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

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

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

All present enzymatic activity of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-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 (-)Ftc-Dp, PDB code: 4qwe 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) 19.73 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.698, 102.432, 52.460, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 25.1

Other elements in 4qwe:

The structure of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-Dp also contains other interesting chemical elements:

Fluorine (F) 1 atom

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

Calcium binding site 1 out of 3 in 4qwe

Go back to Calcium Binding Sites List in 4qwe
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 (-)Ftc-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 (-)Ftc-Dp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:66.1
occ:1.00
 OE2 A:GLU106 2.5 45.6 1.0
O3B A:FTD701 2.6 74.1 1.0
O A:HOH977 2.9 63.4 1.0
OD1 A:ASP7 3.1 34.2 1.0
CA A:CA703 3.1 41.1 1.0
OD2 A:ASP7 3.2 45.9 1.0
OD2 A:ASP105 3.4 37.0 1.0
CD A:GLU106 3.4 41.5 1.0
C3' C:DC13 3.4 83.9 1.0
CG A:ASP7 3.5 39.8 1.0
CG A:GLU106 3.6 38.6 1.0
OD1 A:ASP105 3.6 39.6 1.0
PB A:FTD701 3.8 76.7 1.0
CG A:ASP105 3.9 37.2 1.0
O3' C:DC13 4.0 84.4 1.0
O1B A:FTD701 4.2 83.8 1.0
O5' C:DC13 4.3 85.9 1.0
C2' C:DC13 4.3 78.8 1.0
O2A A:FTD701 4.3 76.3 1.0
NZ A:LYS159 4.3 68.1 1.0
C5' C:DC13 4.4 85.9 1.0
C4' C:DC13 4.4 83.6 1.0
O A:HOH969 4.5 68.6 1.0
OE1 A:GLU106 4.5 41.7 1.0
O1A A:FTD701 4.6 71.1 1.0
O A:ASP105 4.8 30.3 1.0
C5' A:FTD701 4.9 76.8 1.0
CB A:ASP7 4.9 34.2 1.0

Calcium binding site 2 out of 3 in 4qwe

Go back to Calcium Binding Sites List in 4qwe
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 (-)Ftc-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 (-)Ftc-Dp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:41.1
occ:1.00
 O3B A:FTD701 2.2 74.1 1.0
O1A A:FTD701 2.3 71.1 1.0
O A:PHE8 2.3 35.0 1.0
OD1 A:ASP105 2.3 39.6 1.0
OD1 A:ASP7 2.4 34.2 1.0
O A:HOH855 3.0 43.8 1.0
CA A:CA702 3.1 66.1 1.0
CG A:ASP105 3.4 37.2 1.0
PB A:FTD701 3.5 76.7 1.0
C A:PHE8 3.5 33.3 1.0
PA A:FTD701 3.6 75.7 1.0
CG A:ASP7 3.6 39.8 1.0
O2A A:FTD701 3.7 76.3 1.0
O2B A:FTD701 3.9 78.9 1.0
O A:HOH803 4.0 38.7 1.0
OD2 A:ASP105 4.0 37.0 1.0
N A:PHE8 4.0 33.1 1.0
OD2 A:ASP7 4.2 45.9 1.0
CA A:PHE8 4.3 34.0 1.0
C5' A:FTD701 4.3 76.8 1.0
C A:ASP7 4.3 35.5 1.0
N A:TYR10 4.4 34.6 1.0
O5' A:FTD701 4.4 81.5 1.0
N A:ASP9 4.4 34.1 1.0
CA A:ASP9 4.5 35.3 1.0
CB A:ASP105 4.5 32.0 1.0
O A:ASP105 4.6 30.3 1.0
C A:ASP9 4.6 33.8 1.0
NZ A:LYS159 4.7 68.1 1.0
N A:PHE11 4.7 34.6 1.0
O1B A:FTD701 4.7 83.8 1.0
CB A:ASP7 4.7 34.2 1.0
O A:ASP7 4.8 35.9 1.0
CB A:PHE8 4.8 31.6 1.0
O3A A:FTD701 4.8 87.7 1.0
CA A:ASP7 4.9 34.8 1.0
CB A:PHE11 5.0 33.5 1.0

Calcium binding site 3 out of 3 in 4qwe

Go back to Calcium Binding Sites List in 4qwe
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 (-)Ftc-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 (-)Ftc-Dp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:56.2
occ:1.00
 O A:ALA181 2.5 66.1 1.0
O A:ILE186 2.5 44.5 1.0
O A:HOH933 2.6 59.1 1.0
O A:HOH879 2.8 48.9 1.0
C A:ALA181 3.6 67.9 1.0
C A:ILE186 3.7 45.8 1.0
CA A:ALA181 4.3 69.2 1.0
CA A:GLY187 4.3 51.3 1.0
N A:GLY187 4.5 48.0 1.0
CB A:ALA181 4.5 78.0 1.0
N A:ASP182 4.6 58.6 1.0
OP1 C:DT12 4.7 54.0 1.0
CA A:ASP182 4.8 51.5 1.0
CA A:ILE186 4.8 41.5 1.0
C A:GLY187 4.8 53.1 1.0
CB A:ILE186 4.9 42.7 1.0
O A:VAL183 4.9 43.1 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: Wed Jul 9 01:48:19 2025

Last articles

Na in 6A8B
Na in 6A82
Na in 6A4W
Na in 6A83
Na in 6A5S
Na in 6A4Q
Na in 6A4L
Na in 6A4P
Na in 6A4N
Na in 6A47
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy