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Calcium in PDB 2jei: 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: 2jei 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) 29.10 / 2.39
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.492, 103.717, 52.621, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 27.1

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 2jei). 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: 2jei:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2jei

Go back to Calcium Binding Sites List in 2jei
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:Ca1000

b:94.4
occ:1.00
O5' P:DT14 2.3 70.8 0.8
O P:HOH2015 2.7 67.3 1.0
OP2 P:DT14 2.8 68.9 0.8
C2' P:DT14 2.9 79.7 1.0
O1A A:DGT2475 2.9 47.7 1.0
O A:HOH2085 3.0 39.9 1.0
P P:DT14 3.1 68.3 1.0
C3' P:DT14 3.2 80.6 0.1
O2A A:DGT2475 3.4 50.2 1.0
C5' P:DT14 3.5 76.0 0.9
C6 P:DT14 3.6 78.5 0.3
C4' P:DT14 3.7 79.3 0.5
PA A:DGT2475 3.7 40.8 1.0
OP1 P:DT14 3.9 66.7 1.0
C1' P:DT14 3.9 79.2 1.0
O A:HOH2087 3.9 39.9 1.0
O4' P:DT14 4.0 80.1 0.3
N1 P:DT14 4.2 79.5 0.1
O A:HOH2088 4.3 45.5 1.0
O3' P:DC13 4.3 64.2 1.0
C2' P:DC13 4.4 57.0 1.0
O3' P:DT14 4.5 80.9 1.0
C5 P:DT14 4.6 77.7 0.9
C7 P:DT14 4.7 78.0 0.9
O5' A:DGT2475 4.8 43.4 1.0
C3' P:DC13 4.9 58.7 1.0
O3A A:DGT2475 4.9 46.3 1.0

Calcium binding site 2 out of 4 in 2jei

Go back to Calcium Binding Sites List in 2jei
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:Ca1001

b:35.1
occ:1.00
O A:PHE8 2.4 27.5 1.0
O2G A:DGT2475 2.5 38.1 1.0
OD2 A:ASP105 2.5 26.1 1.0
OD2 A:ASP7 2.6 39.5 1.0
O3A A:DGT2475 2.7 46.3 1.0
O1B A:DGT2475 2.8 43.2 1.0
CG A:ASP7 3.3 39.5 1.0
PA A:DGT2475 3.4 40.8 1.0
PB A:DGT2475 3.4 37.5 1.0
O2A A:DGT2475 3.4 50.2 1.0
CA A:CA1002 3.5 49.6 1.0
OD1 A:ASP7 3.5 42.8 1.0
PG A:DGT2475 3.5 37.3 1.0
C A:PHE8 3.6 28.4 1.0
CG A:ASP105 3.6 28.3 1.0
O5' A:DGT2475 3.6 43.4 1.0
O3B A:DGT2475 3.7 42.7 1.0
OD1 A:ASP105 4.1 32.2 1.0
N A:PHE8 4.1 31.2 1.0
O3G A:DGT2475 4.2 42.5 1.0
N A:TYR10 4.4 25.9 1.0
C A:ASP7 4.4 34.5 1.0
C5' A:DGT2475 4.4 43.1 1.0
CA A:PHE8 4.4 31.0 1.0
N A:ASP9 4.5 29.4 1.0
CA A:ASP9 4.5 28.7 1.0
CB A:ASP7 4.5 37.4 1.0
C A:ASP9 4.6 27.9 1.0
O2B A:DGT2475 4.7 46.2 1.0
O A:HOH2088 4.7 45.5 1.0
N A:PHE11 4.7 29.1 1.0
O A:ASP7 4.8 37.8 1.0
CB A:ASP105 4.8 28.1 1.0
O1G A:DGT2475 4.8 41.8 1.0
O A:ASP105 4.8 30.6 1.0
CA A:ASP7 4.9 35.0 1.0
O1A A:DGT2475 4.9 47.7 1.0
CB A:PHE11 5.0 26.2 1.0

Calcium binding site 3 out of 4 in 2jei

Go back to Calcium Binding Sites List in 2jei
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:Ca1002

b:49.6
occ:1.00
O2A A:DGT2475 2.5 50.2 1.0
O A:HOH2088 2.6 45.5 1.0
OD1 A:ASP105 2.6 32.2 1.0
OE2 A:GLU106 2.6 51.9 1.0
OD2 A:ASP7 2.8 39.5 1.0
O3' P:DT14 3.0 80.9 1.0
OD1 A:ASP7 3.2 42.8 1.0
CG A:ASP7 3.3 39.5 1.0
OD2 A:ASP105 3.3 26.1 1.0
CG A:ASP105 3.3 28.3 1.0
CD A:GLU106 3.5 47.7 1.0
PA A:DGT2475 3.5 40.8 1.0
CA A:CA1001 3.5 35.1 1.0
C3' P:DT14 3.5 80.6 0.1
O5' A:DGT2475 3.6 43.4 1.0
CB A:GLU106 4.0 36.3 1.0
CG A:GLU106 4.0 43.9 1.0
C4' P:DT14 4.2 79.3 0.5
O3A A:DGT2475 4.3 46.3 1.0
OG A:SER103 4.3 37.3 1.0
OE1 A:GLU106 4.4 51.5 1.0
O A:ASP105 4.4 30.6 1.0
C5' P:DT14 4.4 76.0 0.9
O A:HOH2010 4.6 45.3 1.0
C A:ASP105 4.6 30.8 1.0
CB A:ASP7 4.6 37.4 1.0
O2G A:DGT2475 4.7 38.1 1.0
O5' P:DT14 4.7 70.8 0.8
CB A:ASP105 4.7 28.1 1.0
O1A A:DGT2475 4.8 47.7 1.0
C2' P:DT14 4.9 79.7 1.0
N A:GLU106 4.9 32.4 1.0
O A:HOH2042 4.9 62.4 1.0
C5' A:DGT2475 5.0 43.1 1.0

Calcium binding site 4 out of 4 in 2jei

Go back to Calcium Binding Sites List in 2jei
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
A:Ca1003

b:56.7
occ:1.00
O A:HOH2054 2.6 37.0 1.0
O P:HOH2014 2.6 51.8 1.0
O A:ALA181 2.7 43.8 1.0
O A:HOH2011 2.7 51.8 1.0
O A:ILE186 2.7 38.3 1.0
C A:ALA181 3.8 44.0 1.0
C A:ILE186 3.9 37.4 1.0
OP1 P:DC13 4.1 41.3 1.0
OP2 P:DC13 4.2 41.4 1.0
CA A:GLY187 4.3 39.0 1.0
N A:GLY187 4.5 38.3 1.0
O A:VAL183 4.6 38.7 1.0
CA A:ALA181 4.7 43.7 1.0
CA A:ASP182 4.7 42.9 1.0
N A:ASP182 4.7 44.1 1.0
P P:DC13 4.8 39.1 1.0
C A:GLY187 4.9 41.4 1.0
CA A:ILE186 4.9 37.2 1.0
CB A:ALA181 4.9 44.2 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: Sat Dec 12 03:42:02 2020

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