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Calcium in PDB 3b0y: K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp

Enzymatic activity of K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp

All present enzymatic activity of K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp:
2.7.7.7;

Protein crystallography data

The structure of K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp, PDB code: 3b0y was solved by S.Nakane, N.Nakagawa, R.Masui, S.Kuramitsu, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.942, 53.224, 84.864, 90.00, 107.65, 90.00
R / Rfree (%) 17.5 / 20.5

Other elements in 3b0y:

The structure of K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp (pdb code 3b0y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp, PDB code: 3b0y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3b0y

Go back to Calcium Binding Sites List in 3b0y
Calcium binding site 1 out of 4 in the K263D Mutant of Polx 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 K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca578

b:9.8
occ:1.00
 OD2 A:ASP200 2.3 11.2 1.0
O1G A:DGT576 2.3 10.8 1.0
O2B A:DGT576 2.4 10.1 1.0
OD1 A:ASP198 2.4 11.0 1.0
O1A A:DGT576 2.4 10.8 1.0
O A:ASP198 2.4 11.1 1.0
O A:HOH638 2.5 10.5 1.0
CG A:ASP200 3.3 8.9 1.0
C A:ASP198 3.4 10.4 1.0
PB A:DGT576 3.5 10.8 1.0
PG A:DGT576 3.6 10.7 1.0
CG A:ASP198 3.6 10.4 1.0
PA A:DGT576 3.6 10.7 1.0
OD1 A:ASP200 3.7 11.1 1.0
O3A A:DGT576 3.8 10.8 1.0
CA A:CA579 3.8 11.0 1.0
O3B A:DGT576 3.9 10.6 1.0
N A:ASP198 3.9 10.9 1.0
O A:HOH597 4.0 17.2 1.0
CA A:ASP198 4.1 10.4 1.0
O3G A:DGT576 4.1 9.9 1.0
N A:LEU199 4.3 9.8 1.0
O A:HOH596 4.3 10.2 1.0
CB A:ASP198 4.4 10.8 1.0
C A:GLY197 4.5 11.7 1.0
OD2 A:ASP198 4.5 16.1 1.0
OG A:SER188 4.5 9.2 1.0
C5' A:DGT576 4.6 11.6 1.0
CA A:LEU199 4.6 9.8 1.0
N A:SER188 4.6 8.4 1.0
O5' A:DGT576 4.6 10.8 1.0
CB A:ASP200 4.6 9.3 1.0
O2A A:DGT576 4.7 13.2 1.0
C A:LEU199 4.7 9.5 1.0
N A:ASP200 4.7 9.4 1.0
CA A:GLY187 4.8 9.3 1.0
O2G A:DGT576 4.8 12.4 1.0
O1B A:DGT576 4.8 11.9 1.0
CA A:GLY197 5.0 11.3 1.0
N A:GLY197 5.0 10.4 1.0

Calcium binding site 2 out of 4 in 3b0y

Go back to Calcium Binding Sites List in 3b0y
Calcium binding site 2 out of 4 in the K263D Mutant of Polx 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 K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca579

b:11.0
occ:1.00
 OD2 A:ASP243 2.3 13.4 1.0
OD1 A:ASP200 2.4 11.1 1.0
O A:HOH689 2.4 17.9 1.0
O A:HOH661 2.4 17.7 1.0
OD2 A:ASP198 2.5 16.1 1.0
O1A A:DGT576 2.5 10.8 1.0
OD1 A:ASP198 2.5 11.0 1.0
CG A:ASP198 2.8 10.4 1.0
CG A:ASP200 3.4 8.9 1.0
CG A:ASP243 3.4 11.1 1.0
PA A:DGT576 3.6 10.7 1.0
OD2 A:ASP200 3.7 11.2 1.0
CA A:CA578 3.8 9.8 1.0
O2A A:DGT576 4.0 13.2 1.0
O5' A:DGT576 4.0 10.8 1.0
CB A:ASP243 4.0 10.4 1.0
O A:HOH863 4.2 24.4 1.0
CB A:ASP198 4.3 10.8 1.0
OD1 A:ASP243 4.4 13.8 1.0
O A:HOH862 4.4 23.9 1.0
C5' A:DGT576 4.4 11.6 1.0
O A:HOH670 4.5 16.5 1.0
CB A:ASP200 4.7 9.3 1.0
O A:HOH597 4.8 17.2 1.0
O A:HOH876 5.0 20.3 1.0
O3A A:DGT576 5.0 10.8 1.0

Calcium binding site 3 out of 4 in 3b0y

Go back to Calcium Binding Sites List in 3b0y
Calcium binding site 3 out of 4 in the K263D Mutant of Polx 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 K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca580

b:13.8
occ:1.00
 O A:LEU177 2.7 12.2 1.0
O A:ARG175 2.7 13.2 1.0
O A:VAL180 2.7 11.6 1.0
O A:HOH781 2.8 25.5 1.0
C A:LEU177 3.7 13.2 1.0
O A:HOH704 3.7 18.6 1.0
C A:ARG175 3.8 12.2 1.0
C A:VAL180 3.8 10.9 1.0
C A:ALA176 3.9 12.9 1.0
O A:ALA176 4.1 14.1 1.0
N A:LEU177 4.1 13.1 1.0
CA A:ALA176 4.1 12.2 1.0
N A:VAL180 4.2 12.5 1.0
CB A:VAL180 4.3 11.3 1.0
CA A:VAL180 4.3 11.0 1.0
N A:ALA176 4.4 12.1 1.0
CA A:PRO178 4.4 15.0 1.0
N A:PRO178 4.5 13.8 1.0
CA A:LEU177 4.5 13.1 1.0
N A:GLY179 4.6 17.5 1.0
C A:PRO178 4.8 16.1 1.0
O A:HOH727 4.8 21.2 1.0
CG1 A:VAL180 4.9 10.9 1.0
CA A:ARG175 5.0 10.8 1.0
N A:GLU181 5.0 10.9 1.0

Calcium binding site 4 out of 4 in 3b0y

Go back to Calcium Binding Sites List in 3b0y
Calcium binding site 4 out of 4 in the K263D Mutant of Polx 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 K263D Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca581

b:42.2
occ:1.00
 O A:MET56 2.5 37.4 1.0
O A:LEU58 2.7 36.6 1.0
O A:VAL61 2.9 33.8 1.0
C A:MET56 3.6 37.1 1.0
N A:VAL61 3.8 34.6 1.0
C A:VAL61 3.8 34.0 1.0
C A:LEU58 3.8 36.6 1.0
N A:GLY60 4.0 35.4 1.0
C A:GLU57 4.3 38.0 1.0
CA A:VAL61 4.3 34.1 1.0
N A:LEU58 4.3 37.4 1.0
CA A:MET56 4.4 36.5 1.0
O A:GLU57 4.5 38.0 1.0
CA A:PRO59 4.5 36.0 1.0
C A:PRO59 4.5 35.6 1.0
N A:GLU57 4.5 37.9 1.0
C A:GLY60 4.6 35.0 1.0
N A:PRO59 4.6 36.3 1.0
CA A:GLU57 4.7 38.2 1.0
CA A:LEU58 4.7 36.9 1.0
N A:GLY62 4.8 34.3 1.0
CA A:GLY60 4.8 35.0 1.0
CB A:VAL61 4.9 34.2 1.0
CB A:MET56 4.9 36.7 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 08:07:06 2024

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