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Calcium in PDB 2va3: 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: 2va3 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) 30.17 / 2.98
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.620, 103.566, 52.645, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 28.2

Other elements in 2va3:

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) 2 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 2va3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 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: 2va3:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2va3

Go back to Calcium Binding Sites List in 2va3
Calcium binding site 1 out of 3 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:88.6
occ:1.00
 O P:HOH2009 2.3 85.2 1.0
O2A A:DGT1344 2.6 65.4 1.0
OD2 A:ASP105 2.9 49.3 1.0
C5' A:DGT1344 3.0 66.4 1.0
OE2 A:GLU106 3.0 61.6 1.0
O5' A:DGT1344 3.0 66.5 1.0
OD1 A:ASP105 3.0 50.7 1.0
CD A:GLU106 3.2 59.8 1.0
PA A:DGT1344 3.2 65.0 1.0
CG A:ASP105 3.4 49.1 1.0
O A:HOH2043 3.5 18.8 1.0
CG A:GLU106 3.6 56.4 1.0
OE1 A:GLU106 3.7 61.4 1.0
O1A A:DGT1344 3.8 64.8 1.0
OD1 A:ASP7 3.9 47.3 1.0
C4' A:DGT1344 4.2 68.4 1.0
O3' P:DA13 4.2 60.6 1.0
OG A:SER103 4.3 56.1 1.0
O4' A:DGT1344 4.4 69.0 1.0
CA A:CA1346 4.4 46.7 1.0
O3A A:DGT1344 4.7 66.3 1.0
CB A:SER103 4.7 50.9 1.0
O2B A:DGT1344 4.8 68.3 1.0
CB A:ASP105 4.9 46.9 1.0
CG A:ASP7 4.9 45.6 1.0

Calcium binding site 2 out of 3 in 2va3

Go back to Calcium Binding Sites List in 2va3
Calcium binding site 2 out of 3 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:46.7
occ:1.00
 O2B A:DGT1344 2.4 68.3 1.0
OD2 A:ASP105 2.5 49.3 1.0
O A:PHE8 2.6 40.9 1.0
O3G A:DGT1344 2.8 71.6 1.0
OD2 A:ASP7 3.0 49.2 1.0
OD1 A:ASP7 3.1 47.3 1.0
O2A A:DGT1344 3.1 65.4 1.0
CG A:ASP7 3.2 45.6 1.0
PB A:DGT1344 3.5 66.5 1.0
C A:PHE8 3.5 38.5 1.0
C5' A:DGT1344 3.6 66.4 1.0
CG A:ASP105 3.6 49.1 1.0
PG A:DGT1344 3.7 73.7 1.0
O3B A:DGT1344 3.8 70.8 1.0
O3A A:DGT1344 3.8 66.3 1.0
PA A:DGT1344 3.8 65.0 1.0
N A:PHE8 4.0 39.2 1.0
CB A:ASP105 4.1 46.9 1.0
O5' A:DGT1344 4.2 66.5 1.0
C A:ASP7 4.2 41.9 1.0
CA A:PHE8 4.2 37.2 1.0
O1G A:DGT1344 4.3 74.1 1.0
CA A:CA1345 4.4 88.6 1.0
N A:ASP9 4.4 37.8 1.0
N A:TYR10 4.4 36.0 1.0
CB A:ASP7 4.4 43.8 1.0
O A:ASP7 4.6 42.9 1.0
CA A:ASP9 4.6 38.3 1.0
OD1 A:ASP105 4.6 50.7 1.0
CA A:ASP7 4.7 43.2 1.0
C A:ASP9 4.7 37.7 1.0
C4' A:DGT1344 4.7 68.4 1.0
N A:PHE11 4.8 33.3 1.0
O1B A:DGT1344 4.8 64.5 1.0
O A:ASP105 4.9 46.5 1.0
CB A:PHE8 4.9 34.4 1.0

Calcium binding site 3 out of 3 in 2va3

Go back to Calcium Binding Sites List in 2va3
Calcium binding site 3 out of 3 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
A:Ca1347

b:0.5
occ:1.00
 O P:HOH2008 2.2 33.0 1.0
O P:HOH2011 2.3 94.6 1.0
O A:HOH2010 2.3 63.1 1.0
O A:HOH2022 2.6 21.8 1.0
O P:HOH2007 2.7 0.6 1.0
O A:HOH2021 3.0 43.0 1.0
O A:ALA181 3.3 57.7 1.0
O A:ILE186 4.3 50.0 1.0
OP2 P:DA13 4.4 53.0 1.0
OP1 P:DA13 4.4 52.1 1.0
C A:ALA181 4.4 57.5 1.0
O P:HOH2010 4.5 60.4 1.0
CA A:ASP182 4.5 55.5 1.0
C A:ASP182 4.9 52.3 1.0
P P:DA13 4.9 52.3 1.0
N A:ASP182 5.0 56.5 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 17:51:57 2024

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