Manganese in PDB 6vfc: Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min)
Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min)
All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min):
2.7.7.7;
Protein crystallography data
The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min), PDB code: 6vfc
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)
|
33.55 /
1.59
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.333,
62.44,
119.336,
90,
90,
90
|
R / Rfree (%)
|
17.2 /
19.2
|
Other elements in 6vfc:
The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min) also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min)
(pdb code 6vfc). 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 Product State Ternary Complex, 50 Mm MN2+ (2160 Min), PDB code: 6vfc:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 6vfc
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Manganese Binding Sites List in 6vfc
Manganese binding site 1 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 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 Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:20.5
occ:1.00
|
OD1
|
A:ASP330
|
2.0
|
21.8
|
0.5
|
O
|
A:HOH602
|
2.1
|
28.9
|
1.0
|
O3
|
A:PO4507
|
2.1
|
16.6
|
0.8
|
OD1
|
A:ASP330
|
2.2
|
20.8
|
0.6
|
OD2
|
A:ASP332
|
2.2
|
17.8
|
1.0
|
O
|
A:HOH620
|
2.3
|
18.5
|
1.0
|
OP1
|
P:8GM5
|
2.6
|
22.4
|
0.8
|
CG
|
A:ASP330
|
2.7
|
19.8
|
0.5
|
OD2
|
A:ASP330
|
2.9
|
23.4
|
0.5
|
CG
|
A:ASP332
|
3.1
|
18.6
|
1.0
|
CG
|
A:ASP330
|
3.2
|
20.2
|
0.6
|
P
|
A:PO4507
|
3.2
|
30.2
|
0.8
|
O1
|
A:PO4507
|
3.4
|
33.0
|
0.8
|
OD1
|
A:ASP332
|
3.4
|
19.7
|
1.0
|
OD2
|
A:ASP330
|
3.4
|
24.4
|
0.6
|
MN
|
P:MN101
|
3.5
|
20.6
|
0.8
|
P
|
P:8GM5
|
3.6
|
22.5
|
0.8
|
O5'
|
P:8GM5
|
3.8
|
23.1
|
0.8
|
O4
|
A:PO4507
|
3.8
|
38.1
|
0.8
|
O
|
A:HOH604
|
3.8
|
49.6
|
1.0
|
O
|
A:ASP330
|
3.8
|
13.9
|
0.5
|
O
|
A:HOH656
|
4.0
|
41.0
|
1.0
|
C5'
|
P:8GM5
|
4.1
|
23.8
|
0.8
|
CE1
|
A:HIS329
|
4.1
|
28.5
|
0.6
|
ND1
|
A:HIS329
|
4.1
|
27.4
|
0.6
|
CB
|
A:ASP330
|
4.2
|
17.4
|
0.5
|
O
|
P:HOH201
|
4.2
|
21.6
|
0.5
|
C
|
A:ASP330
|
4.3
|
13.9
|
0.5
|
O
|
A:HOH613
|
4.3
|
17.1
|
1.0
|
N
|
A:GLY320
|
4.3
|
18.6
|
1.0
|
OP2
|
P:8GM5
|
4.4
|
21.9
|
0.8
|
O
|
A:ASP330
|
4.4
|
14.2
|
0.6
|
O
|
A:HOH601
|
4.4
|
22.9
|
1.0
|
O2
|
A:PO4507
|
4.4
|
24.9
|
0.8
|
CB
|
A:ASP332
|
4.4
|
14.1
|
1.0
|
CA
|
A:GLY319
|
4.5
|
17.7
|
1.0
|
C
|
A:ASP330
|
4.5
|
14.1
|
0.6
|
CB
|
A:ASP330
|
4.5
|
16.1
|
0.6
|
N
|
A:ASP330
|
4.8
|
16.9
|
0.6
|
CA
|
A:ASP330
|
4.8
|
16.0
|
0.5
|
O3'
|
P:DA4
|
4.8
|
24.6
|
1.0
|
CA
|
A:ASP330
|
4.9
|
15.4
|
0.6
|
N
|
A:ASP332
|
4.9
|
14.1
|
1.0
|
N
|
A:VAL331
|
4.9
|
17.1
|
1.0
|
|
Manganese binding site 2 out
of 8 in 6vfc
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Manganese Binding Sites List in 6vfc
Manganese binding site 2 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 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 Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn502
b:41.7
occ:0.81
|
O
|
A:HOH834
|
2.1
|
38.8
|
0.7
|
O
|
A:HOH797
|
2.2
|
37.7
|
0.7
|
O
|
A:HOH798
|
2.2
|
40.0
|
0.8
|
NE2
|
A:HIS152
|
2.4
|
49.6
|
1.0
|
CD2
|
A:HIS152
|
3.2
|
48.9
|
1.0
|
CE1
|
A:HIS152
|
3.4
|
51.4
|
1.0
|
O
|
A:HOH670
|
4.4
|
31.5
|
1.0
|
CG
|
A:HIS152
|
4.4
|
46.5
|
1.0
|
O
|
A:HOH816
|
4.5
|
43.0
|
1.0
|
O
|
A:PRO190
|
4.5
|
33.3
|
1.0
|
ND1
|
A:HIS152
|
4.5
|
50.4
|
1.0
|
O
|
A:THR150
|
4.6
|
26.7
|
1.0
|
|
Manganese binding site 3 out
of 8 in 6vfc
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Manganese Binding Sites List in 6vfc
Manganese binding site 3 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 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 Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn503
b:41.2
occ:0.66
|
OP3
|
D:DG1
|
2.2
|
35.2
|
1.0
|
O
|
D:HOH217
|
2.3
|
42.5
|
0.9
|
O
|
D:HOH218
|
2.4
|
36.5
|
0.7
|
ND1
|
A:HIS208
|
2.5
|
31.3
|
1.0
|
O
|
D:HOH209
|
2.5
|
35.7
|
0.9
|
CE1
|
A:HIS208
|
3.4
|
32.7
|
1.0
|
P
|
D:DG1
|
3.4
|
28.8
|
1.0
|
CG
|
A:HIS208
|
3.4
|
28.1
|
1.0
|
O
|
D:HOH214
|
3.5
|
42.5
|
1.0
|
CB
|
A:HIS208
|
3.7
|
25.1
|
1.0
|
OP1
|
D:DG1
|
3.7
|
28.6
|
1.0
|
OP2
|
D:DG1
|
4.1
|
27.3
|
1.0
|
NE2
|
A:HIS208
|
4.4
|
30.5
|
1.0
|
CD2
|
A:HIS208
|
4.5
|
30.7
|
1.0
|
O5'
|
D:DG1
|
4.6
|
26.8
|
1.0
|
CA
|
A:HIS208
|
4.6
|
24.4
|
1.0
|
C5'
|
D:DG1
|
5.0
|
25.1
|
1.0
|
|
Manganese binding site 4 out
of 8 in 6vfc
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Manganese Binding Sites List in 6vfc
Manganese binding site 4 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 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 Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn504
b:56.6
occ:0.80
|
O
|
A:HOH737
|
1.9
|
49.2
|
0.7
|
O
|
A:HOH603
|
2.1
|
48.9
|
0.8
|
O
|
A:HOH826
|
2.3
|
43.0
|
0.7
|
NE2
|
A:HIS219
|
2.3
|
47.6
|
1.0
|
OE2
|
A:GLU215
|
2.9
|
66.5
|
1.0
|
CD2
|
A:HIS219
|
3.1
|
46.6
|
1.0
|
CE1
|
A:HIS219
|
3.4
|
49.4
|
1.0
|
OE1
|
A:GLU215
|
3.5
|
67.2
|
1.0
|
CD
|
A:GLU215
|
3.6
|
61.0
|
1.0
|
OE1
|
A:GLU218
|
3.7
|
69.0
|
1.0
|
OE2
|
A:GLU218
|
3.8
|
71.0
|
1.0
|
CD
|
A:GLU218
|
3.9
|
68.0
|
1.0
|
CG
|
A:HIS219
|
4.4
|
45.3
|
1.0
|
ND1
|
A:HIS219
|
4.4
|
48.5
|
1.0
|
CG
|
A:GLU218
|
5.0
|
58.1
|
1.0
|
|
Manganese binding site 5 out
of 8 in 6vfc
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Manganese Binding Sites List in 6vfc
Manganese binding site 5 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 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 Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn505
b:25.8
occ:0.67
|
O
|
A:HOH802
|
2.0
|
34.6
|
1.0
|
O
|
T:HOH204
|
2.2
|
31.4
|
1.0
|
OE2
|
A:GLU386
|
2.2
|
31.8
|
1.0
|
O
|
A:HOH757
|
2.3
|
38.3
|
1.0
|
NE2
|
A:HIS459
|
2.3
|
39.1
|
1.0
|
OE1
|
A:GLU386
|
2.5
|
41.4
|
1.0
|
CD
|
A:GLU386
|
2.7
|
36.4
|
1.0
|
CD2
|
A:HIS459
|
3.2
|
42.3
|
1.0
|
CE1
|
A:HIS459
|
3.3
|
40.5
|
1.0
|
O
|
A:HOH734
|
4.2
|
29.4
|
1.0
|
OP1
|
T:DC8
|
4.2
|
26.0
|
1.0
|
CG
|
A:GLU386
|
4.3
|
39.2
|
1.0
|
O
|
A:HOH638
|
4.4
|
24.8
|
1.0
|
CG
|
A:HIS459
|
4.4
|
35.2
|
1.0
|
ND1
|
A:HIS459
|
4.4
|
38.7
|
1.0
|
C5'
|
T:DC8
|
4.5
|
20.7
|
1.0
|
OE1
|
A:GLN426
|
4.6
|
26.8
|
1.0
|
|
Manganese binding site 6 out
of 8 in 6vfc
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Manganese Binding Sites List in 6vfc
Manganese binding site 6 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 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 Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Mn101
b:56.7
occ:0.75
|
N7
|
T:DG2
|
2.3
|
24.8
|
0.6
|
N7
|
T:DG2
|
2.3
|
24.4
|
0.5
|
O
|
T:HOH211
|
2.4
|
37.8
|
1.0
|
O
|
T:HOH201
|
2.8
|
36.2
|
0.8
|
C8
|
T:DG2
|
3.1
|
24.4
|
0.5
|
C8
|
T:DG2
|
3.1
|
24.5
|
0.6
|
C5
|
T:DG2
|
3.2
|
23.4
|
0.6
|
C5
|
T:DG2
|
3.5
|
23.4
|
0.5
|
O6
|
T:DG2
|
3.6
|
23.0
|
0.6
|
C6
|
T:DG2
|
3.8
|
22.4
|
0.6
|
O6
|
T:DG2
|
3.9
|
22.4
|
0.5
|
C6
|
T:DG2
|
4.1
|
22.4
|
0.5
|
O
|
T:HOH213
|
4.2
|
40.5
|
1.0
|
O
|
D:HOH216
|
4.2
|
43.1
|
0.8
|
N9
|
T:DG2
|
4.3
|
24.6
|
0.6
|
N9
|
T:DG2
|
4.3
|
24.4
|
0.5
|
C4
|
T:DG2
|
4.3
|
22.8
|
0.6
|
O6
|
T:DG3
|
4.4
|
22.7
|
1.0
|
C4
|
T:DG2
|
4.5
|
23.0
|
0.5
|
OP2
|
T:DG2
|
4.6
|
33.0
|
0.5
|
C2'
|
T:DC1
|
4.7
|
29.3
|
0.4
|
C6
|
T:DC1
|
4.9
|
21.4
|
0.4
|
C5
|
T:DC1
|
5.0
|
21.1
|
0.6
|
|
Manganese binding site 7 out
of 8 in 6vfc
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Manganese Binding Sites List in 6vfc
Manganese binding site 7 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 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 Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Mn101
b:20.6
occ:0.83
|
OP1
|
P:8GM5
|
1.6
|
22.4
|
0.8
|
OD2
|
A:ASP330
|
1.8
|
24.4
|
0.6
|
OD2
|
A:ASP418
|
2.0
|
17.1
|
1.0
|
OD1
|
A:ASP332
|
2.1
|
19.7
|
1.0
|
O
|
A:HOH601
|
2.2
|
22.9
|
1.0
|
OD1
|
A:ASP330
|
2.4
|
21.8
|
0.5
|
CG
|
A:ASP330
|
2.8
|
20.2
|
0.6
|
P
|
P:8GM5
|
3.0
|
22.5
|
0.8
|
CG
|
A:ASP418
|
3.0
|
17.8
|
1.0
|
O3'
|
P:DA4
|
3.1
|
24.6
|
1.0
|
CG
|
A:ASP332
|
3.2
|
18.6
|
1.0
|
OD1
|
A:ASP330
|
3.2
|
20.8
|
0.6
|
CG
|
A:ASP330
|
3.2
|
19.8
|
0.5
|
MN
|
A:MN501
|
3.5
|
20.5
|
1.0
|
OD2
|
A:ASP332
|
3.6
|
17.8
|
1.0
|
CB
|
A:ASP418
|
3.7
|
16.0
|
1.0
|
OP2
|
P:8GM5
|
3.9
|
21.9
|
0.8
|
OD1
|
A:ASP418
|
3.9
|
17.9
|
1.0
|
CB
|
A:ASP330
|
3.9
|
17.4
|
0.5
|
CB
|
A:ASP330
|
4.0
|
16.1
|
0.6
|
OD2
|
A:ASP330
|
4.1
|
23.4
|
0.5
|
C5'
|
P:DA4
|
4.1
|
27.3
|
1.0
|
CE1
|
A:HIS329
|
4.2
|
28.5
|
0.6
|
C3'
|
P:DA4
|
4.2
|
27.1
|
1.0
|
O5'
|
P:8GM5
|
4.2
|
23.1
|
0.8
|
C4'
|
P:DA4
|
4.3
|
27.9
|
1.0
|
O
|
P:HOH201
|
4.3
|
21.6
|
0.5
|
NH2
|
A:ARG416
|
4.4
|
19.6
|
1.0
|
O
|
A:HOH602
|
4.4
|
28.9
|
1.0
|
CB
|
A:ASP332
|
4.4
|
14.1
|
1.0
|
C5'
|
P:8GM5
|
4.5
|
23.8
|
0.8
|
OP1
|
P:DA4
|
4.6
|
24.2
|
1.0
|
O
|
A:VAL331
|
4.7
|
16.8
|
1.0
|
N
|
A:ASP418
|
4.8
|
13.8
|
1.0
|
CZ3
|
A:TRP434
|
4.8
|
23.7
|
1.0
|
NE2
|
A:HIS329
|
4.8
|
30.9
|
0.6
|
O5'
|
P:DA4
|
4.8
|
23.0
|
1.0
|
CA
|
A:ASP418
|
4.9
|
15.1
|
1.0
|
CA
|
A:ASP332
|
4.9
|
15.0
|
1.0
|
C
|
A:VAL331
|
4.9
|
17.0
|
1.0
|
|
Manganese binding site 8 out
of 8 in 6vfc
Go back to
Manganese Binding Sites List in 6vfc
Manganese binding site 8 out
of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 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 Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn101
b:58.5
occ:0.66
|
O
|
D:HOH216
|
2.2
|
43.1
|
0.8
|
N7
|
D:DG1
|
2.3
|
21.3
|
1.0
|
O
|
D:HOH210
|
2.6
|
35.4
|
0.8
|
C8
|
D:DG1
|
3.1
|
21.3
|
1.0
|
C5
|
D:DG1
|
3.4
|
19.4
|
1.0
|
O6
|
D:DG1
|
3.8
|
21.5
|
1.0
|
C6
|
D:DG1
|
4.0
|
20.0
|
1.0
|
N4
|
D:DC2
|
4.3
|
23.8
|
1.0
|
O
|
D:HOH202
|
4.4
|
41.7
|
1.0
|
N9
|
D:DG1
|
4.4
|
19.6
|
1.0
|
C4
|
D:DG1
|
4.5
|
19.9
|
1.0
|
O
|
T:HOH211
|
4.6
|
37.8
|
1.0
|
OP2
|
D:DG1
|
4.6
|
27.3
|
1.0
|
CG
|
A:ARG175
|
4.9
|
28.4
|
1.0
|
O
|
A:HOH804
|
5.0
|
27.6
|
1.0
|
C4
|
D:DC2
|
5.0
|
22.5
|
1.0
|
|
Reference:
J.A.Jamsen,
A.Sassa,
D.D.Shock,
W.A.Beard,
S.H.Wilson.
Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min) To Be Published.
Page generated: Sun Oct 6 07:32:12 2024
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