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Calcium in PDB 4dsk: Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium

Enzymatic activity of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium

All present enzymatic activity of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium, PDB code: 4dsk was solved by J.H.Gan, R.Abdur, H.H.Liu, J.Sheng, J.Caton-Willians, A.S.Soares, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.16 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.692, 93.339, 106.363, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 24.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium (pdb code 4dsk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium, PDB code: 4dsk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4dsk

Go back to Calcium Binding Sites List in 4dsk
Calcium binding site 1 out of 4 in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca101

b:61.6
occ:0.60
 O B:HOH201 2.3 46.1 0.6
O A:POP1001 2.3 56.8 0.6
OP1 B:DG14 2.5 27.4 1.0
O2 A:POP1001 2.7 56.9 0.6
P1 A:POP1001 3.1 57.7 0.6
P B:DG14 3.5 23.2 1.0
CA A:CA1002 3.6 51.5 0.6
P2 A:POP1001 3.6 57.7 0.6
O5' B:DG14 3.9 23.6 1.0
O5 A:POP1001 3.9 56.8 0.6
O1 A:POP1001 4.1 57.2 0.6
OP2 B:DG14 4.1 28.7 1.0
C5' B:DG14 4.2 18.6 1.0
O3 A:POP1001 4.2 55.8 0.6
O6 A:POP1001 4.2 57.2 0.6
O A:HOH1284 4.2 41.1 1.0
OE2 A:GLU831 4.3 44.1 1.0
C3' B:DG14 4.7 27.7 1.0
O4 A:POP1001 4.8 56.5 0.6
O3' B:DC13 4.8 25.5 1.0
CG2 A:ILE628 4.9 24.4 1.0

Calcium binding site 2 out of 4 in 4dsk

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Calcium binding site 2 out of 4 in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:51.5
occ:0.60
 OD1 A:ASP830 2.5 26.0 1.0
OE2 A:GLU831 2.8 44.1 1.0
O A:POP1001 2.8 56.8 0.6
O5 A:POP1001 3.0 56.8 0.6
P2 A:POP1001 3.3 57.7 0.6
CD A:GLU831 3.4 43.0 1.0
CG A:ASP830 3.4 28.1 1.0
O4 A:POP1001 3.5 56.5 0.6
O3' B:DG14 3.5 33.0 1.0
CA B:CA101 3.6 61.6 0.6
O3 A:POP1001 3.7 55.8 0.6
OD2 A:ASP830 3.7 30.9 1.0
CG A:GLU831 3.7 32.9 1.0
C3' B:DG14 3.8 27.7 1.0
P1 A:POP1001 3.8 57.7 0.6
CB A:GLU831 4.0 26.3 1.0
CB A:ASP653 4.2 25.4 1.0
C4' B:DG14 4.2 26.6 1.0
C5' B:DG14 4.2 18.6 1.0
OE1 A:GLU831 4.3 47.0 1.0
O2 A:POP1001 4.5 56.9 0.6
O A:VAL828 4.6 21.1 1.0
C A:ASP830 4.6 22.9 1.0
N A:GLU831 4.7 24.1 1.0
O A:ASP830 4.7 21.8 1.0
O6 A:POP1001 4.7 57.2 0.6
CG A:ASP653 4.8 30.6 1.0
CB A:ASP830 4.8 22.6 1.0
OD2 A:ASP653 4.9 37.7 1.0
OP1 B:DG14 4.9 27.4 1.0
O A:HOH1284 4.9 41.1 1.0
O5' B:DG14 4.9 23.6 1.0
CA A:GLU831 5.0 25.4 1.0

Calcium binding site 3 out of 4 in 4dsk

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Calcium binding site 3 out of 4 in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:57.7
occ:1.00
 O A:HOH1257 2.5 38.1 1.0
O A:HOH1367 2.6 48.3 1.0
O A:HOH1240 2.6 56.7 1.0
O A:HOH1186 2.7 24.8 1.0
O A:LEU858 2.8 26.6 1.0
O A:VAL860 3.8 24.2 1.0
C A:LEU858 3.9 26.3 1.0
N A:LEU858 4.0 26.9 1.0
CG2 A:THR857 4.1 32.7 1.0
C A:VAL860 4.2 24.6 1.0
N A:PRO861 4.5 24.1 1.0
CA A:PRO861 4.5 24.2 1.0
CA A:LEU858 4.6 26.2 1.0
C A:THR857 4.7 28.0 1.0
N A:VAL860 4.8 23.9 1.0
CA A:THR857 4.8 29.3 1.0
C A:ARG859 4.8 25.4 1.0
N A:ARG859 4.9 25.9 1.0

Calcium binding site 4 out of 4 in 4dsk

Go back to Calcium Binding Sites List in 4dsk
Calcium binding site 4 out of 4 in the Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Fragment Dna Polymerase I From Bacillus Stearothermophilus with Duplex Dna, Ppi and Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:71.2
occ:1.00
 O A:HOH1112 2.3 48.9 1.0
O A:HOH1342 2.4 44.0 1.0
OD1 A:ASP354 2.6 42.7 1.0
OE1 A:GLN356 3.0 47.2 1.0
CG A:ASP354 3.3 39.7 1.0
OD2 A:ASP354 3.4 43.5 1.0
CD A:GLN356 3.5 48.6 1.0
NE2 A:GLN356 3.8 51.1 1.0
CB A:GLN356 4.4 35.9 1.0
CG A:GLN356 4.5 41.6 1.0
CB A:ASP354 4.7 37.7 1.0
O A:VAL307 4.7 39.7 1.0
CD A:PRO355 4.9 37.7 1.0
N A:GLN356 4.9 35.7 1.0

Reference:

J.H.Gan, R.Abdur, H.H.Liu, J.Sheng, J.Caton-Willians, A.S.Soares, Z.Huang. Biochemical and Structural Insights Into the Fidelity of Bacillus Stearothermophilus Dna Polymerase To Be Published.
Page generated: Tue Jul 8 19:33:16 2025

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