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Calcium in PDB 2v9w: Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand

Enzymatic activity of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand

All present enzymatic activity of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand:
2.7.7.7;

Protein crystallography data

The structure of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand, PDB code: 2v9w was solved by A.Irimia, P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.51 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.704, 186.744, 52.730, 90.00, 110.06, 90.00
R / Rfree (%) 21.8 / 29

Other elements in 2v9w:

The structure of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand (pdb code 2v9w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand, PDB code: 2v9w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2v9w

Go back to Calcium Binding Sites List in 2v9w
Calcium binding site 1 out of 4 in the Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1345

b:50.8
occ:1.00
 O3B A:DCT1347 2.4 62.0 1.0
OD2 A:ASP105 2.5 49.5 1.0
O A:PHE8 2.5 46.2 1.0
OD1 A:ASP7 2.7 50.8 1.0
O1A A:DCT1347 2.8 69.8 1.0
OD2 A:ASP7 2.9 47.1 1.0
CG A:ASP7 3.0 49.1 1.0
O1G A:DCT1347 3.1 58.9 1.0
PG A:DCT1347 3.2 59.5 1.0
O2B A:DCT1347 3.3 66.0 1.0
O2G A:DCT1347 3.3 60.5 1.0
PB A:DCT1347 3.4 65.8 1.0
C A:PHE8 3.5 47.9 1.0
CG A:ASP105 3.5 49.2 1.0
N A:PHE8 3.8 47.7 1.0
PA A:DCT1347 4.0 70.2 1.0
CA A:CA1346 4.0 49.5 1.0
O3A A:DCT1347 4.0 68.4 1.0
O A:ASP105 4.0 47.3 1.0
CA A:PHE8 4.1 46.7 1.0
O A:ASP9 4.1 58.5 1.0
C A:ASP7 4.1 48.2 1.0
CB A:ASP105 4.3 47.2 1.0
OD1 A:ASP105 4.3 52.2 1.0
C A:ASP9 4.3 55.5 1.0
CB A:ASP7 4.3 48.1 1.0
C5' A:DCT1347 4.5 62.8 1.0
N A:ASP9 4.5 52.2 1.0
CB A:PHE8 4.6 43.4 1.0
O3G A:DCT1347 4.6 58.1 1.0
CA A:ASP7 4.6 47.3 1.0
N A:TYR10 4.6 53.0 1.0
O A:ASP7 4.6 50.2 1.0
O1B A:DCT1347 4.7 65.4 1.0
CA A:TYR10 4.7 52.1 1.0
O5' A:DCT1347 4.7 67.7 1.0
CA A:ASP9 4.7 55.0 1.0

Calcium binding site 2 out of 4 in 2v9w

Go back to Calcium Binding Sites List in 2v9w
Calcium binding site 2 out of 4 in the Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1346

b:49.5
occ:1.00
 O1A A:DCT1347 2.6 69.8 1.0
OE1 A:GLU106 2.6 62.9 1.0
OD2 A:ASP7 2.8 47.1 1.0
O A:HOH2059 3.1 29.9 1.0
CD A:GLU106 3.1 59.6 1.0
CG A:GLU106 3.5 55.3 1.0
OD1 A:ASP105 3.6 52.2 1.0
C3' C:DG13 3.7 96.5 1.0
PA A:DCT1347 3.7 70.2 1.0
OD2 A:ASP105 3.9 49.5 1.0
OE2 A:GLU106 4.0 60.9 1.0
CA A:CA1345 4.0 50.8 1.0
O2A A:DCT1347 4.0 70.7 1.0
CG A:ASP7 4.1 49.1 1.0
CG A:ASP105 4.1 49.2 1.0
O1G A:DCT1347 4.1 58.9 1.0
C5' A:DCT1347 4.2 62.8 1.0
O3' C:DG13 4.2 96.2 1.0
O5' A:DCT1347 4.4 67.7 1.0
C2' C:DG13 4.4 96.4 1.0
NZ A:LYS152 4.4 42.5 1.0
O A:ASP105 4.6 47.3 1.0
O5' C:DG13 4.7 0.9 1.0
OD1 A:ASP7 4.7 50.8 1.0
OG A:SER103 4.7 33.2 1.0
CB A:GLU106 4.8 50.4 1.0
C4' C:DG13 4.9 97.1 1.0

Calcium binding site 3 out of 4 in 2v9w

Go back to Calcium Binding Sites List in 2v9w
Calcium binding site 3 out of 4 in the Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1344

b:55.5
occ:1.00
 O3B B:DCT1346 2.5 67.3 1.0
O B:PHE8 2.5 36.5 1.0
OD2 B:ASP105 2.6 45.1 1.0
O1G B:DCT1346 2.7 63.6 1.0
O2B B:DCT1346 2.8 71.8 1.0
O1A B:DCT1346 3.0 77.3 1.0
OD2 B:ASP7 3.0 44.5 1.0
PG B:DCT1346 3.1 63.3 1.0
OD1 B:ASP7 3.2 43.9 1.0
PB B:DCT1346 3.2 70.6 1.0
CG B:ASP7 3.3 43.9 1.0
C B:PHE8 3.6 36.7 1.0
O2G B:DCT1346 3.6 64.7 1.0
CG B:ASP105 3.6 45.5 1.0
OE2 B:GLU106 3.8 46.5 1.0
PA B:DCT1346 3.8 75.4 1.0
O3A B:DCT1346 3.8 72.8 1.0
O5' B:DCT1346 3.8 72.3 1.0
N B:PHE8 4.0 38.5 1.0
CB B:ASP105 4.1 43.4 1.0
N B:TYR10 4.2 40.3 1.0
CA B:PHE8 4.3 37.2 1.0
CA B:CA1345 4.4 63.6 1.0
O B:HOH2048 4.4 50.4 1.0
C B:ASP7 4.5 40.6 1.0
O3G B:DCT1346 4.5 59.8 1.0
N B:PHE11 4.5 41.4 1.0
O1B B:DCT1346 4.5 70.0 1.0
CB B:PHE8 4.6 37.0 1.0
N B:ASP9 4.6 36.8 1.0
OD1 B:ASP105 4.6 49.0 1.0
CB B:ASP7 4.7 41.0 1.0
O B:ASP105 4.7 37.9 1.0
CA B:ASP9 4.7 37.4 1.0
C B:ASP9 4.7 38.2 1.0
CA B:TYR10 4.8 41.2 1.0
CB B:PHE11 4.9 41.1 1.0
CA B:ASP7 4.9 40.4 1.0
O B:ASP7 5.0 41.8 1.0

Calcium binding site 4 out of 4 in 2v9w

Go back to Calcium Binding Sites List in 2v9w
Calcium binding site 4 out of 4 in the Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex Structure of Sulfolobus Solfataricus DPO4 and Dna Duplex Containing A Hydrophobic Thymine Isostere 2,4- Difluorotoluene Nucleotide in the Template Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1345

b:63.6
occ:1.00
 O1A B:DCT1346 2.4 77.3 1.0
OE1 B:GLU106 2.6 48.7 1.0
OE2 B:GLU106 2.7 46.5 1.0
CD B:GLU106 3.0 47.7 1.0
O B:HOH2011 3.0 46.1 1.0
C3' E:DG13 3.1 84.2 1.0
C5' E:DG13 3.2 84.7 1.0
PA B:DCT1346 3.2 75.4 1.0
OD2 B:ASP105 3.2 45.1 1.0
C2' E:DG13 3.4 85.1 1.0
O5' B:DCT1346 3.5 72.3 1.0
OD2 B:ASP7 3.5 44.5 1.0
O2A B:DCT1346 3.5 74.2 1.0
C4' E:DG13 3.7 84.7 1.0
OD1 B:ASP105 3.9 49.0 1.0
CG B:ASP105 4.0 45.5 1.0
O1G B:DCT1346 4.1 63.6 1.0
O3' E:DG13 4.3 81.3 1.0
CA B:CA1344 4.4 55.5 1.0
CG B:GLU106 4.4 45.9 1.0
C5' B:DCT1346 4.4 66.6 1.0
O5' E:DG13 4.5 86.3 1.0
C1' E:DG13 4.7 85.5 1.0
O3A B:DCT1346 4.7 72.8 1.0
O4' E:DG13 4.7 85.9 1.0
CG B:ASP7 4.8 43.9 1.0
C8 E:DG13 4.8 85.5 1.0
OG B:SER103 4.9 43.7 1.0

Reference:

A.Irimia, R.L.Eoff, P.S.Pallan, F.P.Guengerich, M.Egli. Structure and Activity of Y-Class Dna Polymerase DPO4 From Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4- Difluorotoluene. J.Biol.Chem. V. 282 36421 2007.
ISSN: ISSN 0021-9258
PubMed: 17951245
DOI: 10.1074/JBC.M707267200
Page generated: Fri Jul 12 17:51:58 2024

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