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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

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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

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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

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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

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