Calcium in PDB 2xgq: Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna
Enzymatic activity of Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna
All present enzymatic activity of Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna:
2.7.7.7;
Protein crystallography data
The structure of Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna, PDB code: 2xgq
was solved by
S.Schneider,
S.Schorr,
T.Carell,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.30 /
2.70
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
103.525,
103.525,
292.657,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.7 /
26.4
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna
(pdb code 2xgq). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the
Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna, PDB code: 2xgq:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
Calcium binding site 1 out
of 7 in 2xgq
Go back to
Calcium Binding Sites List in 2xgq
Calcium binding site 1 out
of 7 in the Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca600
b:78.7
occ:1.00
|
CA
|
A:CA601
|
3.0
|
81.2
|
1.0
|
OE1
|
A:GLU156
|
3.1
|
33.6
|
1.0
|
OD2
|
A:ASP155
|
3.3
|
31.0
|
1.0
|
OD1
|
A:ASP155
|
3.4
|
33.0
|
1.0
|
CG
|
A:ASP155
|
3.8
|
28.7
|
1.0
|
CD
|
A:GLU156
|
4.2
|
30.8
|
1.0
|
OG
|
A:SER153
|
4.6
|
29.7
|
1.0
|
OE2
|
A:GLU156
|
4.9
|
31.8
|
1.0
|
|
Calcium binding site 2 out
of 7 in 2xgq
Go back to
Calcium Binding Sites List in 2xgq
Calcium binding site 2 out
of 7 in the Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca601
b:81.2
occ:1.00
|
OD2
|
A:ASP30
|
2.9
|
31.1
|
1.0
|
OE1
|
A:GLU156
|
2.9
|
33.6
|
1.0
|
CA
|
A:CA600
|
3.0
|
78.7
|
1.0
|
OD1
|
A:ASP30
|
3.0
|
32.3
|
1.0
|
O
|
A:HOH2002
|
3.2
|
50.2
|
1.0
|
CG
|
A:ASP30
|
3.3
|
28.6
|
1.0
|
OD1
|
A:ASP155
|
3.5
|
33.0
|
1.0
|
CG
|
A:ASP155
|
3.9
|
28.7
|
1.0
|
OD2
|
A:ASP155
|
3.9
|
31.0
|
1.0
|
CD
|
A:GLU156
|
3.9
|
30.8
|
1.0
|
CG
|
A:GLU156
|
4.3
|
27.5
|
1.0
|
ND2
|
A:ASN32
|
4.4
|
35.5
|
1.0
|
O
|
A:MET31
|
4.7
|
26.4
|
1.0
|
CB
|
A:ASP30
|
4.8
|
26.1
|
1.0
|
CB
|
A:ASP155
|
4.9
|
26.0
|
1.0
|
OE2
|
A:GLU156
|
5.0
|
31.8
|
1.0
|
|
Calcium binding site 3 out
of 7 in 2xgq
Go back to
Calcium Binding Sites List in 2xgq
Calcium binding site 3 out
of 7 in the Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca602
b:66.1
occ:1.00
|
OD1
|
A:ASP289
|
2.7
|
23.9
|
1.0
|
OD2
|
A:ASP289
|
3.0
|
23.2
|
1.0
|
CG
|
A:ASP289
|
3.2
|
23.0
|
1.0
|
OG1
|
A:THR231
|
3.5
|
28.0
|
1.0
|
CB
|
A:ASP232
|
4.4
|
24.7
|
1.0
|
CB
|
A:ASP289
|
4.7
|
23.6
|
1.0
|
CE
|
A:LYS3
|
4.7
|
56.7
|
1.0
|
OD2
|
A:ASP232
|
4.7
|
28.5
|
1.0
|
OD2
|
A:ASP234
|
4.8
|
19.3
|
1.0
|
CB
|
A:THR231
|
4.8
|
26.1
|
1.0
|
OD1
|
A:ASP234
|
4.9
|
20.4
|
1.0
|
|
Calcium binding site 4 out
of 7 in 2xgq
Go back to
Calcium Binding Sites List in 2xgq
Calcium binding site 4 out
of 7 in the Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca600
b:68.5
occ:1.00
|
OE1
|
B:GLU156
|
2.5
|
36.6
|
1.0
|
OD1
|
B:ASP30
|
2.8
|
32.1
|
1.0
|
CA
|
B:CA601
|
2.9
|
81.9
|
1.0
|
OD1
|
B:ASP155
|
3.0
|
32.4
|
1.0
|
OD2
|
B:ASP30
|
3.0
|
34.3
|
1.0
|
CG
|
B:ASP30
|
3.3
|
31.0
|
1.0
|
CD
|
B:GLU156
|
3.5
|
34.2
|
1.0
|
CG
|
B:ASP155
|
3.6
|
28.9
|
1.0
|
OD2
|
B:ASP155
|
3.6
|
31.1
|
1.0
|
CG
|
B:GLU156
|
3.9
|
30.5
|
1.0
|
OP1
|
Q:DG13
|
4.6
|
0.8
|
1.0
|
OE2
|
B:GLU156
|
4.7
|
35.2
|
1.0
|
O
|
B:MET31
|
4.7
|
26.5
|
1.0
|
CB
|
B:ASP30
|
4.8
|
28.3
|
1.0
|
OD1
|
B:ASN32
|
4.8
|
34.2
|
1.0
|
CB
|
B:ASP155
|
4.9
|
27.4
|
1.0
|
|
Calcium binding site 5 out
of 7 in 2xgq
Go back to
Calcium Binding Sites List in 2xgq
Calcium binding site 5 out
of 7 in the Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca601
b:81.9
occ:1.00
|
CA
|
B:CA600
|
2.9
|
68.5
|
1.0
|
OD2
|
B:ASP155
|
2.9
|
31.1
|
1.0
|
OE1
|
B:GLU156
|
3.0
|
36.6
|
1.0
|
OD1
|
B:ASP155
|
3.4
|
32.4
|
1.0
|
CG
|
B:ASP155
|
3.5
|
28.9
|
1.0
|
CD
|
B:GLU156
|
4.0
|
34.2
|
1.0
|
OG
|
B:SER153
|
4.1
|
30.8
|
1.0
|
OP1
|
Q:DG13
|
4.4
|
0.8
|
1.0
|
CG
|
B:GLU156
|
4.7
|
30.5
|
1.0
|
OE2
|
B:GLU156
|
4.8
|
35.2
|
1.0
|
CB
|
B:SER153
|
4.8
|
32.0
|
1.0
|
|
Calcium binding site 6 out
of 7 in 2xgq
Go back to
Calcium Binding Sites List in 2xgq
Calcium binding site 6 out
of 7 in the Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca602
b:70.6
occ:1.00
|
OD2
|
B:ASP289
|
2.9
|
36.2
|
1.0
|
OD1
|
B:ASP289
|
3.0
|
37.2
|
1.0
|
NZ
|
B:LYS3
|
3.1
|
58.9
|
1.0
|
CG
|
B:ASP289
|
3.3
|
36.0
|
1.0
|
OG1
|
B:THR231
|
3.6
|
37.6
|
1.0
|
CE
|
B:LYS3
|
3.7
|
56.2
|
1.0
|
O
|
B:HOH2032
|
4.4
|
39.2
|
1.0
|
CB
|
B:ASP232
|
4.5
|
33.7
|
1.0
|
OD2
|
B:ASP234
|
4.6
|
30.1
|
1.0
|
CB
|
B:ASP289
|
4.7
|
35.6
|
1.0
|
OD1
|
B:ASP234
|
4.8
|
31.0
|
1.0
|
OD2
|
B:ASP232
|
4.8
|
36.7
|
1.0
|
CB
|
B:THR231
|
4.8
|
38.2
|
1.0
|
OD2
|
B:ASP235
|
4.9
|
33.8
|
1.0
|
CD
|
B:LYS3
|
4.9
|
56.7
|
1.0
|
|
Calcium binding site 7 out
of 7 in 2xgq
Go back to
Calcium Binding Sites List in 2xgq
Calcium binding site 7 out
of 7 in the Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Structure of Yeast Dna Polymerase Eta in Complex with C8-N-Acetyl-2- Aminoanthracene Containing Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca603
b:65.8
occ:1.00
|
O
|
B:GLY98
|
2.4
|
44.8
|
1.0
|
OE1
|
B:GLU417
|
2.9
|
43.5
|
1.0
|
OE2
|
B:GLU417
|
3.0
|
42.7
|
1.0
|
CD
|
B:GLU417
|
3.3
|
41.0
|
1.0
|
C
|
B:GLY98
|
3.6
|
43.6
|
1.0
|
CA
|
B:GLY98
|
4.1
|
44.4
|
1.0
|
N
|
B:GLU99
|
4.7
|
42.2
|
1.0
|
CG
|
B:GLU417
|
4.9
|
38.0
|
1.0
|
CA
|
B:GLU99
|
5.0
|
41.5
|
1.0
|
|
Reference:
S.Schorr,
S.Schneider,
K.Lammens,
K.P.Hopfner,
T.Carell.
Mechanism of Replication Blocking and Bypass of Y-Family Polymerase Eta By Bulky Acetylaminofluorene Dna Adducts. Proc.Natl.Acad.Sci.Usa V. 107 20720 2010.
ISSN: ISSN 0027-8424
PubMed: 21076032
DOI: 10.1073/PNAS.1008894107
Page generated: Fri Jul 12 19:05:13 2024
|