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

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

The structure of Structure of 9N-I Dna Polymerase Incorporation with 3'-Cl in the Active Site, PDB code: 6isi 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)	40.24 / 3.20
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	205.204, 205.204, 205.204, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 29

The binding sites of Calcium atom in the Structure of 9N-I Dna Polymerase Incorporation with 3'-Cl in the Active Site (pdb code 6isi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of 9N-I Dna Polymerase Incorporation with 3'-Cl in the Active Site, PDB code: 6isi:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of 9N-I Dna Polymerase Incorporation with 3'-Cl 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'-Cl in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:96.3 occ:1.00 O A:HOH908 3.0 47.2 1.0 OH A:TYR594 3.5 77.2 1.0 CE1 A:HIS545 3.6 75.7 1.0 OH A:TYR583 3.7 87.4 1.0 NH1 A:ARG606 3.9 92.8 1.0 NE2 A:HIS545 3.9 75.3 1.0 CE2 A:TYR594 4.2 78.2 1.0 CG A:TYR402 4.3 80.5 1.0 CZ A:TYR594 4.3 77.7 1.0 CZ A:TYR583 4.4 87.5 1.0 CD2 A:TYR402 4.5 80.6 1.0 CD1 A:TYR402 4.5 80.5 1.0 CB A:TYR402 4.7 81.0 1.0 CE2 A:TYR583 4.7 87.3 1.0 CE2 A:TYR402 4.8 80.2 1.0 CE1 A:TYR402 4.8 80.6 1.0 ND1 A:HIS545 4.9 75.9 1.0 CZ A:ARG606 4.9 92.9 1.0 CZ A:TYR402 5.0 80.3 1.0

Calcium binding site 2 out of 4 in the Structure of 9N-I Dna Polymerase Incorporation with 3'-Cl 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'-Cl in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:0.6 occ:1.00 OE1 A:GLU578 2.4 0.5 1.0 O11 A:PPV801 2.9 0.2 1.0 OE2 A:GLU580 3.3 97.2 1.0 OO5 A:B0U804 3.3 0.5 1.0 CD A:GLU578 3.5 0.8 1.0 O10 A:B0U804 3.7 0.5 1.0 C9 A:B0U804 3.7 1.0 1.0 OE2 A:GLU578 3.9 0.5 1.0 P1 A:PPV801 4.1 0.5 1.0 CD A:GLU580 4.2 95.6 1.0 OE1 A:GLU580 4.3 97.3 1.0 O21 A:PPV801 4.4 0.5 1.0 OPP A:PPV801 4.5 0.9 1.0 CB A:ARG406 4.7 98.3 1.0 CG A:GLU578 4.7 99.2 1.0 CG A:ARG406 4.8 1.0 1.0 C8 A:B0U804 5.0 0.2 1.0

Calcium binding site 3 out of 4 in the Structure of 9N-I Dna Polymerase Incorporation with 3'-Cl in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of 9N-I Dna Polymerase Incorporation with 3'-Cl in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca101 b:99.8 occ:1.00 OP2 D:DG3 2.4 0.9 1.0 OP2 D:DG4 2.5 0.9 1.0 O D:HOH203 2.5 63.7 1.0 P D:DG3 3.7 0.9 1.0 O3' D:DC2 3.9 0.8 1.0 P D:DG4 4.0 0.7 1.0 N7 D:DG4 4.3 98.2 1.0 C8 D:DG4 4.4 99.0 1.0 C3' D:DG3 4.5 0.4 1.0 O5' D:DG3 4.6 0.6 1.0 O3' D:DG3 4.7 0.9 1.0 O5' D:DG4 4.8 0.4 1.0 OP1 D:DG3 4.8 0.7 1.0 OP1 D:DG4 4.9 0.1 1.0

Calcium binding site 4 out of 4 in the Structure of 9N-I Dna Polymerase Incorporation with 3'-Cl in the Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of 9N-I Dna Polymerase Incorporation with 3'-Cl in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca102 b:0.5 occ:1.00 C8 D:DG3 4.2 0.4 1.0 CA A:GLY495 4.2 91.4 1.0 OG1 A:THR349 4.2 0.8 1.0 C2' D:DC2 4.4 0.7 1.0 N7 D:DG3 4.4 0.9 1.0 C A:GLY495 4.6 92.4 1.0 C2 D:DC2 4.7 0.4 1.0 O2 D:DC2 4.7 0.6 1.0 O A:SER492 4.7 93.6 1.0 N1 D:DC2 4.8 0.5 1.0 N A:TYR496 4.8 92.9 1.0 O4' D:DG3 4.9 0.8 1.0 N9 D:DG3 5.0 0.5 1.0 C1' D:DC2 5.0 0.4 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