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Calcium in PDB 6ur9: Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, Dideoxy Primer, 3'-Amino-Ddgtp (Ngtp), and CA2+

Enzymatic activity of Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, Dideoxy Primer, 3'-Amino-Ddgtp (Ngtp), and CA2+

All present enzymatic activity of Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, Dideoxy Primer, 3'-Amino-Ddgtp (Ngtp), and CA2+:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, Dideoxy Primer, 3'-Amino-Ddgtp (Ngtp), and CA2+, PDB code: 6ur9 was solved by W.Zhang, V.S.Lelyveld, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.81 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.629, 108.069, 149.748, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, Dideoxy Primer, 3'-Amino-Ddgtp (Ngtp), and CA2+ (pdb code 6ur9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, Dideoxy Primer, 3'-Amino-Ddgtp (Ngtp), and CA2+, PDB code: 6ur9:

Calcium binding site 1 out of 1 in 6ur9

Go back to Calcium Binding Sites List in 6ur9
Calcium binding site 1 out of 1 in the Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, Dideoxy Primer, 3'-Amino-Ddgtp (Ngtp), and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, Dideoxy Primer, 3'-Amino-Ddgtp (Ngtp), and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:45.0
occ:1.00
 O A:TYR654 2.3 28.0 1.0
OD2 A:ASP830 2.4 43.8 1.0
OD2 A:ASP653 2.4 46.7 1.0
O1G A:NG3901 2.5 62.3 1.0
O1A A:NG3901 2.5 38.5 1.0
O2B A:NG3901 2.8 40.3 1.0
O A:HOH1006 3.3 34.7 1.0
CG A:ASP830 3.5 30.4 1.0
CG A:ASP653 3.5 41.9 1.0
C A:TYR654 3.5 25.5 1.0
PG A:NG3901 3.7 62.6 1.0
PA A:NG3901 3.8 44.9 1.0
PB A:NG3901 3.8 51.3 1.0
CB A:ASP653 3.9 27.3 1.0
OD1 A:ASP830 4.0 32.1 1.0
O3B A:NG3901 4.2 63.0 1.0
O3A A:NG3901 4.3 49.9 1.0
N A:TYR654 4.3 25.5 1.0
O2G A:NG3901 4.4 56.1 1.0
N A:SER655 4.4 26.6 1.0
CA A:SER655 4.4 29.0 1.0
CA A:TYR654 4.5 30.9 1.0
C A:ASP653 4.6 31.9 1.0
OD1 A:ASP653 4.6 39.9 1.0
C5' A:NG3901 4.6 43.1 1.0
O2A A:NG3901 4.6 43.7 1.0
N A:GLN656 4.7 27.3 1.0
O3G A:NG3901 4.7 54.4 1.0
O5' A:NG3901 4.7 40.1 1.0
CB A:ASP830 4.7 33.9 1.0
CA A:ASP653 4.9 32.0 1.0

Reference:

V.S.Lelyveld, W.Zhang, J.W.Szostak. Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, Dideoxy Primer, 3'-Amino-Ddgtp (Ngtp), and CA2+ To Be Published.
Page generated: Wed Jul 9 18:37:06 2025

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