0
|
O3B
|
A:8GT508
|
3.4
|
21.5
|
1.0
|
OD1
|
A:ASP332
|
3.4
|
17.9
|
1.0
|
OD2
|
A:ASP330
|
3.5
|
21.4
|
1.0
|
MN
|
A:MN501
|
3.6
|
19.4
|
1.0
|
PA
|
A:8GT508
|
3.7
|
31.9
|
1.0
|
O3A
|
A:8GT508
|
3.8
|
25.2
|
1.0
|
O3G
|
A:8GT508
|
3.9
|
23.6
|
1.0
|
O
|
A:ASP330
|
4.1
|
19.2
|
1.0
|
ND1
|
A:HIS329
|
4.2
|
25.6
|
1.0
|
CE1
|
A:HIS329
|
4.2
|
25.4
|
1.0
|
O
|
A:HOH645
|
4.3
|
18.8
|
1.0
|
N
|
A:GLY320
|
4.3
|
19.7
|
1.0
|
C
|
A:ASP330
|
4.3
|
18.7
|
1.0
|
O
|
A:HOH777
|
4.3
|
23.6
|
1.0
|
CB
|
A:ASP332
|
4.5
|
15.6
|
1.0
|
O2G
|
A:8GT508
|
4.5
|
24.1
|
1.0
|
CB
|
A:ASP330
|
4.5
|
15.8
|
1.0
|
CA
|
A:GLY319
|
4.5
|
20.3
|
1.0
|
O1B
|
A:8GT508
|
4.5
|
21.8
|
1.0
|
O1A
|
A:8GT508
|
4.6
|
40.2
|
1.0
|
N
|
A:ASP330
|
4.6
|
18.7
|
1.0
|
CA
|
A:ASP330
|
4.7
|
17.4
|
1.0
|
O5'
|
A:8GT508
|
4.8
|
44.6
|
1.0
|
N
|
A:ASP332
|
4.8
|
15.7
|
1.0
|
N
|
A:VAL331
|
4.9
|
18.3
|
1.0
|
O
|
A:HOH785
|
4.9
|
21.5
|
1.0
|
O
|
P:HOH106
|
4.9
|
19.9
|
1.0
|
C
|
A:GLY319
|
5.0
|
17.9
|
1.0
|
|
Manganese binding site 3 out
of 8 in 6vfa
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Manganese Binding Sites List in 6vfa
Manganese binding site 3 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct 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-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn503
b:37.4
occ:0.62
|
O
|
A:HOH816
|
1.9
|
37.3
|
0.8
|
O
|
A:HOH742
|
2.0
|
38.9
|
0.8
|
NE2
|
A:HIS152
|
2.1
|
54.5
|
1.0
|
CE1
|
A:HIS152
|
2.9
|
54.4
|
1.0
|
O
|
A:HOH616
|
3.2
|
51.3
|
1.0
|
CD2
|
A:HIS152
|
3.2
|
52.2
|
1.0
|
ND1
|
A:HIS152
|
4.1
|
54.0
|
1.0
|
CG
|
A:HIS152
|
4.3
|
50.5
|
1.0
|
O
|
A:PRO190
|
4.4
|
34.3
|
1.0
|
O
|
A:HOH630
|
4.4
|
29.6
|
1.0
|
O
|
A:THR150
|
4.5
|
27.3
|
1.0
|
|
Manganese binding site 4 out
of 8 in 6vfa
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Manganese Binding Sites List in 6vfa
Manganese binding site 4 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct 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-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn504
b:31.2
occ:0.50
|
O
|
D:HOH212
|
2.0
|
38.3
|
1.0
|
OP3
|
D:DG1
|
2.1
|
35.9
|
1.0
|
O
|
D:HOH215
|
2.2
|
44.4
|
1.0
|
O
|
A:HOH795
|
2.3
|
45.6
|
1.0
|
ND1
|
A:HIS208
|
2.3
|
32.6
|
1.0
|
CE1
|
A:HIS208
|
3.2
|
33.9
|
1.0
|
CG
|
A:HIS208
|
3.3
|
31.5
|
1.0
|
P
|
D:DG1
|
3.4
|
30.4
|
1.0
|
OP1
|
D:DG1
|
3.7
|
28.2
|
1.0
|
CB
|
A:HIS208
|
3.7
|
27.9
|
1.0
|
O
|
D:HOH210
|
4.0
|
40.1
|
1.0
|
OP2
|
D:DG1
|
4.1
|
28.4
|
1.0
|
O
|
D:HOH205
|
4.1
|
43.6
|
1.0
|
NE2
|
A:HIS208
|
4.3
|
32.8
|
1.0
|
CD2
|
A:HIS208
|
4.4
|
32.9
|
1.0
|
O5'
|
D:DG1
|
4.5
|
25.8
|
1.0
|
CA
|
A:HIS208
|
4.7
|
28.4
|
1.0
|
C5'
|
D:DG1
|
4.8
|
25.8
|
1.0
|
|
Manganese binding site 5 out
of 8 in 6vfa
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Manganese Binding Sites List in 6vfa
Manganese binding site 5 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct 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-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn505
b:83.1
occ:1.00
|
NE2
|
A:HIS219
|
2.3
|
52.7
|
1.0
|
O
|
A:HOH787
|
2.4
|
50.2
|
1.0
|
OE1
|
A:GLU218
|
3.0
|
62.2
|
1.0
|
CE1
|
A:HIS219
|
3.1
|
53.5
|
1.0
|
CD2
|
A:HIS219
|
3.4
|
52.1
|
1.0
|
CD
|
A:GLU218
|
4.1
|
59.8
|
1.0
|
ND1
|
A:HIS219
|
4.3
|
53.8
|
1.0
|
CG
|
A:HIS219
|
4.4
|
52.7
|
1.0
|
CB
|
A:GLU218
|
4.7
|
47.3
|
1.0
|
OE2
|
A:GLU218
|
4.7
|
60.6
|
1.0
|
CG
|
A:GLU218
|
5.0
|
54.0
|
1.0
|
|
Manganese binding site 6 out
of 8 in 6vfa
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Manganese Binding Sites List in 6vfa
Manganese binding site 6 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct 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-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn506
b:36.9
occ:0.55
|
O
|
A:HOH809
|
2.0
|
42.3
|
0.8
|
O
|
T:HOH201
|
2.2
|
42.2
|
1.0
|
OE2
|
A:GLU386
|
2.3
|
42.3
|
1.0
|
O
|
A:HOH783
|
2.3
|
39.6
|
0.9
|
NE2
|
A:HIS459
|
2.5
|
43.9
|
1.0
|
CD
|
A:GLU386
|
3.0
|
42.6
|
1.0
|
OE1
|
A:GLU386
|
3.0
|
45.3
|
1.0
|
CD2
|
A:HIS459
|
3.1
|
50.2
|
1.0
|
CE1
|
A:HIS459
|
3.7
|
44.0
|
1.0
|
OP1
|
T:DC8
|
4.1
|
37.9
|
1.0
|
O
|
A:HOH684
|
4.3
|
31.2
|
1.0
|
CG
|
A:HIS459
|
4.4
|
39.6
|
1.0
|
C5'
|
T:DC8
|
4.4
|
32.6
|
1.0
|
CG
|
A:GLU386
|
4.5
|
38.5
|
1.0
|
O
|
A:HOH723
|
4.5
|
41.2
|
1.0
|
OE1
|
A:GLN426
|
4.6
|
30.4
|
1.0
|
ND1
|
A:HIS459
|
4.6
|
43.1
|
1.0
|
O
|
A:HOH789
|
4.9
|
45.1
|
1.0
|
O5'
|
T:DC8
|
5.0
|
33.9
|
1.0
|
|
Manganese binding site 7 out
of 8 in 6vfa
Go back to
Manganese Binding Sites List in 6vfa
Manganese binding site 7 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct 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-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Mn101
b:55.5
occ:0.79
|
O
|
T:HOH226
|
2.1
|
55.0
|
1.0
|
N7
|
T:DG2
|
2.3
|
30.0
|
1.0
|
O
|
T:HOH203
|
2.3
|
36.8
|
0.9
|
O
|
T:HOH210
|
2.6
|
49.5
|
1.0
|
C8
|
T:DG2
|
3.2
|
26.9
|
1.0
|
C5
|
T:DG2
|
3.4
|
25.4
|
1.0
|
O6
|
T:DG2
|
3.7
|
26.1
|
1.0
|
C6
|
T:DG2
|
3.9
|
24.4
|
1.0
|
O
|
T:HOH215
|
4.0
|
48.4
|
1.0
|
O6
|
T:DG3
|
4.3
|
27.6
|
1.0
|
N9
|
T:DG2
|
4.4
|
25.6
|
1.0
|
C4
|
T:DG2
|
4.5
|
23.2
|
1.0
|
OP2
|
T:DG2
|
4.8
|
45.1
|
1.0
|
|
Manganese binding site 8 out
of 8 in 6vfa
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Manganese Binding Sites List in 6vfa
Manganese binding site 8 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct 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-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn101
b:84.6
occ:0.98
|
N7
|
D:DG1
|
2.2
|
22.2
|
1.0
|
O
|
D:HOH217
|
2.5
|
40.7
|
1.0
|
O
|
D:HOH201
|
3.0
|
44.7
|
1.0
|
C8
|
D:DG1
|
3.1
|
22.4
|
1.0
|
C5
|
D:DG1
|
3.2
|
22.6
|
1.0
|
O6
|
D:DG1
|
3.5
|
22.5
|
1.0
|
C6
|
D:DG1
|
3.8
|
22.8
|
1.0
|
N4
|
D:DC2
|
4.2
|
23.7
|
1.0
|
N9
|
D:DG1
|
4.3
|
22.5
|
1.0
|
C4
|
D:DG1
|
4.4
|
20.3
|
1.0
|
O
|
D:HOH208
|
4.4
|
42.8
|
1.0
|
O
|
T:HOH203
|
4.6
|
36.8
|
0.9
|
OP2
|
D:DG1
|
4.8
|
28.4
|
1.0
|
CG
|
A:ARG175
|
4.8
|
24.8
|
1.0
|
O
|
A:HOH804
|
4.8
|
32.5
|
1.0
|
C4
|
D:DC2
|
4.9
|
24.8
|
1.0
|
|
Reference:
J.A.Jamsen,
A.Sassa,
D.D.Shock,
W.A.Beard,
S.H.Wilson.
Dna Polymerase Mu, 8-Oxorgtp:Ct Ground State Ternary Complex, 50 Mm MN2+ (15 Min) To Be Published.
Page generated: Sun Oct 6 07:32:12 2024
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