Magnesium in PDB 6pz3: Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue
Enzymatic activity of Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue
All present enzymatic activity of Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue:
2.7.7.7;
Protein crystallography data
The structure of Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue, PDB code: 6pz3
was solved by
O.Rechkoblit,
A.K.Aggarwal,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.53 /
2.40
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.221,
98.221,
81.348,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.4 /
21.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue
(pdb code 6pz3). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the
Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue, PDB code: 6pz3:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 6pz3
Go back to
Magnesium Binding Sites List in 6pz3
Magnesium binding site 1 out
of 2 in the Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:32.0
occ:1.00
|
OD1
|
A:ASP13
|
2.0
|
30.1
|
1.0
|
O1B
|
A:XG4501
|
2.0
|
34.8
|
1.0
|
O1G
|
A:XG4501
|
2.1
|
30.7
|
1.0
|
O1A
|
A:XG4501
|
2.1
|
35.3
|
1.0
|
OD1
|
A:ASP115
|
2.2
|
36.5
|
1.0
|
O
|
A:MET14
|
2.3
|
27.9
|
1.0
|
CG
|
A:ASP13
|
2.9
|
29.3
|
1.0
|
H5'
|
A:XG4501
|
3.0
|
45.0
|
1.0
|
PB
|
A:XG4501
|
3.1
|
34.0
|
1.0
|
MG
|
A:MG503
|
3.1
|
42.4
|
1.0
|
CG
|
A:ASP115
|
3.1
|
35.0
|
1.0
|
PA
|
A:XG4501
|
3.3
|
37.5
|
1.0
|
OD2
|
A:ASP13
|
3.3
|
32.0
|
1.0
|
PG
|
A:XG4501
|
3.4
|
34.8
|
1.0
|
C
|
A:MET14
|
3.5
|
28.6
|
1.0
|
N3A
|
A:XG4501
|
3.5
|
40.0
|
1.0
|
OD2
|
A:ASP115
|
3.5
|
36.3
|
1.0
|
O3B
|
A:XG4501
|
3.6
|
38.5
|
1.0
|
HZ2
|
A:LYS231
|
3.8
|
42.0
|
1.0
|
C5'
|
A:XG4501
|
3.8
|
37.6
|
1.0
|
H
|
A:MET14
|
3.9
|
30.8
|
1.0
|
N
|
A:MET14
|
3.9
|
25.8
|
1.0
|
HZ3
|
A:LYS231
|
4.0
|
42.0
|
1.0
|
O5'
|
A:XG4501
|
4.0
|
43.9
|
1.0
|
O
|
A:HOH615
|
4.0
|
37.7
|
1.0
|
H5'A
|
A:XG4501
|
4.0
|
45.0
|
1.0
|
H
|
A:PHE17
|
4.1
|
30.2
|
1.0
|
HB2
|
A:PHE17
|
4.1
|
31.1
|
1.0
|
HO3'
|
P:DT8
|
4.1
|
48.3
|
1.0
|
HB2
|
A:MET14
|
4.1
|
35.9
|
1.0
|
HA
|
A:ASP15
|
4.2
|
34.9
|
1.0
|
O2G
|
A:XG4501
|
4.2
|
38.1
|
1.0
|
CB
|
A:ASP13
|
4.2
|
22.5
|
1.0
|
CA
|
A:MET14
|
4.2
|
30.2
|
1.0
|
C
|
A:ASP13
|
4.3
|
22.9
|
1.0
|
H
|
A:CYS16
|
4.3
|
34.2
|
1.0
|
NZ
|
A:LYS231
|
4.3
|
35.1
|
1.0
|
CB
|
A:ASP115
|
4.4
|
30.0
|
1.0
|
HB2
|
A:ASP115
|
4.4
|
35.9
|
1.0
|
O2B
|
A:XG4501
|
4.4
|
38.4
|
1.0
|
HN3A
|
A:XG4501
|
4.4
|
47.9
|
1.0
|
HB3
|
A:ASP13
|
4.5
|
26.9
|
1.0
|
O3G
|
A:XG4501
|
4.5
|
36.4
|
1.0
|
N
|
A:ASP15
|
4.5
|
28.6
|
1.0
|
O2A
|
A:XG4501
|
4.6
|
39.8
|
1.0
|
N
|
A:CYS16
|
4.6
|
28.6
|
1.0
|
HA
|
A:ASP13
|
4.6
|
30.4
|
1.0
|
CA
|
A:ASP13
|
4.7
|
25.4
|
1.0
|
HE3
|
A:LYS231
|
4.7
|
48.8
|
1.0
|
CA
|
A:ASP15
|
4.7
|
29.2
|
1.0
|
O
|
A:ASP115
|
4.7
|
30.6
|
1.0
|
CB
|
A:MET14
|
4.8
|
30.0
|
1.0
|
O
|
A:ASP13
|
4.8
|
25.9
|
1.0
|
OE2
|
A:GLU116
|
4.8
|
39.9
|
1.0
|
HB3
|
A:ASP115
|
4.8
|
35.9
|
1.0
|
N
|
A:PHE17
|
4.8
|
25.3
|
1.0
|
C
|
A:ASP15
|
4.8
|
28.5
|
1.0
|
O3'
|
P:DT8
|
4.9
|
40.4
|
1.0
|
HB2
|
A:ASP13
|
4.9
|
26.9
|
1.0
|
HA
|
A:CYS16
|
4.9
|
37.3
|
1.0
|
CB
|
A:PHE17
|
4.9
|
26.0
|
1.0
|
HB3
|
A:PHE17
|
4.9
|
31.1
|
1.0
|
HZ1
|
A:LYS231
|
5.0
|
42.0
|
1.0
|
H3'
|
A:XG4501
|
5.0
|
43.2
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 6pz3
Go back to
Magnesium Binding Sites List in 6pz3
Magnesium binding site 2 out
of 2 in the Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Polymerase Eta-Catalyzed Insertion of Correct G Opposite Template Cytarabine (Arac) Residue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg503
b:42.4
occ:1.00
|
HO3'
|
P:DT8
|
1.7
|
48.3
|
1.0
|
OE2
|
A:GLU116
|
1.9
|
39.9
|
1.0
|
OD2
|
A:ASP13
|
2.1
|
32.0
|
1.0
|
O1A
|
A:XG4501
|
2.1
|
35.3
|
1.0
|
O
|
A:HOH615
|
2.1
|
37.7
|
1.0
|
OD2
|
A:ASP115
|
2.1
|
36.3
|
1.0
|
O3'
|
P:DT8
|
2.5
|
40.4
|
1.0
|
H3'
|
P:DT8
|
2.7
|
46.1
|
1.0
|
CG
|
A:ASP115
|
2.9
|
35.0
|
1.0
|
CG
|
A:ASP13
|
3.0
|
29.3
|
1.0
|
C3'
|
P:DT8
|
3.1
|
38.5
|
1.0
|
MG
|
A:MG502
|
3.1
|
32.0
|
1.0
|
CD
|
A:GLU116
|
3.1
|
37.1
|
1.0
|
OD1
|
A:ASP115
|
3.1
|
36.5
|
1.0
|
PA
|
A:XG4501
|
3.2
|
37.5
|
1.0
|
OD1
|
A:ASP13
|
3.4
|
30.1
|
1.0
|
HG
|
A:SER113
|
3.4
|
38.2
|
1.0
|
H5'A
|
A:XG4501
|
3.4
|
45.0
|
1.0
|
HB3
|
A:GLU116
|
3.4
|
38.9
|
1.0
|
O5'
|
A:XG4501
|
3.7
|
43.9
|
1.0
|
O2A
|
A:XG4501
|
3.7
|
39.8
|
1.0
|
H5'
|
A:XG4501
|
3.8
|
45.0
|
1.0
|
HG2
|
A:GLU116
|
3.8
|
40.5
|
1.0
|
C5'
|
A:XG4501
|
3.8
|
37.6
|
1.0
|
CG
|
A:GLU116
|
3.9
|
33.9
|
1.0
|
H4'
|
P:DT8
|
3.9
|
44.4
|
1.0
|
OE1
|
A:GLU116
|
4.0
|
35.8
|
1.0
|
C4'
|
P:DT8
|
4.0
|
37.1
|
1.0
|
OG
|
A:SER113
|
4.0
|
31.9
|
1.0
|
H5''
|
P:DT8
|
4.1
|
49.8
|
1.0
|
CB
|
A:GLU116
|
4.1
|
32.5
|
1.0
|
C2'
|
P:DT8
|
4.3
|
38.2
|
1.0
|
CB
|
A:ASP13
|
4.4
|
22.5
|
1.0
|
H2''
|
P:DT8
|
4.4
|
45.8
|
1.0
|
CB
|
A:ASP115
|
4.4
|
30.0
|
1.0
|
O1G
|
A:XG4501
|
4.4
|
30.7
|
1.0
|
HB2
|
A:ASP13
|
4.5
|
26.9
|
1.0
|
O1B
|
A:XG4501
|
4.5
|
34.8
|
1.0
|
C
|
A:ASP115
|
4.5
|
27.8
|
1.0
|
O
|
A:ASP115
|
4.5
|
30.6
|
1.0
|
HA
|
A:ASP13
|
4.6
|
30.4
|
1.0
|
C5'
|
P:DT8
|
4.6
|
41.5
|
1.0
|
HO2A
|
A:XG4501
|
4.6
|
47.6
|
1.0
|
HB3
|
A:ASP115
|
4.6
|
35.9
|
1.0
|
N3A
|
A:XG4501
|
4.7
|
40.0
|
1.0
|
H
|
A:ASP115
|
4.7
|
34.4
|
1.0
|
N
|
A:GLU116
|
4.7
|
30.8
|
1.0
|
H2'
|
P:DT8
|
4.8
|
45.8
|
1.0
|
HG3
|
A:GLU116
|
4.8
|
40.5
|
1.0
|
HB2
|
A:GLU116
|
4.8
|
38.9
|
1.0
|
H
|
A:MET14
|
4.9
|
30.8
|
1.0
|
HZ3
|
A:LYS224
|
4.9
|
47.8
|
1.0
|
CA
|
A:ASP115
|
4.9
|
30.3
|
1.0
|
H
|
A:GLU116
|
5.0
|
36.9
|
1.0
|
HB2
|
A:ASP115
|
5.0
|
35.9
|
1.0
|
CA
|
A:ASP13
|
5.0
|
25.4
|
1.0
|
|
Reference:
O.Rechkoblit,
R.E.Johnson,
A.Buku,
L.Prakash,
S.Prakash,
A.K.Aggarwal.
Structural Insights Into Mutagenicity of Anticancer Nucleoside Analog Cytarabine During Replication By Dna Polymerase Eta. Sci Rep V. 9 16400 2019.
ISSN: ESSN 2045-2322
PubMed: 31704958
DOI: 10.1038/S41598-019-52703-7
Page generated: Tue Oct 1 15:21:18 2024
|