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Calcium in PDB 2jef: The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State and X-Ray Crystallography of Correct and Incorrect Pairing

Enzymatic activity of The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State and X-Ray Crystallography of Correct and Incorrect Pairing

All present enzymatic activity of The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State and X-Ray Crystallography of Correct and Incorrect Pairing:
2.7.7.7;

Protein crystallography data

The structure of The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State and X-Ray Crystallography of Correct and Incorrect Pairing, PDB code: 2jef was solved by R.L.Eoff, K.C.Angel, I.D.Kosekov, M.Egli, F.P.Guengerich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.99 / 2.17
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.990, 102.660, 52.880, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 26.7

Calcium Binding Sites:

The binding sites of Calcium atom in the The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State and X-Ray Crystallography of Correct and Incorrect Pairing (pdb code 2jef). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State and X-Ray Crystallography of Correct and Incorrect Pairing, PDB code: 2jef:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2jef

Go back to Calcium Binding Sites List in 2jef
Calcium binding site 1 out of 3 in the The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State and X-Ray Crystallography of Correct and Incorrect Pairing


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State and X-Ray Crystallography of Correct and Incorrect Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1344

b:44.3
occ:1.00
 O P:HOH2019 2.4 31.4 1.0
OD1 A:ASP105 2.6 27.3 1.0
O2A A:DGT1343 2.7 25.3 1.0
OD2 A:ASP7 2.8 30.8 1.0
OE1 A:GLU106 2.9 41.2 1.0
C5' P:DOC14 3.2 53.5 1.0
OD2 A:ASP105 3.3 28.1 1.0
CG A:ASP105 3.3 28.7 1.0
OD1 A:ASP7 3.4 35.4 1.0
CG A:ASP7 3.4 31.3 1.0
CA A:CA1345 3.5 26.4 1.0
C3' P:DOC14 3.6 52.6 1.0
PA A:DGT1343 3.8 27.7 1.0
C4' P:DOC14 3.9 53.6 1.0
CD A:GLU106 3.9 38.9 1.0
O5' A:DGT1343 4.2 24.2 1.0
CB A:GLU106 4.2 31.1 1.0
OP1 P:DOC14 4.2 50.6 1.0
C5' A:DGT1343 4.3 23.2 1.0
CG A:GLU106 4.3 37.8 1.0
O5' P:DOC14 4.3 51.6 1.0
O1A A:DGT1343 4.4 28.7 1.0
O A:ASP105 4.4 23.1 1.0
OG A:SER103 4.6 27.5 1.0
C A:ASP105 4.7 24.9 1.0
P P:DOC14 4.7 50.0 1.0
C2' P:DOC14 4.7 51.7 1.0
CB A:ASP105 4.8 25.0 1.0
CB A:ASP7 4.8 27.1 1.0
O1B A:DGT1343 4.8 29.3 1.0
O2G A:DGT1343 4.9 25.2 1.0
OE2 A:GLU106 5.0 43.5 1.0
N A:GLU106 5.0 25.2 1.0

Calcium binding site 2 out of 3 in 2jef

Go back to Calcium Binding Sites List in 2jef
Calcium binding site 2 out of 3 in the The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State and X-Ray Crystallography of Correct and Incorrect Pairing


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State and X-Ray Crystallography of Correct and Incorrect Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1345

b:26.4
occ:1.00
 O1B A:DGT1343 2.4 29.3 1.0
O2G A:DGT1343 2.4 25.2 1.0
O A:PHE8 2.4 22.6 1.0
OD2 A:ASP105 2.4 28.1 1.0
OD2 A:ASP7 2.5 30.8 1.0
O2A A:DGT1343 2.5 25.3 1.0
CG A:ASP7 3.4 31.3 1.0
CA A:CA1344 3.5 44.3 1.0
C A:PHE8 3.6 24.1 1.0
PB A:DGT1343 3.6 25.7 1.0
CG A:ASP105 3.6 28.7 1.0
PG A:DGT1343 3.6 26.2 1.0
PA A:DGT1343 3.7 27.7 1.0
OD1 A:ASP7 3.8 35.4 1.0
O3A A:DGT1343 4.0 25.7 1.0
O3B A:DGT1343 4.0 27.6 1.0
N A:PHE8 4.0 25.6 1.0
OD1 A:ASP105 4.1 27.3 1.0
O3G A:DGT1343 4.1 28.5 1.0
C5' A:DGT1343 4.2 23.2 1.0
C A:ASP7 4.2 25.8 1.0
CA A:PHE8 4.3 25.5 1.0
O5' A:DGT1343 4.5 24.2 1.0
CB A:ASP7 4.5 27.1 1.0
N A:ASP9 4.5 25.6 1.0
O A:ASP7 4.5 22.2 1.0
N A:TYR10 4.5 22.1 1.0
CA A:ASP9 4.6 24.7 1.0
O P:HOH2019 4.7 31.4 1.0
C A:ASP9 4.7 22.6 1.0
CA A:ASP7 4.7 26.1 1.0
CB A:ASP105 4.8 25.0 1.0
O A:ASP105 4.8 23.1 1.0
N A:PHE11 4.8 23.6 1.0
O1G A:DGT1343 4.9 29.2 1.0
O2B A:DGT1343 4.9 25.9 1.0
CB A:PHE8 5.0 21.7 1.0
O1A A:DGT1343 5.0 28.7 1.0

Calcium binding site 3 out of 3 in 2jef

Go back to Calcium Binding Sites List in 2jef
Calcium binding site 3 out of 3 in the The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State and X-Ray Crystallography of Correct and Incorrect Pairing


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Molecular Basis of Selectivity of Nucleotide Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State and X-Ray Crystallography of Correct and Incorrect Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1346

b:41.9
occ:1.00
 O A:ALA181 2.4 36.1 1.0
O A:HOH2089 2.5 47.5 1.0
O P:HOH2015 2.6 24.8 1.0
O A:ILE186 2.6 30.1 1.0
O P:HOH2016 2.7 32.1 1.0
C A:ALA181 3.5 35.0 1.0
C A:ILE186 3.9 31.6 1.0
CA A:ALA181 4.2 33.8 1.0
OP2 P:DC13 4.4 30.7 1.0
CB A:ALA181 4.4 33.7 1.0
CA A:GLY187 4.4 33.5 1.0
N A:ASP182 4.5 35.5 1.0
OP1 P:DC13 4.5 33.0 1.0
CA A:ASP182 4.6 34.2 1.0
N A:GLY187 4.6 32.4 1.0
O A:VAL183 4.8 28.0 1.0
C A:GLY187 4.9 33.1 1.0
CA A:ILE186 4.9 30.7 1.0
CB A:ILE186 4.9 32.1 1.0

Reference:

R.L.Eoff, K.C.Angel, M.Egli, F.P.Guengerich. Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase DPO4: Steady-State and Pre-Steady-State Kinetics and X-Ray Crystallography of Correct and Incorrect Pairing. J.Biol.Chem. V. 282 13573 2007.
ISSN: ISSN 0021-9258
PubMed: 17337730
DOI: 10.1074/JBC.M700656200
Page generated: Fri Jul 12 13:41:25 2024

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