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Calcium in PDB 4qw9: Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-Ppnp

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

All present enzymatic activity of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and (-)Ftc-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 (-)Ftc-Ppnp, PDB code: 4qw9 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) 29.18 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.800, 101.900, 52.540, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 27

Other elements in 4qw9:

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

Fluorine (F) 2 atoms

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-Ppnp (pdb code 4qw9). 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-Ppnp, PDB code: 4qw9:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4qw9

Go back to Calcium Binding Sites List in 4qw9
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-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 (-)Ftc-Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:85.4
occ:1.00
 O2A A:0G4701 2.4 0.8 0.5
O2B A:0G4701 2.5 0.4 0.5
OD2 A:ASP105 2.5 74.9 1.0
OD2 A:ASP7 2.5 80.3 1.0
OE2 A:GLU106 2.6 78.6 1.0
O A:HOH828 2.7 92.0 1.0
O A:HOH850 3.0 0.0 1.0
CD A:GLU106 3.3 75.2 1.0
C3' C:DC13 3.3 0.8 1.0
CG A:ASP7 3.4 79.3 1.0
OD1 A:ASP7 3.5 80.3 1.0
O2B A:0G4701 3.5 0.6 0.5
PA A:0G4701 3.5 99.9 0.5
CG A:GLU106 3.5 74.5 1.0
O3A A:0G4701 3.6 0.8 0.5
CA A:CA703 3.6 67.8 1.0
O3' C:DC13 3.7 0.7 1.0
CG A:ASP105 3.8 74.8 1.0
PB A:0G4701 3.8 0.0 0.5
O A:HOH871 4.0 0.6 1.0
O5' C:DC13 4.0 0.2 1.0
O3G A:0G4701 4.1 0.3 0.5
PB A:0G4701 4.1 0.7 0.5
O1B A:0G4701 4.1 1.0 0.5
OE1 A:GLU106 4.2 75.1 1.0
C5' C:DC13 4.3 1.0 1.0
C4' C:DC13 4.3 0.8 1.0
C2' C:DC13 4.3 0.8 1.0
O1A A:0G4701 4.4 0.1 0.5
O A:HOH834 4.4 83.8 1.0
O1A A:0G4701 4.4 0.2 0.5
CB A:ASP105 4.5 70.7 1.0
O3A A:0G4701 4.6 0.3 0.5
O1B A:0G4701 4.6 0.4 0.5
OD1 A:ASP105 4.7 79.0 1.0
NZ A:LYS159 4.7 93.4 1.0
O5' A:0G4701 4.8 97.7 0.5
CB A:ASP7 4.8 78.8 1.0
NZ A:LYS152 4.9 76.4 1.0
C5' A:0G4701 5.0 0.5 0.5

Calcium binding site 2 out of 3 in 4qw9

Go back to Calcium Binding Sites List in 4qw9
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-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 (-)Ftc-Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:67.8
occ:1.00
 O3G A:0G4701 2.0 0.3 0.5
O1A A:0G4701 2.1 0.1 0.5
O A:PHE8 2.1 78.2 1.0
OD1 A:ASP7 2.2 80.3 1.0
O2B A:0G4701 2.6 0.4 0.5
OD2 A:ASP105 2.6 74.9 1.0
O2B A:0G4701 2.7 0.6 0.5
OD1 A:ASP105 2.8 79.0 1.0
CG A:ASP105 3.0 74.8 1.0
CG A:ASP7 3.2 79.3 1.0
O3A A:0G4701 3.3 0.8 0.5
C A:PHE8 3.3 80.0 1.0
O2C A:0G4701 3.4 0.8 0.5
O3G A:0G4701 3.5 0.8 0.5
PB A:0G4701 3.5 0.7 0.5
PG A:0G4701 3.5 0.8 0.5
CA A:CA702 3.6 85.4 1.0
PA A:0G4701 3.6 99.6 0.5
O A:HOH802 3.7 75.7 1.0
OD2 A:ASP7 3.8 80.3 1.0
N A:PHE8 3.8 78.9 1.0
PG A:0G4701 3.8 0.6 0.5
PB A:0G4701 3.9 0.0 0.5
CA A:PHE8 4.1 79.8 1.0
N3B A:0G4701 4.1 0.3 0.5
C A:ASP7 4.2 80.1 1.0
O3A A:0G4701 4.2 0.3 0.5
O1G A:0G4701 4.2 0.1 0.5
N A:ASP9 4.3 82.8 1.0
N3B A:0G4701 4.3 0.4 0.5
CB A:ASP7 4.4 78.8 1.0
CA A:ASP9 4.4 84.3 1.0
O A:HOH831 4.4 0.5 1.0
O2A A:0G4701 4.4 0.8 0.5
CB A:ASP105 4.5 70.7 1.0
O2C A:0G4701 4.5 0.1 0.5
O5' A:0G4701 4.5 0.1 0.5
PA A:0G4701 4.5 99.9 0.5
N A:TYR10 4.6 83.0 1.0
C5' A:0G4701 4.6 0.5 0.5
O2A A:0G4701 4.6 0.8 0.5
CB A:PHE8 4.6 78.0 1.0
CA A:ASP7 4.6 78.2 1.0
O A:ASP105 4.7 70.3 1.0
O A:ASP7 4.7 81.0 1.0
C A:ASP9 4.7 83.7 1.0
NZ A:LYS159 4.8 93.4 1.0
N A:PHE11 4.8 78.1 1.0
CB A:PHE11 4.9 76.1 1.0
C5' A:0G4701 5.0 0.7 0.5
O1B A:0G4701 5.0 0.4 0.5

Calcium binding site 3 out of 3 in 4qw9

Go back to Calcium Binding Sites List in 4qw9
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-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 (-)Ftc-Ppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:90.2
occ:1.00
 O A:ALA181 2.6 94.0 1.0
O A:HOH820 2.8 81.8 1.0
O C:HOH104 2.8 0.7 1.0
O A:ILE186 3.3 83.0 1.0
C A:ALA181 3.7 95.0 1.0
CA A:ASP182 4.4 92.2 1.0
N A:ASP182 4.4 94.3 1.0
C A:ILE186 4.5 83.2 1.0
CA A:ALA181 4.6 97.3 1.0
CB A:ALA181 4.7 97.3 1.0
OP1 C:DT12 4.9 0.4 1.0
C A:ASP182 4.9 87.6 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 12:32:03 2024

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