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Calcium in PDB 3b0x: K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp

Enzymatic activity of K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp

All present enzymatic activity of K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp:
2.7.7.7;

Protein crystallography data

The structure of K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp, PDB code: 3b0x 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 / 1.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.088, 53.202, 84.859, 90.00, 107.65, 90.00
R / Rfree (%) 17.1 / 19.8

Other elements in 3b0x:

The structure of K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp (pdb code 3b0x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the K263A Mutant of Polx From Thermus Thermophilus HB8 Complexed with Ca- Dgtp, PDB code: 3b0x:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3b0x

Go back to Calcium Binding Sites List in 3b0x
Calcium binding site 1 out of 4 in the K263A 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 K263A 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:10.6
occ:1.00
 OD2 A:ASP200 2.3 11.9 1.0
O1G A:DGT583 2.3 11.6 1.0
O2B A:DGT583 2.4 9.9 1.0
OD1 A:ASP198 2.4 11.8 1.0
O1A A:DGT583 2.4 11.3 1.0
O A:ASP198 2.4 11.5 1.0
O A:HOH675 2.5 12.0 1.0
CG A:ASP200 3.3 9.2 1.0
C A:ASP198 3.4 10.7 1.0
PB A:DGT583 3.5 11.1 1.0
PG A:DGT583 3.5 11.3 1.0
CG A:ASP198 3.6 11.2 1.0
PA A:DGT583 3.6 11.2 1.0
OD1 A:ASP200 3.7 11.5 1.0
O3A A:DGT583 3.7 11.1 1.0
CA A:CA579 3.8 11.9 1.0
O3B A:DGT583 3.9 11.4 1.0
N A:ASP198 3.9 11.1 1.0
O A:HOH617 4.0 17.6 1.0
CA A:ASP198 4.1 10.7 1.0
O3G A:DGT583 4.1 11.7 1.0
N A:LEU199 4.3 10.2 1.0
O A:HOH600 4.3 10.3 1.0
CB A:ASP198 4.4 11.2 1.0
C A:GLY197 4.5 12.2 1.0
OG A:SER188 4.5 9.4 1.0
OD2 A:ASP198 4.5 16.7 1.0
C5' A:DGT583 4.5 12.6 1.0
CA A:LEU199 4.6 10.0 1.0
CB A:ASP200 4.6 9.6 1.0
O5' A:DGT583 4.6 11.4 1.0
N A:SER188 4.7 8.0 1.0
N A:ASP200 4.7 9.1 1.0
C A:LEU199 4.7 9.1 1.0
O2A A:DGT583 4.7 13.5 1.0
CA A:GLY187 4.8 8.8 1.0
O2G A:DGT583 4.8 13.3 1.0
O1B A:DGT583 4.8 11.4 1.0
CA A:GLY197 5.0 12.0 1.0
N A:GLY197 5.0 10.3 1.0

Calcium binding site 2 out of 4 in 3b0x

Go back to Calcium Binding Sites List in 3b0x
Calcium binding site 2 out of 4 in the K263A 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 K263A 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:11.9
occ:1.00
 O A:HOH726 2.3 20.9 1.0
O A:HOH704 2.4 21.3 1.0
OD1 A:ASP200 2.4 11.5 1.0
OD2 A:ASP243 2.4 13.6 1.0
O1A A:DGT583 2.5 11.3 1.0
OD2 A:ASP198 2.5 16.7 1.0
OD1 A:ASP198 2.5 11.8 1.0
CG A:ASP198 2.8 11.2 1.0
CG A:ASP200 3.4 9.2 1.0
CG A:ASP243 3.5 12.4 1.0
PA A:DGT583 3.6 11.2 1.0
OD2 A:ASP200 3.7 11.9 1.0
CA A:CA578 3.8 10.6 1.0
O2A A:DGT583 4.0 13.5 1.0
O5' A:DGT583 4.0 11.4 1.0
CB A:ASP243 4.1 10.8 1.0
O A:HOH939 4.1 25.2 1.0
CB A:ASP198 4.3 11.2 1.0
O A:HOH1090 4.3 29.5 1.0
C5' A:DGT583 4.4 12.6 1.0
OD1 A:ASP243 4.4 13.1 1.0
O A:HOH651 4.5 15.9 1.0
CB A:ASP200 4.7 9.6 1.0
O A:HOH617 4.7 17.6 1.0
O3A A:DGT583 5.0 11.1 1.0

Calcium binding site 3 out of 4 in 3b0x

Go back to Calcium Binding Sites List in 3b0x
Calcium binding site 3 out of 4 in the K263A 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 K263A 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:13.2
occ:1.00
 O A:LEU177 2.7 12.4 1.0
O A:ARG175 2.7 12.6 1.0
O A:VAL180 2.7 11.1 1.0
O A:HOH791 2.8 23.1 1.0
C A:LEU177 3.6 12.2 1.0
O A:HOH715 3.8 17.0 1.0
C A:ARG175 3.8 11.3 1.0
C A:ALA176 3.8 12.9 1.0
C A:VAL180 3.8 9.9 1.0
O A:ALA176 4.0 13.3 1.0
N A:LEU177 4.1 11.5 1.0
CA A:ALA176 4.1 11.7 1.0
N A:VAL180 4.1 11.2 1.0
CB A:VAL180 4.3 10.4 1.0
CA A:VAL180 4.3 10.4 1.0
CA A:PRO178 4.4 13.9 1.0
N A:PRO178 4.4 12.9 1.0
N A:ALA176 4.4 11.6 1.0
CA A:LEU177 4.5 12.3 1.0
N A:GLY179 4.6 15.8 1.0
C A:PRO178 4.8 14.7 1.0
O A:HOH803 4.8 20.6 1.0
CG1 A:VAL180 4.9 10.4 1.0
CA A:ARG175 5.0 10.5 1.0
N A:GLU181 5.0 10.2 1.0

Calcium binding site 4 out of 4 in 3b0x

Go back to Calcium Binding Sites List in 3b0x
Calcium binding site 4 out of 4 in the K263A 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 K263A 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:39.5
occ:1.00
 O A:MET56 2.4 36.2 1.0
O A:LEU58 2.7 36.6 1.0
O A:VAL61 2.9 34.8 1.0
C A:MET56 3.5 36.0 1.0
N A:VAL61 3.7 34.8 1.0
C A:VAL61 3.8 34.8 1.0
C A:LEU58 3.8 36.7 1.0
N A:GLY60 4.0 35.2 1.0
C A:GLU57 4.3 37.9 1.0
CA A:VAL61 4.3 34.9 1.0
CA A:MET56 4.3 35.3 1.0
O A:GLU57 4.4 38.1 1.0
N A:LEU58 4.4 37.5 1.0
N A:GLU57 4.5 36.9 1.0
CA A:PRO59 4.5 35.9 1.0
C A:PRO59 4.5 35.4 1.0
C A:GLY60 4.5 35.0 1.0
N A:PRO59 4.6 36.3 1.0
CA A:GLU57 4.6 37.8 1.0
CA A:GLY60 4.7 34.8 1.0
CA A:LEU58 4.7 37.2 1.0
CB A:VAL61 4.8 34.8 1.0
N A:GLY62 4.8 35.4 1.0
CB A:MET56 4.9 35.4 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 08:06:10 2024

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