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Calcium in PDB 4qwc: Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and L-Dcdp

Enzymatic activity of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and L-Dcdp

All present enzymatic activity of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and L-Dcdp:
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 L-Dcdp, PDB code: 4qwc was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.46 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.440, 101.930, 105.400, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 27.7

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 L-Dcdp (pdb code 4qwc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 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 L-Dcdp, PDB code: 4qwc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4qwc

Go back to Calcium Binding Sites List in 4qwc
Calcium binding site 1 out of 5 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and L-Dcdp


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 L-Dcdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:43.3
occ:1.00
 OAE A:LTP405 2.2 79.0 1.0
O A:PHE8 2.2 40.9 1.0
OD2 A:ASP105 2.3 35.8 1.0
OAJ A:LTP405 2.3 55.1 1.0
OD1 A:ASP7 2.3 41.2 1.0
CA A:CA402 2.9 88.5 1.0
O A:HOH535 3.4 41.4 0.5
CG A:ASP7 3.4 42.8 1.0
PAI A:LTP405 3.4 58.4 1.0
C A:PHE8 3.5 41.8 1.0
PAF A:LTP405 3.5 76.0 1.0
CG A:ASP105 3.5 34.8 1.0
OAH A:LTP405 3.7 64.9 1.0
OD2 A:ASP7 3.8 45.2 1.0
OAL A:LTP405 3.9 62.5 1.0
CAM A:LTP405 3.9 59.9 1.0
NZ A:LYS159 4.0 65.1 1.0
O A:HOH502 4.0 65.9 1.0
OD1 A:ASP105 4.1 35.7 1.0
N A:PHE8 4.2 39.9 1.0
OBB A:LTP405 4.2 70.8 1.0
N A:TYR10 4.3 42.1 1.0
N A:ASP9 4.3 43.9 1.0
CA A:ASP9 4.4 44.6 1.0
CA A:PHE8 4.4 40.8 1.0
C A:ASP7 4.4 42.0 1.0
C A:ASP9 4.5 43.5 1.0
O A:HOH559 4.6 62.5 1.0
CB A:ASP105 4.6 33.7 1.0
OAG A:LTP405 4.6 73.5 1.0
O A:ASP105 4.6 34.4 1.0
CB A:ASP7 4.7 41.3 1.0
O A:ASP7 4.8 43.7 1.0
OAK A:LTP405 4.8 60.0 1.0
N A:PHE11 4.8 37.0 1.0
CB A:PHE11 4.9 34.2 1.0
CA A:ASP7 5.0 41.6 1.0

Calcium binding site 2 out of 5 in 4qwc

Go back to Calcium Binding Sites List in 4qwc
Calcium binding site 2 out of 5 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and L-Dcdp


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 L-Dcdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:88.5
occ:1.00
 CA A:CA401 2.9 43.3 1.0
OD2 A:ASP105 3.0 35.8 1.0
OD1 A:ASP105 3.0 35.7 1.0
OD1 A:ASP7 3.1 41.2 1.0
O A:HOH559 3.1 62.5 1.0
OAE A:LTP405 3.1 79.0 1.0
OD2 A:ASP7 3.2 45.2 1.0
CG A:ASP105 3.3 34.8 1.0
O A:HOH525 3.4 57.5 0.5
CG A:ASP7 3.5 42.8 1.0
CG A:GLU106 3.6 40.8 1.0
CAM A:LTP405 3.7 59.9 1.0
CD A:GLU106 3.8 42.8 1.0
OBB A:LTP405 3.9 70.8 1.0
PAF A:LTP405 4.1 76.0 1.0
OE1 A:GLU106 4.1 48.0 1.0
OAL A:LTP405 4.1 62.5 1.0
OE2 A:GLU106 4.2 43.1 1.0
OAJ A:LTP405 4.3 55.1 1.0
NZ A:LYS159 4.3 65.1 1.0
O A:ASP105 4.4 34.4 1.0
OP1 B:DOC101 4.7 88.4 1.0
PAI A:LTP405 4.8 58.4 1.0
O A:PHE8 4.8 40.9 1.0
CB A:ASP105 4.8 33.7 1.0
CB A:ASP7 4.9 41.3 1.0
C A:ASP105 4.9 34.0 1.0
OG A:SER103 5.0 29.4 1.0

Calcium binding site 3 out of 5 in 4qwc

Go back to Calcium Binding Sites List in 4qwc
Calcium binding site 3 out of 5 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and L-Dcdp


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 L-Dcdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:96.9
occ:1.00
 OD2 D:ASP294 2.3 95.3 1.0
CG D:ASP294 3.3 94.3 1.0
OD1 D:ASP294 3.4 97.8 1.0
OP2 E:DA10 4.2 86.6 1.0
NH2 D:ARG328 4.2 0.0 1.0
O D:ILE295 4.5 79.5 1.0
CB D:ASP294 4.7 94.5 1.0
OP1 E:DA10 4.8 92.0 1.0
P E:DA10 4.9 88.4 1.0
C3' E:DG9 5.0 94.8 1.0

Calcium binding site 4 out of 5 in 4qwc

Go back to Calcium Binding Sites List in 4qwc
Calcium binding site 4 out of 5 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and L-Dcdp


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 L-Dcdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:86.4
occ:1.00
 OD2 D:ASP7 2.9 45.9 1.0
CA D:CA403 2.9 52.2 1.0
OAE D:LTP405 3.0 68.3 1.0
OD2 D:ASP105 3.2 47.1 1.0
OD1 D:ASP7 3.2 43.4 1.0
CG D:ASP7 3.3 44.7 1.0
OBB D:LTP405 3.4 67.1 1.0
OE2 D:GLU106 3.6 46.6 1.0
CG D:GLU106 3.7 45.8 1.0
CD D:GLU106 3.7 47.7 1.0
PAF D:LTP405 3.8 70.7 1.0
OD1 D:ASP105 3.8 44.8 1.0
CAM D:LTP405 3.8 69.0 1.0
CG D:ASP105 3.9 44.9 1.0
O D:HOH544 3.9 63.4 1.0
NZ D:LYS159 4.1 64.0 1.0
OAL D:LTP405 4.2 71.8 1.0
OAJ D:LTP405 4.3 61.2 1.0
OE1 D:GLU106 4.5 55.2 1.0
NZ D:LYS152 4.7 43.5 1.0
CB D:ASP7 4.7 45.6 1.0
PAI D:LTP405 4.7 63.7 1.0
OAH D:LTP405 4.8 65.4 1.0
O D:ASP105 4.9 42.5 1.0
O D:HOH535 4.9 58.7 1.0
O D:PHE8 5.0 42.8 1.0
OAG D:LTP405 5.0 68.2 1.0

Calcium binding site 5 out of 5 in 4qwc

Go back to Calcium Binding Sites List in 4qwc
Calcium binding site 5 out of 5 in the Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and L-Dcdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ternary Crystal Structures of A Y-Family Dna Polymerase DPO4 From Sulfolobus Solfataricus in Complex with Dna and L-Dcdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca403

b:52.2
occ:1.00
 OAE D:LTP405 2.2 68.3 1.0
OAJ D:LTP405 2.2 61.2 1.0
OD1 D:ASP7 2.2 43.4 1.0
O D:PHE8 2.3 42.8 1.0
OD2 D:ASP105 2.3 47.1 1.0
CA D:CA402 2.9 86.4 1.0
CG D:ASP7 3.3 44.7 1.0
PAI D:LTP405 3.4 63.7 1.0
PAF D:LTP405 3.4 70.7 1.0
C D:PHE8 3.5 44.5 1.0
CG D:ASP105 3.6 44.9 1.0
OD2 D:ASP7 3.6 45.9 1.0
O D:HOH502 3.7 50.3 1.0
OAH D:LTP405 3.7 65.4 1.0
O D:HOH509 3.8 58.6 1.0
OAL D:LTP405 3.9 71.8 1.0
CAM D:LTP405 3.9 69.0 1.0
OBB D:LTP405 4.1 67.1 1.0
N D:PHE8 4.3 43.8 1.0
N D:TYR10 4.3 43.8 1.0
NZ D:LYS159 4.3 64.0 1.0
CA D:ASP9 4.4 48.1 1.0
N D:ASP9 4.4 46.8 1.0
OD1 D:ASP105 4.4 44.8 1.0
CA D:PHE8 4.5 43.8 1.0
C D:ASP7 4.5 45.1 1.0
CB D:ASP105 4.5 43.2 1.0
C D:ASP9 4.5 45.3 1.0
O D:ASP105 4.6 42.5 1.0
OAG D:LTP405 4.7 68.2 1.0
CB D:ASP7 4.7 45.6 1.0
OAK D:LTP405 4.7 63.4 1.0
N D:PHE11 4.7 39.9 1.0
O D:ASP7 4.8 47.1 1.0
CA D:ASP7 5.0 45.2 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 12:32:34 2024

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