Atomistry » Calcium » PDB 4qn5-4r90 » 4qwd
Atomistry »
  Calcium »
    PDB 4qn5-4r90 »
      4qwd »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy