Magnesium in PDB 7ksw: Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN)
Enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN)
All present enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN):
2.7.7.7;
Protein crystallography data
The structure of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN), PDB code: 7ksw
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)
|
35.00 /
1.49
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.043,
68.736,
110.548,
90,
90,
90
|
R / Rfree (%)
|
15.4 /
17.2
|
Other elements in 7ksw:
The structure of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN) also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN)
(pdb code 7ksw). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN), PDB code: 7ksw:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 7ksw
Go back to
Magnesium Binding Sites List in 7ksw
Magnesium binding site 1 out
of 3 in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:15.4
occ:1.00
|
OD2
|
A:ASP330
|
1.7
|
20.2
|
0.5
|
OD2
|
A:ASP418
|
2.1
|
20.3
|
1.0
|
OD1
|
A:ASP332
|
2.2
|
16.1
|
1.0
|
OP1
|
P:DG5
|
2.2
|
12.9
|
0.6
|
O
|
A:HOH602
|
2.3
|
28.8
|
1.0
|
O2A
|
A:DGT505
|
2.6
|
15.2
|
0.4
|
O3'
|
P:DA4
|
2.6
|
16.6
|
0.6
|
OD1
|
A:ASP330
|
2.7
|
16.3
|
0.6
|
O3'
|
P:DA4
|
2.7
|
21.1
|
0.4
|
CG
|
A:ASP330
|
2.8
|
21.3
|
0.5
|
P
|
P:DG5
|
3.0
|
12.3
|
0.6
|
OD1
|
A:ASP330
|
3.2
|
17.0
|
0.5
|
CG
|
A:ASP332
|
3.2
|
15.4
|
1.0
|
CG
|
A:ASP418
|
3.2
|
16.6
|
1.0
|
CG
|
A:ASP330
|
3.4
|
18.7
|
0.6
|
OD2
|
A:ASP332
|
3.5
|
14.7
|
1.0
|
MG
|
A:MG502
|
3.5
|
14.6
|
1.0
|
PA
|
A:DGT505
|
3.5
|
16.4
|
0.4
|
C3'
|
P:DA4
|
3.8
|
17.7
|
0.6
|
C3'
|
P:DA4
|
3.9
|
17.6
|
0.4
|
CB
|
A:ASP418
|
3.9
|
15.5
|
1.0
|
O1A
|
A:DGT505
|
3.9
|
15.1
|
0.4
|
C4'
|
P:DA4
|
3.9
|
15.8
|
0.6
|
C5'
|
P:DA4
|
4.0
|
17.2
|
0.4
|
C5'
|
P:DA4
|
4.0
|
16.2
|
0.6
|
OP2
|
P:DG5
|
4.0
|
15.9
|
0.6
|
OD2
|
A:ASP330
|
4.0
|
23.7
|
0.6
|
O5'
|
A:DGT505
|
4.0
|
16.1
|
0.4
|
C4'
|
P:DA4
|
4.1
|
16.5
|
0.4
|
CB
|
A:ASP330
|
4.1
|
15.8
|
0.5
|
CB
|
A:ASP330
|
4.2
|
17.8
|
0.6
|
OD1
|
A:ASP418
|
4.2
|
16.8
|
1.0
|
O5'
|
P:DG5
|
4.2
|
13.2
|
0.6
|
CE1
|
A:HIS329
|
4.3
|
36.6
|
0.5
|
C5'
|
P:DG5
|
4.4
|
15.6
|
0.6
|
C5'
|
A:DGT505
|
4.4
|
12.9
|
0.4
|
OP1
|
P:DA4
|
4.5
|
18.0
|
0.4
|
CB
|
A:ASP332
|
4.5
|
13.3
|
1.0
|
NH2
|
A:ARG416
|
4.5
|
17.2
|
1.0
|
O5'
|
P:DA4
|
4.7
|
17.0
|
0.6
|
OP1
|
P:DA4
|
4.7
|
18.9
|
0.6
|
O12
|
A:PPV506
|
4.8
|
20.6
|
0.6
|
O2G
|
A:DGT505
|
4.8
|
20.2
|
0.4
|
O5'
|
P:DA4
|
4.8
|
18.2
|
0.4
|
CZ3
|
A:TRP434
|
4.8
|
18.7
|
1.0
|
NE2
|
A:HIS329
|
4.9
|
38.3
|
0.5
|
O
|
A:VAL331
|
4.9
|
15.8
|
1.0
|
C2'
|
P:DA4
|
4.9
|
18.5
|
0.6
|
|
Magnesium binding site 2 out
of 3 in 7ksw
Go back to
Magnesium Binding Sites List in 7ksw
Magnesium binding site 2 out
of 3 in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:14.6
occ:1.00
|
O2A
|
A:DGT505
|
1.6
|
15.2
|
0.4
|
O2B
|
A:DGT505
|
2.0
|
14.5
|
0.4
|
O2G
|
A:DGT505
|
2.0
|
20.2
|
0.4
|
O11
|
A:PPV506
|
2.1
|
14.8
|
0.6
|
OD1
|
A:ASP330
|
2.1
|
16.3
|
0.6
|
OD2
|
A:ASP332
|
2.2
|
14.7
|
1.0
|
O
|
A:HOH623
|
2.2
|
19.3
|
1.0
|
OD1
|
A:ASP330
|
2.3
|
17.0
|
0.5
|
OP1
|
P:DG5
|
2.4
|
12.9
|
0.6
|
O12
|
A:PPV506
|
2.4
|
20.6
|
0.6
|
PA
|
A:DGT505
|
2.8
|
16.4
|
0.4
|
PB
|
A:DGT505
|
2.9
|
17.1
|
0.4
|
O3A
|
A:DGT505
|
3.1
|
15.9
|
0.4
|
CG
|
A:ASP330
|
3.1
|
18.7
|
0.6
|
PG
|
A:DGT505
|
3.2
|
22.9
|
0.4
|
CG
|
A:ASP332
|
3.2
|
15.4
|
1.0
|
CG
|
A:ASP330
|
3.3
|
21.3
|
0.5
|
O3B
|
A:DGT505
|
3.3
|
18.9
|
0.4
|
P1
|
A:PPV506
|
3.4
|
15.4
|
0.6
|
OD2
|
A:ASP330
|
3.4
|
23.7
|
0.6
|
MG
|
A:MG501
|
3.5
|
15.4
|
1.0
|
OD1
|
A:ASP332
|
3.5
|
16.1
|
1.0
|
OD2
|
A:ASP330
|
3.6
|
20.2
|
0.5
|
P
|
P:DG5
|
3.7
|
12.3
|
0.6
|
OPP
|
A:PPV506
|
3.7
|
16.6
|
0.6
|
P2
|
A:PPV506
|
3.8
|
22.6
|
0.6
|
O5'
|
A:DGT505
|
3.8
|
16.1
|
0.4
|
C5'
|
A:DGT505
|
3.8
|
12.9
|
0.4
|
O
|
A:HOH654
|
3.8
|
25.3
|
0.6
|
O
|
A:ASP330
|
4.0
|
17.1
|
0.5
|
O1A
|
A:DGT505
|
4.0
|
15.1
|
0.4
|
CE1
|
A:HIS329
|
4.0
|
36.6
|
0.5
|
O3G
|
A:DGT505
|
4.1
|
21.6
|
0.4
|
C5'
|
P:DG5
|
4.1
|
15.6
|
0.6
|
ND1
|
A:HIS329
|
4.2
|
38.2
|
0.5
|
O21
|
A:PPV506
|
4.2
|
17.6
|
0.6
|
O5'
|
P:DG5
|
4.2
|
13.2
|
0.6
|
O
|
A:HOH653
|
4.3
|
16.4
|
1.0
|
O1B
|
A:DGT505
|
4.4
|
14.9
|
0.4
|
O1G
|
A:DGT505
|
4.4
|
32.0
|
0.4
|
O
|
A:ASP330
|
4.4
|
14.0
|
0.6
|
N
|
A:GLY320
|
4.4
|
12.3
|
1.0
|
CB
|
A:ASP330
|
4.4
|
17.8
|
0.6
|
O
|
A:HOH613
|
4.4
|
25.7
|
0.6
|
O
|
A:HOH602
|
4.4
|
28.8
|
1.0
|
C
|
A:ASP330
|
4.4
|
14.3
|
0.5
|
O31
|
A:PPV506
|
4.5
|
16.7
|
0.6
|
O22
|
A:PPV506
|
4.5
|
32.6
|
0.6
|
C
|
A:ASP330
|
4.6
|
14.5
|
0.6
|
CB
|
A:ASP332
|
4.6
|
13.3
|
1.0
|
CB
|
A:ASP330
|
4.6
|
15.8
|
0.5
|
O
|
A:HOH654
|
4.6
|
14.6
|
0.4
|
OP2
|
P:DG5
|
4.6
|
15.9
|
0.6
|
CA
|
A:GLY319
|
4.7
|
12.6
|
1.0
|
O3'
|
P:DA4
|
4.7
|
16.6
|
0.6
|
O32
|
A:PPV506
|
4.8
|
32.0
|
0.6
|
N
|
A:ASP330
|
4.8
|
14.4
|
0.5
|
O3'
|
P:DA4
|
4.8
|
21.1
|
0.4
|
CA
|
A:ASP330
|
4.9
|
16.8
|
0.5
|
CA
|
A:ASP330
|
4.9
|
17.0
|
0.6
|
|
Magnesium binding site 3 out
of 3 in 7ksw
Go back to
Magnesium Binding Sites List in 7ksw
Magnesium binding site 3 out
of 3 in the Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Mg101
b:29.8
occ:0.62
|
O1A
|
A:DGT505
|
1.9
|
15.1
|
0.4
|
OP2
|
P:DG5
|
2.1
|
15.9
|
0.6
|
O22
|
A:PPV506
|
2.1
|
32.6
|
0.6
|
O
|
P:HOH215
|
2.1
|
21.3
|
0.6
|
O
|
P:HOH203
|
2.2
|
35.0
|
0.6
|
PA
|
A:DGT505
|
3.3
|
16.4
|
0.4
|
O
|
A:HOH761
|
3.4
|
21.1
|
0.4
|
P
|
P:DG5
|
3.4
|
12.3
|
0.6
|
P2
|
A:PPV506
|
3.6
|
22.6
|
0.6
|
O3A
|
A:DGT505
|
3.8
|
15.9
|
0.4
|
CE1
|
A:HIS329
|
3.8
|
36.6
|
0.5
|
O
|
A:HOH602
|
4.0
|
28.8
|
1.0
|
O
|
A:HOH761
|
4.0
|
24.3
|
0.6
|
OP1
|
P:DG5
|
4.0
|
12.9
|
0.6
|
O
|
A:HOH731
|
4.1
|
24.2
|
1.0
|
O12
|
A:PPV506
|
4.1
|
20.6
|
0.6
|
OPP
|
A:PPV506
|
4.2
|
16.6
|
0.6
|
O
|
A:HOH806
|
4.2
|
23.4
|
0.4
|
O5'
|
A:DGT505
|
4.3
|
16.1
|
0.4
|
O5'
|
P:DG5
|
4.3
|
13.2
|
0.6
|
NE2
|
A:HIS329
|
4.3
|
38.3
|
0.5
|
O2A
|
A:DGT505
|
4.4
|
15.2
|
0.4
|
O3'
|
P:DA4
|
4.4
|
16.6
|
0.6
|
OP2
|
P:DA4
|
4.4
|
19.3
|
0.4
|
OP2
|
P:DA4
|
4.4
|
19.7
|
0.6
|
OP1
|
P:DA4
|
4.6
|
18.0
|
0.4
|
O5'
|
P:DA4
|
4.6
|
17.0
|
0.6
|
C3'
|
P:DA4
|
4.6
|
17.7
|
0.6
|
ND1
|
A:HIS329
|
4.7
|
38.2
|
0.5
|
O32
|
A:PPV506
|
4.7
|
32.0
|
0.6
|
OP1
|
P:DA4
|
4.7
|
18.9
|
0.6
|
P
|
P:DA4
|
4.8
|
17.4
|
0.4
|
O1G
|
A:DGT505
|
4.8
|
32.0
|
0.4
|
P
|
P:DA4
|
4.8
|
17.3
|
0.6
|
O3'
|
P:DA4
|
4.8
|
21.1
|
0.4
|
O5'
|
P:DA4
|
4.8
|
18.2
|
0.4
|
O
|
P:HOH202
|
4.8
|
37.6
|
1.0
|
OD2
|
A:ASP330
|
4.8
|
23.7
|
0.6
|
C3'
|
P:DA4
|
4.9
|
17.6
|
0.4
|
|
Reference:
J.A.Jamsen,
A.Sassa,
D.D.Shock,
W.A.Beard,
S.H.Wilson.
Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN) To Be Published.
Page generated: Wed Oct 2 22:37:11 2024
|