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

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

All present enzymatic activity of The Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State Kinetics 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 Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State Kinetics and X- Ray Crystallography of Correct and Incorrect Pairing, PDB code: 2jej 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) 47.03 / 1.86
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.220, 103.855, 52.740, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 26.5

Calcium Binding Sites:

The binding sites of Calcium atom in the The Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State Kinetics and X- Ray Crystallography of Correct and Incorrect Pairing (pdb code 2jej). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State Kinetics and X- Ray Crystallography of Correct and Incorrect Pairing, PDB code: 2jej:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2jej

Go back to Calcium Binding Sites List in 2jej
Calcium binding site 1 out of 4 in the The Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State Kinetics 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 Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State Kinetics and X- Ray Crystallography of Correct and Incorrect Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1343

b:26.8
occ:1.00
 OE2 A:GLU106 2.4 33.8 1.0
O2A A:DGT1346 2.5 23.2 1.0
OP2 P:DG15 2.5 39.0 1.0
OD2 A:ASP7 2.5 33.4 1.0
O P:HOH2019 2.6 26.6 1.0
OD1 A:ASP105 2.7 32.6 1.0
CD A:GLU106 3.3 32.5 1.0
CG A:GLU106 3.4 35.7 1.0
P P:DG15 3.5 42.7 1.0
CG A:ASP7 3.6 33.1 1.0
CG A:ASP105 3.6 30.0 1.0
CA A:CA1344 3.7 22.6 1.0
PA A:DGT1346 3.7 27.8 1.0
OP1 P:DG15 3.7 40.4 1.0
OD2 A:ASP105 3.9 26.0 1.0
OD1 A:ASP7 4.1 32.7 1.0
O1A A:DGT1346 4.1 26.1 1.0
O A:HOH2132 4.1 38.0 1.0
O5' A:DGT1346 4.2 25.8 1.0
O3' P:DC14 4.3 41.2 1.0
C5' A:DGT1346 4.4 24.6 1.0
CB A:GLU106 4.4 31.1 1.0
OE1 A:GLU106 4.5 29.3 1.0
O A:ASP105 4.5 23.4 1.0
CB A:ASP7 4.7 25.9 1.0
OP2 P:DC14 4.7 41.4 1.0
C A:ASP105 4.7 24.9 1.0
C4' P:DC14 4.8 43.4 1.0
O5' P:DG15 4.8 41.5 1.0
O3G A:DGT1346 4.9 21.9 1.0
C3' P:DC14 5.0 42.6 1.0
OG A:SER103 5.0 36.3 0.0
CB A:ASP105 5.0 29.9 1.0

Calcium binding site 2 out of 4 in 2jej

Go back to Calcium Binding Sites List in 2jej
Calcium binding site 2 out of 4 in the The Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State Kinetics 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 Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State Kinetics and X- Ray Crystallography of Correct and Incorrect Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1344

b:22.6
occ:1.00
 O1B A:DGT1346 2.3 23.0 1.0
O2A A:DGT1346 2.4 23.2 1.0
O A:PHE8 2.4 22.3 1.0
O3G A:DGT1346 2.4 21.9 1.0
OD2 A:ASP105 2.4 26.0 1.0
OD1 A:ASP7 2.5 32.7 1.0
CG A:ASP7 3.2 33.1 1.0
PB A:DGT1346 3.4 22.1 1.0
CG A:ASP105 3.4 30.0 1.0
PA A:DGT1346 3.5 27.8 1.0
OD2 A:ASP7 3.5 33.4 1.0
PG A:DGT1346 3.5 25.2 1.0
C A:PHE8 3.5 23.3 1.0
O3A A:DGT1346 3.7 23.1 1.0
CA A:CA1343 3.7 26.8 1.0
OD1 A:ASP105 3.7 32.6 1.0
O3B A:DGT1346 3.9 23.5 1.0
O A:HOH2132 3.9 38.0 1.0
N A:PHE8 4.0 25.5 1.0
NZ A:LYS159 4.1 47.0 1.0
O1G A:DGT1346 4.1 23.7 1.0
C5' A:DGT1346 4.2 24.6 1.0
CA A:PHE8 4.3 22.9 1.0
C A:ASP7 4.3 23.2 1.0
O5' A:DGT1346 4.4 25.8 1.0
N A:ASP9 4.5 24.7 1.0
CB A:ASP7 4.5 25.9 1.0
CE A:LYS159 4.5 50.1 1.0
N A:TYR10 4.6 22.5 1.0
CA A:ASP9 4.6 22.8 1.0
O1A A:DGT1346 4.7 26.1 1.0
CB A:ASP105 4.7 29.9 1.0
N A:PHE11 4.8 22.6 1.0
O A:ASP105 4.8 23.4 1.0
C A:ASP9 4.8 23.6 1.0
O2B A:DGT1346 4.8 21.2 1.0
CA A:ASP7 4.8 25.7 1.0
O A:ASP7 4.8 28.0 1.0
O P:HOH2019 4.8 26.6 1.0
CB A:PHE8 4.8 22.4 1.0
CB A:PHE11 4.9 21.6 1.0
O2G A:DGT1346 4.9 24.9 1.0

Calcium binding site 3 out of 4 in 2jej

Go back to Calcium Binding Sites List in 2jej
Calcium binding site 3 out of 4 in the The Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State Kinetics 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 Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State Kinetics and X- Ray Crystallography of Correct and Incorrect Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1345

b:44.7
occ:1.00
 O A:ALA181 2.5 37.5 1.0
O P:HOH2016 2.6 34.4 1.0
O A:ILE186 2.7 28.6 1.0
O P:HOH2017 2.7 35.2 1.0
O P:HOH2004 2.9 68.7 1.0
C A:ALA181 3.6 38.7 1.0
C A:ILE186 3.9 30.4 1.0
OP2 P:DC13 4.2 31.1 1.0
CA A:GLY187 4.4 31.3 1.0
CA A:ALA181 4.4 38.8 1.0
CB A:ALA181 4.6 39.5 1.0
N A:GLY187 4.6 29.7 1.0
N A:ASP182 4.6 37.7 1.0
OP1 P:DC13 4.7 33.7 1.0
C A:GLY187 4.8 32.7 1.0
O A:VAL183 4.8 28.8 1.0
CA A:ASP182 4.8 37.4 1.0
CA A:ILE186 5.0 28.7 1.0
P P:DC13 5.0 30.9 1.0

Calcium binding site 4 out of 4 in 2jej

Go back to Calcium Binding Sites List in 2jej
Calcium binding site 4 out of 4 in the The Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State Kinetics 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 4 of The Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine By Sulfolobus Solfataricus Dna Polymerase IV: Steady-State and Pre-Steady-State Kinetics and X- Ray Crystallography of Correct and Incorrect Pairing within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca1016

b:36.0
occ:1.00
 O1A A:DGT1346 2.4 26.1 1.0
OP2 P:DC14 2.6 41.4 1.0
O6 P:DG15 2.7 40.1 1.0
N7 P:DG15 2.7 41.0 1.0
O A:HOH2130 2.8 44.3 1.0
O P:HOH2021 2.8 42.4 1.0
O A:HOH2128 2.8 35.4 1.0
C6 P:DG15 3.3 42.3 1.0
C5 P:DG15 3.3 40.6 1.0
O3' P:DC13 3.4 39.6 1.0
P P:DC14 3.6 41.6 1.0
C8 P:DG15 3.9 40.9 1.0
PA A:DGT1346 4.0 27.8 1.0
O P:HOH2019 4.2 26.6 1.0
O A:HOH2133 4.5 32.6 1.0
O5' A:DGT1346 4.6 25.8 1.0
N7 A:DGT1346 4.6 25.8 1.0
OP1 P:DC14 4.6 39.9 1.0
C3' P:DC13 4.6 35.4 1.0
O3A A:DGT1346 4.6 23.1 1.0
C4 P:DG15 4.6 40.3 1.0
O5' P:DC14 4.7 42.2 1.0
N1 P:DG15 4.7 40.0 1.0
C8 A:DGT1346 4.7 27.5 1.0
C5' P:DC14 4.8 43.6 1.0
O A:HOH2134 4.8 45.6 1.0
C2' P:DC13 4.8 36.4 1.0
O2A A:DGT1346 4.9 23.2 1.0
N9 P:DG15 4.9 41.0 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 13:43:07 2024

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