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Calcium in PDB 2jeg: 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: 2jeg 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) 46.55 / 2.38
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.102, 103.165, 52.632, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 26.3

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

Calcium binding site 1 out of 4 in 2jeg

Go back to Calcium Binding Sites List in 2jeg
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:Ca1345

b:51.3
occ:1.00
 O A:HOH2038 2.3 54.5 1.0
OE2 A:GLU106 2.5 45.6 1.0
O2A A:DGT1344 2.7 34.4 1.0
OD1 A:ASP105 2.8 35.8 1.0
O A:HOH2036 2.8 40.0 1.0
OD2 A:ASP7 2.8 46.4 1.0
OD1 A:ASP7 3.1 43.8 1.0
CG A:ASP7 3.3 40.1 1.0
CD A:GLU106 3.4 44.1 1.0
CG A:ASP105 3.6 32.4 1.0
OD2 A:ASP105 3.6 28.7 1.0
CA A:CA1346 3.7 37.3 1.0
PA A:DGT1344 3.8 33.0 1.0
C4' P:DOC14 4.0 71.0 1.0
O5' P:DOC14 4.1 63.0 1.0
CG A:GLU106 4.1 41.4 1.0
O1A A:DGT1344 4.1 35.5 1.0
O5' A:DGT1344 4.1 32.0 1.0
CB A:GLU106 4.2 36.4 1.0
OE1 A:GLU106 4.3 45.5 1.0
C5' P:DOC14 4.4 66.8 1.0
C5' A:DGT1344 4.4 28.6 1.0
OG A:SER103 4.7 36.1 1.0
NZ A:LYS152 4.7 43.7 1.0
O A:ASP105 4.7 32.1 1.0
CB A:ASP7 4.7 36.9 1.0
O2G A:DGT1344 4.8 29.3 1.0
C3' P:DOC14 4.8 72.9 1.0
C A:ASP105 4.9 31.8 1.0
CB A:ASP105 5.0 31.2 1.0

Calcium binding site 2 out of 4 in 2jeg

Go back to Calcium Binding Sites List in 2jeg
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:Ca1346

b:37.3
occ:1.00
 OD2 A:ASP105 2.3 28.7 1.0
O1B A:DGT1344 2.4 33.4 1.0
O2A A:DGT1344 2.4 34.4 1.0
O2G A:DGT1344 2.4 29.3 1.0
O A:PHE8 2.5 32.3 1.0
OD2 A:ASP7 2.6 46.4 1.0
CG A:ASP7 3.3 40.1 1.0
NZ A:LYS159 3.3 55.8 1.0
CG A:ASP105 3.5 32.4 1.0
C A:PHE8 3.5 31.1 1.0
PB A:DGT1344 3.6 33.0 1.0
PA A:DGT1344 3.6 33.0 1.0
OD1 A:ASP7 3.6 43.8 1.0
PG A:DGT1344 3.7 31.5 1.0
CA A:CA1345 3.7 51.3 1.0
N A:PHE8 3.9 30.5 1.0
O3A A:DGT1344 3.9 33.7 1.0
OD1 A:ASP105 4.0 35.8 1.0
O3B A:DGT1344 4.1 31.5 1.0
CE A:LYS159 4.1 55.5 1.0
C A:ASP7 4.2 33.3 1.0
O3G A:DGT1344 4.2 34.3 1.0
CA A:PHE8 4.2 30.8 1.0
C5' A:DGT1344 4.2 28.6 1.0
CB A:ASP7 4.3 36.9 1.0
N A:ASP9 4.4 31.7 1.0
O5' A:DGT1344 4.4 32.0 1.0
N A:TYR10 4.5 30.1 1.0
CA A:ASP9 4.6 31.5 1.0
O A:ASP7 4.6 33.1 1.0
CA A:ASP7 4.6 34.0 1.0
CB A:ASP105 4.6 31.2 1.0
O A:ASP105 4.6 32.1 1.0
C A:ASP9 4.8 30.9 1.0
O1A A:DGT1344 4.8 35.5 1.0
CB A:PHE8 4.9 28.0 1.0
N A:PHE11 4.9 31.5 1.0
O1G A:DGT1344 4.9 34.5 1.0
O2B A:DGT1344 4.9 34.2 1.0
O A:HOH2038 4.9 54.5 1.0

Calcium binding site 3 out of 4 in 2jeg

Go back to Calcium Binding Sites List in 2jeg
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:Ca1347

b:52.2
occ:1.00
 O A:ALA181 2.4 40.2 1.0
O A:HOH2049 2.5 50.7 1.0
O P:HOH2005 2.6 35.4 1.0
O A:ILE186 2.7 34.7 1.0
O A:HOH2051 2.7 43.5 1.0
O A:HOH2052 2.8 62.3 1.0
C A:ALA181 3.5 42.0 1.0
C A:ILE186 3.9 34.4 1.0
OP2 P:DC13 4.1 45.8 1.0
CA A:ALA181 4.3 43.0 1.0
CA A:GLY187 4.4 35.6 1.0
N A:ASP182 4.5 43.0 1.0
CB A:ALA181 4.5 41.7 1.0
CA A:ASP182 4.6 41.7 1.0
N A:GLY187 4.6 33.6 1.0
OP1 P:DC13 4.6 43.7 1.0
O A:VAL183 4.8 41.6 1.0
C A:GLY187 4.9 36.9 1.0
CA A:ILE186 4.9 34.0 1.0
CB A:ILE186 4.9 35.4 1.0

Calcium binding site 4 out of 4 in 2jeg

Go back to Calcium Binding Sites List in 2jeg
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:Ca1015

b:62.5
occ:1.00
 O1A A:DGT1344 2.5 35.5 1.0
O A:HOH2094 3.0 50.9 1.0
O3' P:DC13 3.1 58.2 1.0
O A:HOH2093 3.4 55.5 1.0
P P:DOC14 3.7 60.2 1.0
OP2 P:DOC14 3.9 61.7 1.0
PA A:DGT1344 4.0 33.0 1.0
C3' P:DC13 4.3 51.2 1.0
N7 A:DGT1344 4.4 31.8 1.0
O5' A:DGT1344 4.4 32.0 1.0
O5' P:DOC14 4.5 63.0 1.0
C2' P:DC13 4.5 50.3 1.0
C8 A:DGT1344 4.5 30.2 1.0
C5' P:DOC14 4.6 66.8 1.0
O3A A:DGT1344 4.7 33.7 1.0
O2A A:DGT1344 5.0 34.4 1.0
OP1 P:DOC14 5.0 65.7 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 13:41:32 2024

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