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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: Sun Jul 14 12:33:49 2024

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