Magnesium in PDB 6vkp: Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg
Enzymatic activity of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg
All present enzymatic activity of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg:
2.7.7.7;
Protein crystallography data
The structure of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg, PDB code: 6vkp
was solved by
H.Jung,
S.Lee,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.55 /
2.54
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.098,
103.69,
99.105,
90,
89.94,
90
|
R / Rfree (%)
|
21 /
26
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg
(pdb code 6vkp). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg, PDB code: 6vkp:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6vkp
Go back to
Magnesium Binding Sites List in 6vkp
Magnesium binding site 1 out
of 4 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:37.3
occ:1.00
|
OD1
|
A:ASP105
|
2.0
|
44.3
|
1.0
|
O
|
P:HOH103
|
2.1
|
42.9
|
1.0
|
O
|
A:HOH507
|
2.2
|
42.9
|
1.0
|
OD2
|
A:ASP7
|
2.2
|
46.8
|
1.0
|
OE2
|
A:GLU106
|
2.5
|
63.8
|
1.0
|
O1A
|
A:DZ4403
|
2.5
|
36.0
|
1.0
|
CG
|
A:GLU106
|
2.7
|
50.7
|
1.0
|
CD
|
A:GLU106
|
3.0
|
50.9
|
1.0
|
CG
|
A:ASP105
|
3.0
|
38.3
|
1.0
|
CG
|
A:ASP7
|
3.3
|
49.1
|
1.0
|
OG
|
A:SER103
|
3.4
|
39.4
|
1.0
|
PA
|
A:DZ4403
|
3.4
|
30.7
|
1.0
|
OD2
|
A:ASP105
|
3.4
|
41.2
|
1.0
|
O2A
|
A:DZ4403
|
3.7
|
35.3
|
1.0
|
OP2
|
P:DG13
|
3.7
|
62.8
|
1.0
|
O5'
|
A:DZ4403
|
3.8
|
34.0
|
1.0
|
OD1
|
A:ASP7
|
3.9
|
46.8
|
1.0
|
MG
|
A:MG402
|
3.9
|
36.1
|
1.0
|
OE1
|
A:GLU106
|
4.2
|
58.9
|
1.0
|
C5'
|
A:DZ4403
|
4.2
|
23.4
|
1.0
|
CB
|
A:GLU106
|
4.2
|
48.0
|
1.0
|
O
|
A:HOH510
|
4.4
|
42.9
|
1.0
|
CB
|
A:ASP105
|
4.4
|
36.5
|
1.0
|
CB
|
A:SER103
|
4.4
|
39.4
|
1.0
|
C
|
A:ASP105
|
4.5
|
42.0
|
1.0
|
CB
|
A:ASP7
|
4.5
|
46.6
|
1.0
|
O
|
A:ASP105
|
4.6
|
37.8
|
1.0
|
N
|
A:GLU106
|
4.6
|
41.5
|
1.0
|
CA
|
A:ASP105
|
4.8
|
42.3
|
1.0
|
O2G
|
A:DZ4403
|
4.8
|
44.6
|
1.0
|
CA
|
A:GLU106
|
4.9
|
39.2
|
1.0
|
O
|
P:HOH101
|
4.9
|
42.9
|
1.0
|
N
|
A:ASP105
|
4.9
|
41.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6vkp
Go back to
Magnesium Binding Sites List in 6vkp
Magnesium binding site 2 out
of 4 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:36.1
occ:1.00
|
O2G
|
A:DZ4403
|
2.0
|
44.6
|
1.0
|
OD1
|
A:ASP7
|
2.1
|
46.8
|
1.0
|
O1A
|
A:DZ4403
|
2.1
|
36.0
|
1.0
|
O
|
A:PHE8
|
2.1
|
43.1
|
1.0
|
OD2
|
A:ASP105
|
2.2
|
41.2
|
1.0
|
O2B
|
A:DZ4403
|
2.2
|
36.1
|
1.0
|
CG
|
A:ASP7
|
3.0
|
49.1
|
1.0
|
PG
|
A:DZ4403
|
3.2
|
42.5
|
1.0
|
PB
|
A:DZ4403
|
3.2
|
37.2
|
1.0
|
CG
|
A:ASP105
|
3.3
|
38.3
|
1.0
|
PA
|
A:DZ4403
|
3.3
|
30.7
|
1.0
|
C
|
A:PHE8
|
3.4
|
41.0
|
1.0
|
OD2
|
A:ASP7
|
3.4
|
46.8
|
1.0
|
O3B
|
A:DZ4403
|
3.5
|
38.8
|
1.0
|
N3A
|
A:DZ4403
|
3.6
|
31.7
|
1.0
|
O1G
|
A:DZ4403
|
3.6
|
42.3
|
1.0
|
OD1
|
A:ASP105
|
3.7
|
44.3
|
1.0
|
O
|
A:HOH510
|
3.7
|
42.9
|
1.0
|
NZ
|
A:LYS159
|
3.9
|
66.8
|
1.0
|
MG
|
A:MG401
|
3.9
|
37.3
|
1.0
|
N
|
A:PHE8
|
3.9
|
45.5
|
1.0
|
C5'
|
A:DZ4403
|
4.0
|
23.4
|
1.0
|
O5'
|
A:DZ4403
|
4.1
|
34.0
|
1.0
|
CA
|
A:PHE8
|
4.2
|
40.0
|
1.0
|
C
|
A:ASP7
|
4.2
|
43.9
|
1.0
|
CE
|
A:LYS159
|
4.3
|
50.7
|
1.0
|
N
|
A:ASP9
|
4.3
|
44.1
|
1.0
|
O
|
A:HOH507
|
4.4
|
42.9
|
1.0
|
CB
|
A:ASP7
|
4.4
|
46.6
|
1.0
|
N
|
A:TYR10
|
4.4
|
34.8
|
1.0
|
CA
|
A:ASP9
|
4.4
|
44.7
|
1.0
|
O2A
|
A:DZ4403
|
4.5
|
35.3
|
1.0
|
O3G
|
A:DZ4403
|
4.5
|
43.4
|
1.0
|
O
|
A:ASP7
|
4.5
|
42.0
|
1.0
|
O1B
|
A:DZ4403
|
4.5
|
34.3
|
1.0
|
CB
|
A:ASP105
|
4.6
|
36.5
|
1.0
|
C
|
A:ASP9
|
4.6
|
38.3
|
1.0
|
N
|
A:PHE11
|
4.8
|
33.0
|
1.0
|
CA
|
A:ASP7
|
4.8
|
42.5
|
1.0
|
CB
|
A:PHE8
|
4.8
|
40.5
|
1.0
|
CB
|
A:PHE11
|
4.9
|
33.0
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6vkp
Go back to
Magnesium Binding Sites List in 6vkp
Magnesium binding site 3 out
of 4 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg401
b:39.8
occ:1.00
|
OD1
|
D:ASP105
|
2.1
|
56.4
|
1.0
|
O
|
B:HOH105
|
2.2
|
46.7
|
1.0
|
OE2
|
D:GLU106
|
2.2
|
62.5
|
1.0
|
OD2
|
D:ASP7
|
2.2
|
46.0
|
1.0
|
O1A
|
D:DZ4403
|
2.4
|
35.7
|
1.0
|
O
|
D:HOH505
|
2.7
|
42.9
|
1.0
|
CG
|
D:ASP105
|
2.9
|
42.8
|
1.0
|
CD
|
D:GLU106
|
3.0
|
51.4
|
1.0
|
OD2
|
D:ASP105
|
3.1
|
42.1
|
1.0
|
CG
|
D:GLU106
|
3.1
|
50.9
|
1.0
|
PA
|
D:DZ4403
|
3.2
|
39.0
|
1.0
|
CG
|
D:ASP7
|
3.3
|
49.0
|
1.0
|
O2A
|
D:DZ4403
|
3.4
|
38.9
|
1.0
|
O5'
|
D:DZ4403
|
3.6
|
34.0
|
1.0
|
OP2
|
B:DG13
|
3.7
|
65.3
|
1.0
|
OG
|
D:SER103
|
3.7
|
43.5
|
1.0
|
OD1
|
D:ASP7
|
3.7
|
46.7
|
1.0
|
MG
|
D:MG402
|
3.8
|
37.0
|
1.0
|
O
|
D:HOH504
|
3.8
|
42.9
|
1.0
|
C5'
|
D:DZ4403
|
3.9
|
24.0
|
1.0
|
OE1
|
D:GLU106
|
4.2
|
58.8
|
1.0
|
CB
|
D:ASP105
|
4.4
|
37.5
|
1.0
|
CB
|
D:GLU106
|
4.5
|
49.5
|
1.0
|
O
|
B:HOH102
|
4.6
|
45.4
|
1.0
|
CB
|
D:ASP7
|
4.6
|
47.7
|
1.0
|
CB
|
D:SER103
|
4.6
|
45.3
|
1.0
|
C
|
D:ASP105
|
4.6
|
41.5
|
1.0
|
O1G
|
D:DZ4403
|
4.6
|
42.0
|
1.0
|
O
|
D:ASP105
|
4.8
|
41.5
|
1.0
|
N
|
D:GLU106
|
4.8
|
45.9
|
1.0
|
N3A
|
D:DZ4403
|
4.8
|
31.4
|
1.0
|
O2B
|
D:DZ4403
|
4.9
|
36.2
|
1.0
|
CA
|
D:ASP105
|
4.9
|
42.5
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6vkp
Go back to
Magnesium Binding Sites List in 6vkp
Magnesium binding site 4 out
of 4 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg402
b:37.0
occ:1.00
|
O
|
D:PHE8
|
2.1
|
48.3
|
1.0
|
O1G
|
D:DZ4403
|
2.1
|
42.0
|
1.0
|
OD1
|
D:ASP7
|
2.1
|
46.7
|
1.0
|
O1A
|
D:DZ4403
|
2.1
|
35.7
|
1.0
|
O2B
|
D:DZ4403
|
2.2
|
36.2
|
1.0
|
OD2
|
D:ASP105
|
2.3
|
42.1
|
1.0
|
CG
|
D:ASP7
|
3.1
|
49.0
|
1.0
|
PG
|
D:DZ4403
|
3.2
|
85.5
|
1.0
|
PB
|
D:DZ4403
|
3.2
|
30.3
|
1.0
|
C
|
D:PHE8
|
3.3
|
44.8
|
1.0
|
O
|
D:HOH504
|
3.3
|
42.9
|
1.0
|
PA
|
D:DZ4403
|
3.3
|
39.0
|
1.0
|
OD2
|
D:ASP7
|
3.4
|
46.0
|
1.0
|
O3G
|
D:DZ4403
|
3.4
|
42.5
|
1.0
|
CG
|
D:ASP105
|
3.5
|
42.8
|
1.0
|
O3B
|
D:DZ4403
|
3.6
|
49.9
|
1.0
|
N3A
|
D:DZ4403
|
3.7
|
31.4
|
1.0
|
MG
|
D:MG401
|
3.8
|
39.8
|
1.0
|
N
|
D:PHE8
|
3.9
|
42.9
|
1.0
|
C5'
|
D:DZ4403
|
4.0
|
24.0
|
1.0
|
OD1
|
D:ASP105
|
4.1
|
56.4
|
1.0
|
CA
|
D:PHE8
|
4.1
|
43.9
|
1.0
|
O5'
|
D:DZ4403
|
4.2
|
34.0
|
1.0
|
NZ
|
D:LYS159
|
4.2
|
70.4
|
1.0
|
CE
|
D:LYS159
|
4.2
|
51.1
|
1.0
|
C
|
D:ASP7
|
4.2
|
45.5
|
1.0
|
N
|
D:ASP9
|
4.2
|
45.2
|
1.0
|
CA
|
D:ASP9
|
4.3
|
48.7
|
1.0
|
CB
|
D:ASP7
|
4.4
|
47.7
|
1.0
|
N
|
D:TYR10
|
4.4
|
40.9
|
1.0
|
O2G
|
D:DZ4403
|
4.5
|
41.5
|
1.0
|
O2A
|
D:DZ4403
|
4.5
|
38.9
|
1.0
|
O
|
D:HOH505
|
4.5
|
42.9
|
1.0
|
O
|
D:ASP7
|
4.5
|
44.4
|
1.0
|
O1B
|
D:DZ4403
|
4.6
|
39.5
|
1.0
|
CB
|
D:ASP105
|
4.6
|
37.5
|
1.0
|
C
|
D:ASP9
|
4.6
|
44.6
|
1.0
|
CB
|
D:PHE8
|
4.8
|
40.7
|
1.0
|
CA
|
D:ASP7
|
4.8
|
44.3
|
1.0
|
N
|
D:PHE11
|
4.8
|
40.9
|
1.0
|
CB
|
D:PHE11
|
4.9
|
35.8
|
1.0
|
|
Reference:
H.Jung,
S.Lee.
Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg To Be Published.
Page generated: Tue Oct 1 22:06:42 2024
|