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Calcium in PDB 4qw8: Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and D-Dctp

Enzymatic activity of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and D-Dctp

All present enzymatic activity of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and D-Dctp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and D-Dctp, PDB code: 4qw8 was solved by V.Gaur, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 2.29
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 98.073, 102.317, 52.495, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 23.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and D-Dctp (pdb code 4qw8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and D-Dctp, PDB code: 4qw8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4qw8

Go back to Calcium Binding Sites List in 4qw8
Calcium binding site 1 out of 3 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and D-Dctp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and D-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:42.3
occ:1.00
 OE2 A:GLU106 2.5 39.2 1.0
O A:HOH801 2.5 37.4 1.0
OD2 A:ASP7 2.6 27.7 1.0
O A:HOH908 2.6 55.0 1.0
OP1 C:DC13 2.6 43.6 1.0
O C:HOH125 2.7 42.6 1.0
CD A:GLU106 3.3 39.0 1.0
CG A:ASP7 3.4 30.4 1.0
P C:DC13 3.7 40.0 1.0
O5' C:DC13 3.7 42.1 1.0
OD1 A:ASP7 3.8 29.0 1.0
CG A:GLU106 3.8 35.7 1.0
O1A A:DCP701 3.9 21.3 1.0
C5' C:DC13 4.1 37.6 1.0
CE A:LYS152 4.1 38.5 1.0
OE1 A:GLU106 4.1 43.6 1.0
NZ A:LYS159 4.2 54.4 1.0
O A:HOH874 4.3 51.8 1.0
NZ A:LYS152 4.5 41.6 1.0
OP2 C:DC13 4.5 43.6 1.0
O C:HOH103 4.6 50.7 1.0
CB A:ASP7 4.6 30.0 1.0
CZ A:PHE5 4.7 30.9 1.0
CA A:CA703 4.7 29.2 1.0
O A:HOH975 4.8 47.2 1.0
OD2 A:ASP105 4.9 31.6 1.0
O2A A:DCP701 4.9 31.8 1.0
O3' C:DT12 4.9 40.0 1.0
C3' C:DC13 4.9 38.2 1.0
PA A:DCP701 4.9 26.2 1.0

Calcium binding site 2 out of 3 in 4qw8

Go back to Calcium Binding Sites List in 4qw8
Calcium binding site 2 out of 3 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and D-Dctp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and D-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:29.2
occ:1.00
 O2B A:DCP701 2.3 32.0 1.0
OD1 A:ASP105 2.4 30.3 1.0
O A:PHE8 2.4 32.2 1.0
OD1 A:ASP7 2.4 29.0 1.0
O1A A:DCP701 2.4 21.3 1.0
O2G A:DCP701 2.5 52.8 1.0
CG A:ASP105 3.5 33.0 1.0
CG A:ASP7 3.5 30.4 1.0
O A:HOH801 3.5 37.4 1.0
C A:PHE8 3.5 32.8 1.0
PB A:DCP701 3.6 31.5 1.0
PA A:DCP701 3.7 26.2 1.0
C5' A:DCP701 3.8 25.8 1.0
PG A:DCP701 3.9 57.2 1.0
OD2 A:ASP7 3.9 27.7 1.0
N A:PHE8 4.0 31.2 1.0
OD2 A:ASP105 4.1 31.6 1.0
O3A A:DCP701 4.1 33.0 1.0
O A:HOH829 4.1 38.6 1.0
O5' A:DCP701 4.2 25.6 1.0
O3B A:DCP701 4.2 43.4 1.0
CA A:PHE8 4.3 31.4 1.0
C A:ASP7 4.4 32.8 1.0
O A:HOH908 4.4 55.0 1.0
N A:ASP9 4.4 34.4 1.0
O1G A:DCP701 4.6 53.0 1.0
CA A:ASP9 4.6 34.0 1.0
CB A:ASP105 4.6 28.4 1.0
CA A:CA702 4.7 42.3 1.0
CB A:ASP7 4.7 30.0 1.0
C A:ASP9 4.7 31.9 1.0
N A:TYR10 4.7 31.5 1.0
CB A:PHE8 4.8 28.7 1.0
O A:ASP7 4.8 35.2 1.0
CE A:LYS159 4.8 52.4 1.0
O1B A:DCP701 4.8 34.5 1.0
N A:PHE11 4.9 29.3 1.0
CA A:ASP7 4.9 31.4 1.0
CB A:PHE11 4.9 26.6 1.0
O A:ASP105 4.9 28.1 1.0
O2A A:DCP701 4.9 31.8 1.0

Calcium binding site 3 out of 3 in 4qw8

Go back to Calcium Binding Sites List in 4qw8
Calcium binding site 3 out of 3 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and D-Dctp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and D-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:56.1
occ:1.00
 O A:ALA181 2.6 47.6 1.0
O A:HOH817 2.8 36.2 1.0
O C:HOH104 2.8 26.5 1.0
O A:HOH937 2.8 53.0 1.0
O A:ILE186 3.2 31.6 1.0
C A:ALA181 3.6 49.0 1.0
CA A:ASP182 4.3 45.5 1.0
N A:ASP182 4.4 47.4 1.0
C A:ILE186 4.4 31.7 1.0
CA A:ALA181 4.6 50.5 1.0
OD1 A:ASP182 4.7 58.7 1.0
CB A:ALA181 4.7 51.7 1.0
OP2 C:DT12 4.7 40.6 1.0
OP1 C:DT12 4.8 41.5 1.0
C A:ASP182 4.9 42.2 1.0
CA A:GLY187 4.9 35.4 1.0

Reference:

V.Gaur, R.Vyas, J.D.Fowler, G.Efthimiopoulos, J.Y.Feng, Z.Suo. Structural and Kinetic Insights Into Binding and Incorporation of L-Nucleotide Analogs By A Y-Family Dna Polymerase. Nucleic Acids Res. V. 42 9984 2014.
ISSN: ISSN 0305-1048
PubMed: 25104018
DOI: 10.1093/NAR/GKU709
Page generated: Sun Jul 14 12:31:56 2024

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