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Calcium in PDB 2xgp: Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna

Enzymatic activity of Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna

All present enzymatic activity of Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna:
2.7.7.7;

Protein crystallography data

The structure of Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna, PDB code: 2xgp was solved by S.Scheider, K.Lammens, S.Schorr, K.P.Hopfner, T.Carell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.76 / 2.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.440, 103.440, 292.350, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 27.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna (pdb code 2xgp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna, PDB code: 2xgp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2xgp

Go back to Calcium Binding Sites List in 2xgp
Calcium binding site 1 out of 8 in the Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1511

b:60.4
occ:1.00
 CA A:CA1512 2.8 70.9 1.0
OD2 A:ASP155 3.2 19.8 1.0
OD1 A:ASP155 3.2 23.6 1.0
CG A:ASP155 3.6 17.2 1.0
OE1 A:GLU156 3.8 23.4 1.0
O A:HOH2016 4.5 19.4 1.0
OP2 P:DG13 4.6 28.6 1.0
CD A:GLU156 4.7 20.0 1.0
OG A:SER153 4.8 18.6 1.0

Calcium binding site 2 out of 8 in 2xgp

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Calcium binding site 2 out of 8 in the Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1512

b:70.9
occ:1.00
 OE1 A:GLU156 2.7 23.4 1.0
CA A:CA1511 2.8 60.4 1.0
OD1 A:ASP30 3.1 26.5 1.0
OD2 A:ASP30 3.2 25.4 1.0
OD1 A:ASP155 3.2 23.6 1.0
CG A:ASP30 3.5 20.4 1.0
CD A:GLU156 3.7 20.0 1.0
CG A:ASP155 3.8 17.2 1.0
OD2 A:ASP155 3.8 19.8 1.0
CG A:GLU156 4.0 15.9 1.0
O A:HOH2016 4.1 19.4 1.0
ND2 A:ASN32 4.8 23.8 1.0
OE2 A:GLU156 4.8 21.0 1.0
O A:MET31 5.0 19.5 1.0

Calcium binding site 3 out of 8 in 2xgp

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Calcium binding site 3 out of 8 in the Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1513

b:50.4
occ:1.00
 OD1 A:ASP289 2.5 17.5 1.0
O A:HOH2026 2.9 11.7 1.0
OD2 A:ASP289 3.1 18.6 1.0
CG A:ASP289 3.2 15.1 1.0
OG1 A:THR231 3.5 15.6 1.0
CB A:ASP232 4.5 11.8 1.0
CB A:ASP289 4.6 13.3 1.0
OD2 A:ASP234 4.7 13.2 1.0
OD1 A:ASP234 4.9 12.1 1.0
OD2 A:ASP232 4.9 16.1 1.0
CB A:THR231 4.9 13.2 1.0

Calcium binding site 4 out of 8 in 2xgp

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Calcium binding site 4 out of 8 in the Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1514

b:3.1
occ:0.50
 OD1 A:ASN32 3.0 25.3 1.0
OG1 A:THR259 3.0 14.2 1.0
O A:THR259 3.3 13.6 1.0
C A:THR259 3.4 13.9 1.0
CB A:PRO280 3.4 26.9 1.0
N A:THR260 3.4 13.9 1.0
CA A:THR260 3.5 14.1 1.0
N A:ASP281 3.5 25.8 1.0
C A:THR260 3.6 14.2 1.0
N A:ASN32 3.6 18.6 1.0
N A:SER261 3.7 14.7 1.0
CG A:ASN32 3.7 21.4 1.0
CB A:THR259 3.7 14.6 1.0
CB A:ASN32 3.7 19.5 1.0
CA A:PRO280 3.8 26.6 1.0
OG A:SER261 4.0 18.9 1.0
C A:PRO280 4.2 25.9 1.0
CA A:THR259 4.2 14.4 1.0
O A:THR260 4.2 14.0 1.0
CA A:ASN32 4.2 18.7 1.0
O A:ASP30 4.2 15.6 1.0
NE2 A:GLN37 4.4 11.6 1.0
CA A:ASP281 4.5 25.5 1.0
C A:MET31 4.7 18.5 1.0
O A:ASN32 4.7 17.7 1.0
CG A:PRO280 4.7 26.6 1.0
CA A:MET31 4.8 17.9 1.0
CA A:SER261 4.8 15.2 1.0
C A:ASN32 4.9 17.8 1.0
ND2 A:ASN32 5.0 23.8 1.0
CB A:SER261 5.0 15.6 1.0

Calcium binding site 5 out of 8 in 2xgp

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Calcium binding site 5 out of 8 in the Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1511

b:69.7
occ:1.00
 OD2 B:ASP30 2.7 23.0 1.0
OE1 B:GLU156 2.8 33.4 1.0
CA B:CA1512 3.1 60.4 1.0
OD1 B:ASP30 3.1 25.2 1.0
OD1 B:ASP155 3.3 28.2 1.0
CG B:ASP30 3.3 20.5 1.0
CD B:GLU156 3.8 28.4 1.0
OP1 Q:DG13 4.0 93.0 1.0
CG B:GLU156 4.0 23.0 1.0
CG B:ASP155 4.1 22.6 1.0
OD2 B:ASP155 4.2 23.9 1.0
O B:HOH2004 4.3 17.5 1.0
C5' Q:DG13 4.6 94.8 1.0
OD1 B:ASN32 4.7 24.6 1.0
CB B:ASP30 4.8 18.2 1.0
OE2 B:GLU156 4.8 30.9 1.0

Calcium binding site 6 out of 8 in 2xgp

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Calcium binding site 6 out of 8 in the Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1512

b:60.4
occ:1.00
 OD2 B:ASP155 2.9 23.9 1.0
CA B:CA1511 3.1 69.7 1.0
OD1 B:ASP155 3.3 28.2 1.0
OE1 B:GLU156 3.4 33.4 1.0
CG B:ASP155 3.5 22.6 1.0
C5' Q:DG13 4.2 94.8 1.0
OP1 Q:DG13 4.4 93.0 1.0
CD B:GLU156 4.5 28.4 1.0
OG B:SER153 4.6 22.7 1.0
CG2 B:ILE154 5.0 20.5 1.0
CB B:ASP155 5.0 20.9 1.0

Calcium binding site 7 out of 8 in 2xgp

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Calcium binding site 7 out of 8 in the Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1513

b:59.9
occ:1.00
 OD1 B:ASP289 2.8 29.9 1.0
OD2 B:ASP289 3.2 27.8 1.0
CG B:ASP289 3.4 26.7 1.0
NZ B:LYS3 3.7 39.7 1.0
OG1 B:THR231 3.7 22.6 1.0
CE B:LYS3 3.8 37.8 1.0
CB B:ASP232 4.4 19.4 1.0
OD2 B:ASP232 4.6 22.0 1.0
CB B:ASP289 4.9 25.4 1.0
CB B:THR231 4.9 23.0 1.0
OD2 B:ASP234 4.9 18.6 1.0
OD1 B:ASP234 4.9 21.1 1.0

Calcium binding site 8 out of 8 in 2xgp

Go back to Calcium Binding Sites List in 2xgp
Calcium binding site 8 out of 8 in the Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Yeast Dna Polymerase Eta in Complex with C8-2-Acetylaminofluorene Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1514

b:53.2
occ:1.00
 O B:GLY98 2.7 21.4 1.0
OE2 B:GLU417 2.8 30.8 1.0
CD B:GLU417 3.6 27.5 1.0
OE1 B:GLU417 3.7 30.9 1.0
C B:GLY98 3.8 21.0 1.0
CA B:GLY98 4.4 20.7 1.0
N B:GLU99 4.8 21.7 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 19:05:04 2024

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