Calcium in PDB 6ish: Structure of 9N-I Dna Polymerase Incorporation with 3'-Al in the Active Site

All present enzymatic activity of Structure of 9N-I Dna Polymerase Incorporation with 3'-Al in the Active Site:
2.7.7.7;

The structure of Structure of 9N-I Dna Polymerase Incorporation with 3'-Al in the Active Site, PDB code: 6ish was solved by S.W.Linwu, M.Maestre-Reyna, M.D.Tsai, Y.H.Tu, W.H.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.99 / 3.30
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	207.654, 207.654, 207.654, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 27.9

The binding sites of Calcium atom in the Structure of 9N-I Dna Polymerase Incorporation with 3'-Al in the Active Site (pdb code 6ish). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of 9N-I Dna Polymerase Incorporation with 3'-Al in the Active Site, PDB code: 6ish:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of 9N-I Dna Polymerase Incorporation with 3'-Al in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of 9N-I Dna Polymerase Incorporation with 3'-Al in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:0.8 occ:1.00 NH1 A:ARG606 3.4 87.9 1.0 OH A:TYR594 3.7 70.1 1.0 CZ A:TYR402 4.2 72.4 1.0 CE2 A:TYR402 4.2 72.6 1.0 CE1 A:TYR402 4.4 72.5 1.0 CE1 A:HIS545 4.5 76.9 1.0 OH A:TYR583 4.5 84.6 1.0 CD2 A:TYR402 4.5 73.3 1.0 OH A:TYR402 4.5 72.1 1.0 CZ A:ARG606 4.5 86.7 1.0 O11 C:B9X101 4.7 72.6 1.0 NE2 A:HIS545 4.7 76.7 1.0 CD1 A:TYR402 4.7 72.8 1.0 CG A:TYR402 4.8 73.3 1.0 CZ A:TYR594 4.8 70.3 1.0

Calcium binding site 2 out of 2 in the Structure of 9N-I Dna Polymerase Incorporation with 3'-Al in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of 9N-I Dna Polymerase Incorporation with 3'-Al in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:0.8 occ:1.00 OD2 A:ASP404 2.9 77.6 1.0 OE2 A:GLU580 3.2 90.4 1.0 O A:PHE405 3.3 82.3 1.0 CG A:ASP404 3.8 77.5 1.0 OE1 A:GLU580 3.8 89.9 1.0 CD A:GLU580 3.9 88.4 1.0 CA A:ARG406 4.0 86.5 1.0 OD1 A:ASP404 4.1 77.6 1.0 C A:PHE405 4.1 82.3 1.0 N A:SER407 4.2 82.7 1.0 N A:ARG406 4.4 85.3 1.0 O A:ASP404 4.6 77.8 1.0 C A:ARG406 4.6 85.0 1.0 OE1 A:GLU578 4.7 98.9 1.0 CB A:ASP404 4.9 77.4 1.0 CB A:ARG406 5.0 89.7 1.0 C A:ASP404 5.0 77.5 1.0

S.W.Linwu, Y.H.Tu, T.Y.Tsai, M.Maestre-Reyna, M.S.Liu, W.J.Wu, J.Y.Huang, H.W.Chi, W.H.Chang, C.F.Chiou, A.H.Wang, J.Lee, M.D.Tsai. Thermococcus Sp. 9°N Dna Polymerase Exhibits 3'-Esterase Activity That Can Be Harnessed For Dna Sequencing. Commun Biol V. 2 224 2019.
ISSN: ESSN 2399-3642
PubMed: 31240262
DOI: 10.1038/S42003-019-0458-7