Calcium in PDB 4qwd: Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp
Enzymatic activity of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp
All present enzymatic activity of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp:
2.7.7.7;
Protein crystallography data
The structure of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp, PDB code: 4qwd
was solved by
V.Gaur,
Z.Suo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.71 /
2.05
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
96.544,
102.483,
52.375,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.5 /
26.2
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp
(pdb code 4qwd). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp, PDB code: 4qwd:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 4qwd
Go back to
Calcium Binding Sites List in 4qwd
Calcium binding site 1 out
of 4 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca702
b:78.0
occ:1.00
|
O2B
|
A:3TT701
|
2.2
|
0.7
|
1.0
|
OE2
|
A:GLU106
|
2.4
|
44.9
|
1.0
|
OD2
|
A:ASP105
|
2.7
|
43.3
|
1.0
|
O
|
C:HOH101
|
2.8
|
64.1
|
1.0
|
OD2
|
A:ASP7
|
2.9
|
37.0
|
1.0
|
OD1
|
A:ASP7
|
3.2
|
37.5
|
1.0
|
CG
|
A:ASP7
|
3.4
|
38.0
|
1.0
|
CD
|
A:GLU106
|
3.4
|
42.8
|
1.0
|
O
|
A:HOH981
|
3.5
|
68.1
|
1.0
|
C3'
|
C:DC13
|
3.5
|
56.9
|
1.0
|
O3G
|
A:3TT701
|
3.5
|
0.4
|
1.0
|
CA
|
A:CA703
|
3.6
|
43.3
|
1.0
|
PB
|
A:3TT701
|
3.6
|
98.7
|
1.0
|
CG
|
A:GLU106
|
3.9
|
40.8
|
1.0
|
O3'
|
C:DC13
|
3.9
|
61.9
|
1.0
|
CG
|
A:ASP105
|
3.9
|
39.6
|
1.0
|
O1B
|
A:3TT701
|
4.0
|
0.3
|
1.0
|
NZ
|
A:LYS159
|
4.1
|
54.5
|
1.0
|
O5'
|
C:DC13
|
4.2
|
59.2
|
1.0
|
O
|
A:HOH971
|
4.2
|
54.5
|
1.0
|
C5'
|
C:DC13
|
4.2
|
55.9
|
1.0
|
O3A
|
A:3TT701
|
4.2
|
80.3
|
1.0
|
C4'
|
C:DC13
|
4.3
|
55.4
|
1.0
|
OE1
|
A:GLU106
|
4.5
|
42.7
|
1.0
|
C2'
|
C:DC13
|
4.5
|
54.8
|
1.0
|
OP1
|
C:DC13
|
4.5
|
60.4
|
1.0
|
NZ
|
A:LYS152
|
4.6
|
41.4
|
1.0
|
OD1
|
A:ASP105
|
4.6
|
43.4
|
1.0
|
CB
|
A:ASP7
|
4.7
|
38.2
|
1.0
|
PG
|
A:3TT701
|
4.8
|
0.8
|
1.0
|
N3B
|
A:3TT701
|
4.8
|
1.0
|
1.0
|
CB
|
A:ASP105
|
4.9
|
38.8
|
1.0
|
|
Calcium binding site 2 out
of 4 in 4qwd
Go back to
Calcium Binding Sites List in 4qwd
Calcium binding site 2 out
of 4 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca703
b:43.3
occ:1.00
|
O
|
A:PHE8
|
2.1
|
40.7
|
1.0
|
O2B
|
A:3TT701
|
2.4
|
0.7
|
1.0
|
OD1
|
A:ASP7
|
2.4
|
37.5
|
1.0
|
O3G
|
A:3TT701
|
2.5
|
0.4
|
1.0
|
OD1
|
A:ASP105
|
2.5
|
43.4
|
1.0
|
OD2
|
A:ASP105
|
2.7
|
43.3
|
1.0
|
O1A
|
A:3TT701
|
2.7
|
73.1
|
1.0
|
O1G
|
A:3TT701
|
2.8
|
0.3
|
1.0
|
CG
|
A:ASP105
|
2.9
|
39.6
|
1.0
|
PG
|
A:3TT701
|
3.0
|
0.8
|
1.0
|
PB
|
A:3TT701
|
3.2
|
98.7
|
1.0
|
N3B
|
A:3TT701
|
3.2
|
1.0
|
1.0
|
C
|
A:PHE8
|
3.3
|
40.5
|
1.0
|
O3A
|
A:3TT701
|
3.4
|
80.3
|
1.0
|
CA
|
A:CA702
|
3.6
|
78.0
|
1.0
|
CG
|
A:ASP7
|
3.6
|
38.0
|
1.0
|
PA
|
A:3TT701
|
3.7
|
68.1
|
1.0
|
N
|
A:PHE8
|
3.9
|
39.4
|
1.0
|
O
|
A:HOH803
|
4.1
|
41.4
|
1.0
|
CA
|
A:PHE8
|
4.1
|
40.1
|
1.0
|
OD2
|
A:ASP7
|
4.1
|
37.0
|
1.0
|
C
|
A:ASP7
|
4.2
|
40.1
|
1.0
|
N
|
A:ASP9
|
4.3
|
40.9
|
1.0
|
N
|
A:TYR10
|
4.4
|
40.4
|
1.0
|
CB
|
A:ASP105
|
4.4
|
38.8
|
1.0
|
CA
|
A:ASP9
|
4.4
|
42.1
|
1.0
|
N
|
A:PHE11
|
4.4
|
35.8
|
1.0
|
O
|
A:ASP105
|
4.4
|
37.5
|
1.0
|
O2G
|
A:3TT701
|
4.5
|
0.1
|
1.0
|
C
|
A:ASP9
|
4.5
|
40.4
|
1.0
|
C5'
|
A:3TT701
|
4.5
|
61.2
|
1.0
|
O5'
|
A:3TT701
|
4.5
|
64.9
|
1.0
|
CB
|
A:PHE8
|
4.5
|
38.0
|
1.0
|
O1B
|
A:3TT701
|
4.6
|
0.3
|
1.0
|
CB
|
A:PHE11
|
4.6
|
33.4
|
1.0
|
O
|
A:ASP7
|
4.7
|
41.5
|
1.0
|
CB
|
A:ASP7
|
4.7
|
38.2
|
1.0
|
CA
|
A:ASP7
|
4.8
|
39.3
|
1.0
|
O2A
|
A:3TT701
|
4.9
|
72.3
|
1.0
|
|
Calcium binding site 3 out
of 4 in 4qwd
Go back to
Calcium Binding Sites List in 4qwd
Calcium binding site 3 out
of 4 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca704
b:54.8
occ:1.00
|
O
|
A:ALA181
|
2.5
|
55.0
|
1.0
|
O
|
A:ILE186
|
2.6
|
44.6
|
1.0
|
O
|
C:HOH113
|
2.7
|
42.4
|
1.0
|
O
|
A:HOH932
|
2.7
|
64.5
|
1.0
|
O
|
C:HOH121
|
2.8
|
49.0
|
1.0
|
C
|
A:ALA181
|
3.6
|
55.7
|
1.0
|
C
|
A:ILE186
|
3.8
|
43.9
|
1.0
|
CA
|
A:GLY187
|
4.2
|
48.1
|
1.0
|
CA
|
A:ALA181
|
4.3
|
58.4
|
1.0
|
O
|
A:HOH990
|
4.4
|
55.3
|
1.0
|
N
|
A:GLY187
|
4.5
|
44.4
|
1.0
|
N
|
A:ASP182
|
4.5
|
52.6
|
1.0
|
CB
|
A:ALA181
|
4.6
|
59.1
|
1.0
|
OP1
|
C:DT12
|
4.7
|
53.5
|
1.0
|
CA
|
A:ASP182
|
4.7
|
49.8
|
1.0
|
C
|
A:GLY187
|
4.8
|
52.1
|
1.0
|
O
|
A:VAL183
|
4.8
|
40.4
|
1.0
|
OP2
|
C:DT12
|
4.9
|
55.8
|
1.0
|
CA
|
A:ILE186
|
4.9
|
42.6
|
1.0
|
CB
|
A:ILE186
|
5.0
|
44.3
|
1.0
|
|
Calcium binding site 4 out
of 4 in 4qwd
Go back to
Calcium Binding Sites List in 4qwd
Calcium binding site 4 out
of 4 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca705
b:75.1
occ:0.50
|
O
|
A:HOH1003
|
2.6
|
69.4
|
1.0
|
O
|
A:HOH992
|
2.7
|
70.8
|
1.0
|
OE2
|
A:GLU127
|
2.7
|
71.1
|
1.0
|
CD
|
A:GLU127
|
3.6
|
70.6
|
1.0
|
OE1
|
A:GLU127
|
3.9
|
70.4
|
1.0
|
CG
|
A:GLU127
|
5.0
|
67.2
|
1.0
|
|
Reference:
V.Gaur,
R.Vyas,
J.D.Fowler,
G.Efthimiopoulos,
J.Y.Feng,
Z.Suo.
Structural and Kinetic Insights Into Binding and Incorporation of L-Nucleotide Analogs By A Y-Family Dna Polymerase. Nucleic Acids Res. V. 42 9984 2014.
ISSN: ISSN 0305-1048
PubMed: 25104018
DOI: 10.1093/NAR/GKU709
Page generated: Sun Jul 14 12:32:37 2024
|