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Calcium in PDB 2va2: 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: 2va2 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) 22.57 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.139, 101.875, 111.062, 90.00, 94.92, 90.00
R / Rfree (%) 21.1 / 25

Other elements in 2va2:

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 2va2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 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: 2va2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2va2

Go back to Calcium Binding Sites List in 2va2
Calcium binding site 1 out of 6 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:Ca1343

b:41.4
occ:1.00
 O A:PHE8 2.4 34.9 1.0
OD1 A:ASP7 2.6 41.9 1.0
O A:HOH2089 2.7 63.3 1.0
O2B A:DCT1345 2.9 74.9 1.0
O3B A:DCT1345 2.9 70.0 1.0
OD2 A:ASP105 3.0 37.8 1.0
O1G A:DCT1345 3.0 69.7 1.0
CG A:ASP7 3.2 40.0 1.0
OD2 A:ASP7 3.3 39.4 1.0
CG A:ASP105 3.5 35.6 1.0
PB A:DCT1345 3.5 72.4 1.0
PG A:DCT1345 3.6 68.1 1.0
O A:HOH2002 3.6 44.4 1.0
C A:PHE8 3.6 33.6 1.0
O1A A:DCT1345 3.7 73.7 1.0
OD1 A:ASP105 3.9 35.9 1.0
N A:PHE8 4.1 33.0 1.0
O2G A:DCT1345 4.2 70.5 1.0
O A:HOH2003 4.2 37.8 1.0
C A:ASP7 4.3 34.6 1.0
CB A:ASP105 4.3 33.8 1.0
CA A:PHE8 4.4 31.8 1.0
O3A A:DCT1345 4.5 74.5 1.0
N A:TYR10 4.5 31.8 1.0
O A:ASP105 4.5 33.2 1.0
CB A:ASP7 4.6 36.2 1.0
N A:ASP9 4.6 33.1 1.0
O1B A:DCT1345 4.6 71.0 1.0
O A:ASP7 4.7 35.6 1.0
CA A:ASP9 4.7 32.6 1.0
PA A:DCT1345 4.7 75.2 1.0
CA A:ASP7 4.8 35.9 1.0
C5' A:DCT1345 4.8 68.2 1.0
C A:ASP9 4.8 31.6 1.0
O3G A:DCT1345 4.9 70.3 1.0
CB A:PHE8 4.9 30.0 1.0
N A:PHE11 4.9 29.3 1.0
OE2 A:GLU106 4.9 39.2 1.0

Calcium binding site 2 out of 6 in 2va2

Go back to Calcium Binding Sites List in 2va2
Calcium binding site 2 out of 6 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:Ca1344

b:87.8
occ:1.00
 O A:HOH2023 2.3 71.1 1.0
O A:HOH2050 2.3 55.3 1.0
O A:ALA181 2.4 56.5 1.0
O A:HOH2048 2.6 55.6 1.0
O A:ILE186 2.7 52.7 1.0
O C:HOH2014 2.9 43.3 1.0
C A:ALA181 3.4 55.5 1.0
C A:ILE186 3.9 52.0 1.0
CA A:ALA181 3.9 55.7 1.0
CB A:ALA181 4.2 54.7 1.0
N A:ASP182 4.4 54.7 1.0
CA A:GLY187 4.5 55.2 1.0
N A:GLY187 4.7 53.4 1.0
CA A:ASP182 4.7 54.1 1.0
O A:VAL183 4.8 48.4 1.0
CB A:ILE186 4.9 49.8 1.0
CA A:ILE186 4.9 49.8 1.0
OP2 C:DT12 5.0 46.4 1.0

Calcium binding site 3 out of 6 in 2va2

Go back to Calcium Binding Sites List in 2va2
Calcium binding site 3 out of 6 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:Ca1346

b:76.4
occ:1.00
 O C:HOH2017 2.6 52.5 1.0
O A:HOH2002 3.0 44.4 1.0
O1A A:DCT1345 3.0 73.7 1.0
O A:HOH2088 3.1 66.2 1.0
O2A A:DCT1345 3.3 75.1 1.0
PA A:DCT1345 3.6 75.2 1.0
O A:HOH2090 3.8 54.6 1.0
O1G A:DCT1345 4.2 69.7 1.0
O5' A:DCT1345 4.5 71.1 1.0
OD1 A:ASP156 4.5 54.5 1.0
OP2 C:DA13 4.6 52.1 1.0
OE2 A:GLU106 4.7 39.2 1.0
C8 C:DA13 4.9 42.1 1.0
C5' A:DCT1345 4.9 68.2 1.0
O3A A:DCT1345 5.0 74.5 1.0
O C:HOH2006 5.0 53.6 1.0

Calcium binding site 4 out of 6 in 2va2

Go back to Calcium Binding Sites List in 2va2
Calcium binding site 4 out of 6 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:Ca1343

b:42.2
occ:1.00
 OD2 B:ASP105 2.3 44.5 1.0
OD1 B:ASP7 2.3 44.3 1.0
O B:PHE8 2.4 38.2 1.0
O3B E:DCT1014 2.7 94.4 1.0
O B:HOH2037 2.7 31.3 1.0
O2B E:DCT1014 3.1 93.1 1.0
O2G E:DCT1014 3.3 94.9 1.0
CG B:ASP7 3.4 41.6 1.0
CG B:ASP105 3.4 42.1 1.0
PB E:DCT1014 3.5 93.6 1.0
C B:PHE8 3.6 38.4 1.0
PG E:DCT1014 3.6 93.9 1.0
OD2 B:ASP7 4.0 42.5 1.0
N B:PHE8 4.0 35.7 1.0
O1G E:DCT1014 4.1 93.6 1.0
O3A E:DCT1014 4.1 92.1 1.0
CB B:ASP105 4.2 37.9 1.0
C B:ASP7 4.2 36.5 1.0
OD1 B:ASP105 4.3 45.7 1.0
CA B:PHE8 4.3 36.3 1.0
O B:ASP105 4.3 37.5 1.0
N B:TYR10 4.5 36.4 1.0
N B:ASP9 4.5 38.7 1.0
CB B:ASP7 4.6 38.8 1.0
O5' E:DCT1014 4.6 89.1 1.0
CA B:ASP7 4.7 37.0 1.0
O B:ASP7 4.7 37.6 1.0
CA B:ASP9 4.7 38.2 1.0
O1B E:DCT1014 4.8 94.8 1.0
O E:HOH2009 4.8 53.9 1.0
C B:ASP9 4.8 36.6 1.0
OE2 B:GLU106 4.8 38.0 1.0
CB B:PHE8 4.9 34.5 1.0
O3G E:DCT1014 4.9 96.0 1.0
CG B:GLU106 5.0 35.5 1.0
N B:PHE11 5.0 35.6 1.0

Calcium binding site 5 out of 6 in 2va2

Go back to Calcium Binding Sites List in 2va2
Calcium binding site 5 out of 6 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 5 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:83.7
occ:1.00
 O B:ALA181 2.4 67.5 1.0
O B:HOH2054 2.5 54.4 1.0
O B:HOH2053 2.5 66.0 1.0
O B:ILE186 2.6 59.9 1.0
O B:HOH2055 2.7 51.4 1.0
C B:ILE186 3.5 59.9 1.0
C B:ALA181 3.6 67.4 1.0
CA B:GLY187 4.0 63.8 1.0
N B:GLY187 4.1 61.4 1.0
CA B:ALA181 4.5 67.1 1.0
N B:ASP182 4.5 67.3 1.0
CA B:ASP182 4.5 66.5 1.0
CA B:ILE186 4.6 58.9 1.0
OP2 E:DT12 4.7 53.3 1.0
O B:VAL183 4.7 61.6 1.0
OP1 E:DT12 4.7 54.6 1.0
N B:ILE186 4.7 58.1 1.0
C B:GLY187 4.7 65.8 1.0
CB B:ILE186 4.8 58.1 1.0
C B:ASP182 4.8 65.0 1.0
CB B:ALA181 4.9 66.6 1.0

Calcium binding site 6 out of 6 in 2va2

Go back to Calcium Binding Sites List in 2va2
Calcium binding site 6 out of 6 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 6 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:Ca3002

b:92.2
occ:1.00
 O1A E:DCT1014 2.2 91.9 1.0
O B:HOH2049 2.8 56.3 1.0
O E:HOH2010 3.0 54.3 1.0
O E:HOH2011 3.6 42.9 1.0
PA E:DCT1014 3.7 91.4 1.0
OP2 E:DA13 3.8 58.6 1.0
O B:HOH2037 4.0 31.3 1.0
NZ B:LYS152 4.1 52.9 1.0
NZ B:LYS159 4.1 64.9 1.0
OD1 B:ASP156 4.3 55.3 1.0
O5' E:DCT1014 4.4 89.1 1.0
O2A E:DCT1014 4.5 91.1 1.0
O3A E:DCT1014 4.5 92.1 1.0
O1G E:DCT1014 4.5 93.6 1.0
C8 E:DA13 4.9 51.0 1.0
CE B:LYS152 4.9 50.4 1.0
OE2 B:GLU106 4.9 38.0 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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