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Calcium in PDB 4qwa: Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Dp

Enzymatic activity of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Dp

All present enzymatic activity of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Dp:
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 (-)3TC-Dp, PDB code: 4qwa 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) 19.94 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.179, 102.644, 52.586, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 24.1

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 (-)3TC-Dp (pdb code 4qwa). 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 (-)3TC-Dp, PDB code: 4qwa:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4qwa

Go back to Calcium Binding Sites List in 4qwa
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 (-)3TC-Dp


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 (-)3TC-Dp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:52.4
occ:1.00
 OD2 A:ASP105 2.5 45.2 1.0
OE2 A:GLU106 2.5 50.6 1.0
O A:HOH633 2.5 69.9 1.0
O2B A:0G8401 2.6 48.9 1.0
OD2 A:ASP7 2.7 51.2 1.0
C3' C:DC13 3.3 74.6 1.0
O3' C:DC13 3.3 79.7 1.0
CD A:GLU106 3.4 46.3 1.0
CG A:ASP7 3.4 49.4 1.0
CA A:CA403 3.5 41.9 1.0
OD1 A:ASP7 3.5 45.9 1.0
CG A:GLU106 3.7 45.2 1.0
CG A:ASP105 3.7 45.1 1.0
PB A:0G8401 3.7 50.2 1.0
O3B A:0G8401 4.0 56.3 1.0
C4' C:DC13 4.3 73.5 1.0
O A:HOH699 4.3 75.5 1.0
O5' C:DC13 4.4 77.3 1.0
C2' C:DC13 4.4 71.6 1.0
C5' C:DC13 4.4 74.7 1.0
CB A:ASP105 4.5 40.9 1.0
OE1 A:GLU106 4.5 44.5 1.0
NZ A:LYS159 4.5 63.8 1.0
OD1 A:ASP105 4.5 47.1 1.0
O3A A:0G8401 4.6 49.2 1.0
NZ A:LYS152 4.8 47.3 1.0
CB A:ASP7 4.8 46.5 1.0
O2A A:0G8401 4.9 39.6 1.0
O1B A:0G8401 5.0 51.3 1.0

Calcium binding site 2 out of 3 in 4qwa

Go back to Calcium Binding Sites List in 4qwa
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 (-)3TC-Dp


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 (-)3TC-Dp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:41.9
occ:1.00
 O2A A:0G8401 2.3 39.6 1.0
O A:PHE8 2.3 44.1 1.0
O2B A:0G8401 2.4 48.9 1.0
OD1 A:ASP7 2.4 45.9 1.0
OD2 A:ASP105 2.6 45.2 1.0
O A:HOH557 2.6 51.6 1.0
OD1 A:ASP105 2.7 47.1 1.0
CG A:ASP105 3.0 45.1 1.0
CA A:CA402 3.5 52.4 1.0
PB A:0G8401 3.5 50.2 1.0
CG A:ASP7 3.5 49.4 1.0
C A:PHE8 3.5 44.1 1.0
PA A:0G8401 3.6 46.1 1.0
O3A A:0G8401 3.9 49.2 1.0
OD2 A:ASP7 3.9 51.2 1.0
O A:HOH503 4.1 46.3 1.0
O1B A:0G8401 4.1 51.3 1.0
N A:PHE8 4.1 42.5 1.0
N A:TYR10 4.2 41.6 1.0
CA A:PHE8 4.4 43.5 1.0
N A:ASP9 4.4 44.4 1.0
CA A:ASP9 4.4 45.0 1.0
C A:ASP7 4.4 44.3 1.0
CB A:ASP105 4.4 40.9 1.0
C5' A:0G8401 4.4 47.3 1.0
C A:ASP9 4.5 42.1 1.0
N A:PHE11 4.5 41.9 1.0
O5' A:0G8401 4.6 48.8 1.0
O1A A:0G8401 4.7 52.0 1.0
CB A:ASP7 4.7 46.5 1.0
O A:ASP105 4.8 39.5 1.0
O A:ASP7 4.8 44.8 1.0
O3B A:0G8401 4.9 56.3 1.0
CB A:PHE11 4.9 38.4 1.0
CB A:PHE8 4.9 43.1 1.0
CA A:ASP7 4.9 43.6 1.0
CA A:TYR10 4.9 42.8 1.0

Calcium binding site 3 out of 3 in 4qwa

Go back to Calcium Binding Sites List in 4qwa
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 (-)3TC-Dp


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 (-)3TC-Dp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:61.5
occ:1.00
 O A:ALA181 2.5 63.3 1.0
O A:HOH645 2.6 72.6 1.0
O A:HOH644 2.6 92.7 1.0
O C:HOH122 2.7 60.6 1.0
O A:HOH583 2.7 56.1 1.0
O A:ILE186 2.7 53.0 1.0
C A:ALA181 3.6 64.4 1.0
C A:ILE186 3.9 51.3 1.0
CA A:GLY187 4.5 58.8 1.0
CA A:ALA181 4.5 67.0 1.0
N A:ASP182 4.6 62.0 1.0
OP1 C:DT12 4.6 69.6 1.0
CA A:ASP182 4.6 58.9 1.0
N A:GLY187 4.7 54.0 1.0
CB A:ALA181 4.7 69.6 1.0
OP2 C:DT12 4.8 68.5 1.0
O A:VAL183 4.8 47.2 1.0
CA A:ILE186 5.0 49.7 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 12:32:22 2024

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