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Calcium in PDB 2br0: Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine

Enzymatic activity of Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine

All present enzymatic activity of Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine:
2.7.7.7;

Protein crystallography data

The structure of Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine, PDB code: 2br0 was solved by A.Irimia, L.V.Loukachevitch, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.81 / 2.17
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.506, 102.072, 52.532, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 26.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine (pdb code 2br0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine, PDB code: 2br0:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2br0

Go back to Calcium Binding Sites List in 2br0
Calcium binding site 1 out of 3 in the Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2001

b:69.3
occ:1.00
 OE2 A:GLU106 2.2 49.5 1.0
OD1 A:ASP7 2.7 34.9 1.0
CD A:GLU106 3.0 45.8 1.0
OD2 A:ASP105 3.2 32.9 1.0
CG A:GLU106 3.3 42.3 1.0
CA A:CA2002 3.4 33.0 1.0
CG A:ASP7 3.5 33.2 1.0
OD1 A:ASP105 3.7 37.0 1.0
OD2 A:ASP7 3.7 30.0 1.0
O A:HOH2041 3.8 65.2 1.0
CG A:ASP105 3.8 35.0 1.0
OE1 A:GLU106 4.0 49.0 1.0
NZ A:LYS159 4.3 47.6 1.0
C5' A:DG1000 4.4 54.4 1.0
CB A:GLU106 4.7 36.3 1.0
CB A:ASP7 4.7 32.0 1.0
O3' P:DC13 4.9 53.0 1.0
O A:ASP105 4.9 27.7 1.0

Calcium binding site 2 out of 3 in 2br0

Go back to Calcium Binding Sites List in 2br0
Calcium binding site 2 out of 3 in the Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2002

b:33.0
occ:1.00
 OD2 A:ASP105 2.3 32.9 1.0
O A:PHE8 2.4 29.3 1.0
OD2 A:ASP7 2.5 30.0 1.0
CA A:CA2001 3.4 69.3 1.0
CG A:ASP7 3.4 33.2 1.0
CG A:ASP105 3.5 35.0 1.0
C A:PHE8 3.5 30.9 1.0
O A:HOH2006 3.6 32.9 1.0
OD1 A:ASP7 3.7 34.9 1.0
O A:HOH2011 3.7 59.2 1.0
C5' A:DG1000 3.8 54.4 1.0
N A:PHE8 4.1 31.3 1.0
O5' A:DG1000 4.2 56.7 1.0
C A:ASP7 4.3 31.5 1.0
OD1 A:ASP105 4.3 37.0 1.0
N A:TYR10 4.4 29.7 1.0
CA A:PHE8 4.4 30.5 1.0
CB A:ASP105 4.4 34.1 1.0
NZ A:LYS159 4.4 47.6 1.0
N A:ASP9 4.5 30.6 1.0
CA A:ASP9 4.5 30.7 1.0
C A:ASP9 4.6 29.7 1.0
O A:ASP105 4.6 27.7 1.0
CB A:ASP7 4.7 32.0 1.0
O A:ASP7 4.7 32.2 1.0
N A:PHE11 4.7 26.8 1.0
CA A:ASP7 4.8 30.5 1.0
CB A:PHE8 4.9 28.8 1.0

Calcium binding site 3 out of 3 in 2br0

Go back to Calcium Binding Sites List in 2br0
Calcium binding site 3 out of 3 in the Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus DPO4. Analysis and Crystal Structures of Multiple Base- Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:50.8
occ:1.00
 O A:ALA181 2.5 41.9 1.0
O P:HOH2004 2.6 58.6 1.0
O A:HOH2053 2.6 49.6 1.0
O P:HOH2013 2.7 48.9 1.0
O P:HOH2014 2.8 46.8 1.0
O A:ILE186 2.9 38.2 1.0
C A:ALA181 3.4 41.8 1.0
C A:ILE186 4.1 38.4 1.0
CA A:ALA181 4.2 42.0 1.0
N A:ASP182 4.3 42.7 1.0
CB A:ALA181 4.4 40.9 1.0
CA A:ASP182 4.5 42.6 1.0
OP1 P:DC13 4.5 41.5 1.0
CA A:GLY187 4.5 40.7 1.0
OP2 P:DC13 4.6 42.4 1.0
O A:VAL183 4.8 38.8 1.0
N A:GLY187 4.8 39.1 1.0
C A:GLY187 4.9 42.1 1.0
OD1 A:ASP182 4.9 55.6 1.0
C A:ASP182 5.0 40.8 1.0

Reference:

H.Zang, A.K.Goodenough, J.Y.Choi, A.Irimia, L.V.Loukachevitch, I.D.Kozekov, K.C.Angel, C.J.Rizzo, M.Egli, F.P.Guengerich. Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus Dna Polymerase DPO4: Analysis and Crystal Structures of Multiple Base Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine. J.Biol.Chem. V. 280 29750 2005.
ISSN: ISSN 0021-9258
PubMed: 15965231
DOI: 10.1074/JBC.M504756200
Page generated: Fri Jul 12 09:10:22 2024

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