Atomistry » Calcium » PDB 2v5d-2vjj » 2va2
Atomistry »
  Calcium »
    PDB 2v5d-2vjj »
      2va2 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy