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Calcium in PDB 3au2: Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp

Enzymatic activity of Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp

All present enzymatic activity of Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp, PDB code: 3au2 was solved by S.Nakane, H.Ishikawa, T.Wakamatsu, N.Nakagawa, R.Masui, S.Kuramitsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.189, 53.286, 84.877, 90.00, 107.52, 90.00
R / Rfree (%) 16.2 / 18.8

Other elements in 3au2:

The structure of Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp also contains other interesting chemical elements:

Zinc (Zn) 3 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp (pdb code 3au2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp, PDB code: 3au2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3au2

Go back to Calcium Binding Sites List in 3au2
Calcium binding site 1 out of 4 in the Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca580

b:12.6
occ:0.90
 OD2 A:ASP200 2.3 13.8 1.0
O1G A:DGT576 2.3 14.2 1.0
O2B A:DGT576 2.4 13.0 1.0
OD1 A:ASP198 2.4 14.8 1.0
O A:ASP198 2.4 14.0 1.0
O1A A:DGT576 2.4 14.3 1.0
O A:HOH725 2.5 14.7 1.0
CG A:ASP200 3.3 12.0 1.0
C A:ASP198 3.4 13.1 1.0
PB A:DGT576 3.5 14.3 1.0
PG A:DGT576 3.5 14.1 1.0
CG A:ASP198 3.6 15.4 1.0
PA A:DGT576 3.6 14.3 1.0
OD1 A:ASP200 3.7 15.3 1.0
O3A A:DGT576 3.7 14.4 1.0
CA A:CA581 3.8 14.0 0.9
O3B A:DGT576 3.9 14.0 1.0
N A:ASP198 3.9 13.4 1.0
O A:HOH694 4.0 20.0 1.0
CA A:ASP198 4.1 13.3 1.0
O3G A:DGT576 4.1 13.8 1.0
O A:HOH699 4.3 12.9 1.0
N A:LEU199 4.3 12.2 1.0
CB A:ASP198 4.4 14.0 1.0
C A:GLY197 4.5 14.8 1.0
OD2 A:ASP198 4.5 19.8 1.0
OG A:SER188 4.5 12.2 1.0
CA A:LEU199 4.6 12.4 1.0
C5' A:DGT576 4.6 15.2 1.0
CB A:ASP200 4.6 11.6 1.0
O5' A:DGT576 4.6 14.2 1.0
N A:SER188 4.7 10.3 1.0
N A:ASP200 4.7 11.2 1.0
O2A A:DGT576 4.7 16.6 1.0
C A:LEU199 4.7 11.4 1.0
CA A:GLY187 4.8 10.8 1.0
O2G A:DGT576 4.8 15.4 1.0
O1B A:DGT576 4.8 14.9 1.0
CA A:GLY197 5.0 14.4 1.0
N A:GLY197 5.0 13.4 1.0

Calcium binding site 2 out of 4 in 3au2

Go back to Calcium Binding Sites List in 3au2
Calcium binding site 2 out of 4 in the Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca581

b:14.0
occ:0.90
 O A:HOH836 2.4 21.6 1.0
OD1 A:ASP200 2.4 15.3 1.0
OD2 A:ASP243 2.4 16.8 1.0
O A:HOH1086 2.4 22.7 1.0
O1A A:DGT576 2.5 14.3 1.0
OD2 A:ASP198 2.5 19.8 1.0
OD1 A:ASP198 2.5 14.8 1.0
CG A:ASP198 2.8 15.4 1.0
CG A:ASP200 3.4 12.0 1.0
CG A:ASP243 3.5 15.3 1.0
PA A:DGT576 3.5 14.3 1.0
OD2 A:ASP200 3.7 13.8 1.0
CA A:CA580 3.8 12.6 0.9
O2A A:DGT576 4.0 16.6 1.0
O5' A:DGT576 4.0 14.2 1.0
CB A:ASP243 4.1 13.2 1.0
O A:HOH898 4.2 29.7 1.0
CB A:ASP198 4.3 14.0 1.0
O A:HOH940 4.3 28.3 1.0
OD1 A:ASP243 4.4 16.9 1.0
C5' A:DGT576 4.4 15.2 1.0
O A:HOH870 4.5 19.9 1.0
CB A:ASP200 4.7 11.6 1.0
O A:HOH694 4.8 20.0 1.0
O A:HOH929 4.9 24.3 1.0
O3A A:DGT576 5.0 14.4 1.0

Calcium binding site 3 out of 4 in 3au2

Go back to Calcium Binding Sites List in 3au2
Calcium binding site 3 out of 4 in the Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca582

b:13.6
occ:0.90
 O A:ARG175 2.6 13.9 1.0
O A:LEU177 2.7 13.5 1.0
O A:VAL180 2.7 12.2 1.0
C A:LEU177 3.6 13.9 1.0
C A:ARG175 3.8 12.6 1.0
C A:VAL180 3.8 11.4 1.0
O A:HOH769 3.8 18.6 1.0
C A:ALA176 3.8 13.9 1.0
O A:ALA176 4.0 14.9 1.0
N A:LEU177 4.1 13.1 1.0
CA A:ALA176 4.1 12.7 1.0
N A:VAL180 4.1 12.5 1.0
CB A:VAL180 4.3 11.7 1.0
CA A:VAL180 4.3 11.9 1.0
CA A:PRO178 4.4 16.4 1.0
N A:ALA176 4.4 12.1 1.0
N A:PRO178 4.4 15.3 1.0
CA A:LEU177 4.5 13.6 1.0
N A:GLY179 4.6 18.1 1.0
C A:PRO178 4.8 16.9 1.0
CG1 A:VAL180 4.9 11.8 1.0
CA A:ARG175 5.0 12.1 1.0
N A:GLU181 5.0 11.9 1.0

Calcium binding site 4 out of 4 in 3au2

Go back to Calcium Binding Sites List in 3au2
Calcium binding site 4 out of 4 in the Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Dna Polymerase X From Thermus Thermophilus HB8 Complexed with Ca-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca583

b:34.2
occ:0.60
 O A:MET56 2.5 38.6 1.0
O A:LEU58 2.7 38.0 1.0
O A:VAL61 2.9 36.7 1.0
C A:MET56 3.5 38.3 1.0
N A:VAL61 3.8 36.5 1.0
C A:LEU58 3.8 38.0 1.0
C A:VAL61 3.8 36.5 1.0
N A:GLY60 4.1 36.6 1.0
C A:GLU57 4.2 39.3 1.0
CA A:MET56 4.3 37.9 1.0
CA A:VAL61 4.3 36.5 1.0
N A:LEU58 4.4 38.9 1.0
O A:GLU57 4.4 39.5 1.0
N A:GLU57 4.5 38.9 1.0
CA A:PRO59 4.5 37.3 1.0
C A:PRO59 4.5 36.8 1.0
N A:PRO59 4.6 37.7 1.0
C A:GLY60 4.6 36.5 1.0
CA A:GLU57 4.6 39.4 1.0
CA A:LEU58 4.7 38.5 1.0
CA A:GLY60 4.8 36.3 1.0
CB A:VAL61 4.8 36.4 1.0
CB A:MET56 4.9 38.1 1.0
N A:GLY62 4.9 36.8 1.0

Reference:

S.Nakane, H.Ishikawa, N.Nakagawa, S.Kuramitsu, R.Masui. The Structural Basis of the Kinetic Mechanism of A Gap-Filling X-Family Dna Polymerase That Binds Mg(2+)-Dntp Before Binding to Dna. J.Mol.Biol. V. 417 179 2012.
ISSN: ISSN 0022-2836
PubMed: 22306405
DOI: 10.1016/J.JMB.2012.01.025
Page generated: Sat Jul 13 07:59:30 2024

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