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

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

All present enzymatic activity of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp:
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-Ppnp, PDB code: 4qwd 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) 19.71 / 2.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.544, 102.483, 52.375, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 26.2

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-Ppnp (pdb code 4qwd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 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-Ppnp, PDB code: 4qwd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4qwd

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


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-Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:78.0
occ:1.00
 O2B A:3TT701 2.2 0.7 1.0
OE2 A:GLU106 2.4 44.9 1.0
OD2 A:ASP105 2.7 43.3 1.0
O C:HOH101 2.8 64.1 1.0
OD2 A:ASP7 2.9 37.0 1.0
OD1 A:ASP7 3.2 37.5 1.0
CG A:ASP7 3.4 38.0 1.0
CD A:GLU106 3.4 42.8 1.0
O A:HOH981 3.5 68.1 1.0
C3' C:DC13 3.5 56.9 1.0
O3G A:3TT701 3.5 0.4 1.0
CA A:CA703 3.6 43.3 1.0
PB A:3TT701 3.6 98.7 1.0
CG A:GLU106 3.9 40.8 1.0
O3' C:DC13 3.9 61.9 1.0
CG A:ASP105 3.9 39.6 1.0
O1B A:3TT701 4.0 0.3 1.0
NZ A:LYS159 4.1 54.5 1.0
O5' C:DC13 4.2 59.2 1.0
O A:HOH971 4.2 54.5 1.0
C5' C:DC13 4.2 55.9 1.0
O3A A:3TT701 4.2 80.3 1.0
C4' C:DC13 4.3 55.4 1.0
OE1 A:GLU106 4.5 42.7 1.0
C2' C:DC13 4.5 54.8 1.0
OP1 C:DC13 4.5 60.4 1.0
NZ A:LYS152 4.6 41.4 1.0
OD1 A:ASP105 4.6 43.4 1.0
CB A:ASP7 4.7 38.2 1.0
PG A:3TT701 4.8 0.8 1.0
N3B A:3TT701 4.8 1.0 1.0
CB A:ASP105 4.9 38.8 1.0

Calcium binding site 2 out of 4 in 4qwd

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


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-Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:43.3
occ:1.00
 O A:PHE8 2.1 40.7 1.0
O2B A:3TT701 2.4 0.7 1.0
OD1 A:ASP7 2.4 37.5 1.0
O3G A:3TT701 2.5 0.4 1.0
OD1 A:ASP105 2.5 43.4 1.0
OD2 A:ASP105 2.7 43.3 1.0
O1A A:3TT701 2.7 73.1 1.0
O1G A:3TT701 2.8 0.3 1.0
CG A:ASP105 2.9 39.6 1.0
PG A:3TT701 3.0 0.8 1.0
PB A:3TT701 3.2 98.7 1.0
N3B A:3TT701 3.2 1.0 1.0
C A:PHE8 3.3 40.5 1.0
O3A A:3TT701 3.4 80.3 1.0
CA A:CA702 3.6 78.0 1.0
CG A:ASP7 3.6 38.0 1.0
PA A:3TT701 3.7 68.1 1.0
N A:PHE8 3.9 39.4 1.0
O A:HOH803 4.1 41.4 1.0
CA A:PHE8 4.1 40.1 1.0
OD2 A:ASP7 4.1 37.0 1.0
C A:ASP7 4.2 40.1 1.0
N A:ASP9 4.3 40.9 1.0
N A:TYR10 4.4 40.4 1.0
CB A:ASP105 4.4 38.8 1.0
CA A:ASP9 4.4 42.1 1.0
N A:PHE11 4.4 35.8 1.0
O A:ASP105 4.4 37.5 1.0
O2G A:3TT701 4.5 0.1 1.0
C A:ASP9 4.5 40.4 1.0
C5' A:3TT701 4.5 61.2 1.0
O5' A:3TT701 4.5 64.9 1.0
CB A:PHE8 4.5 38.0 1.0
O1B A:3TT701 4.6 0.3 1.0
CB A:PHE11 4.6 33.4 1.0
O A:ASP7 4.7 41.5 1.0
CB A:ASP7 4.7 38.2 1.0
CA A:ASP7 4.8 39.3 1.0
O2A A:3TT701 4.9 72.3 1.0

Calcium binding site 3 out of 4 in 4qwd

Go back to Calcium Binding Sites List in 4qwd
Calcium binding site 3 out of 4 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp


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-Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:54.8
occ:1.00
 O A:ALA181 2.5 55.0 1.0
O A:ILE186 2.6 44.6 1.0
O C:HOH113 2.7 42.4 1.0
O A:HOH932 2.7 64.5 1.0
O C:HOH121 2.8 49.0 1.0
C A:ALA181 3.6 55.7 1.0
C A:ILE186 3.8 43.9 1.0
CA A:GLY187 4.2 48.1 1.0
CA A:ALA181 4.3 58.4 1.0
O A:HOH990 4.4 55.3 1.0
N A:GLY187 4.5 44.4 1.0
N A:ASP182 4.5 52.6 1.0
CB A:ALA181 4.6 59.1 1.0
OP1 C:DT12 4.7 53.5 1.0
CA A:ASP182 4.7 49.8 1.0
C A:GLY187 4.8 52.1 1.0
O A:VAL183 4.8 40.4 1.0
OP2 C:DT12 4.9 55.8 1.0
CA A:ILE186 4.9 42.6 1.0
CB A:ILE186 5.0 44.3 1.0

Calcium binding site 4 out of 4 in 4qwd

Go back to Calcium Binding Sites List in 4qwd
Calcium binding site 4 out of 4 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)3TC-Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:75.1
occ:0.50
 O A:HOH1003 2.6 69.4 1.0
O A:HOH992 2.7 70.8 1.0
OE2 A:GLU127 2.7 71.1 1.0
CD A:GLU127 3.6 70.6 1.0
OE1 A:GLU127 3.9 70.4 1.0
CG A:GLU127 5.0 67.2 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 12:32:37 2024

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