Calcium in PDB 7b07: TGOT_6G12 Apo

All present enzymatic activity of TGOT_6G12 Apo:
2.7.7.7;

The structure of TGOT_6G12 Apo, PDB code: 7b07 was solved by C.Samson, P.Legrand, M.Tekpinar, J.Rozenski, M.Abramov, P.Holliger, V.Pinheiro, P.Herdewijn, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.53 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.89, 110.49, 111.77, 90, 90, 90
R / Rfree (%)	26.2 / 26.5

The binding sites of Calcium atom in the TGOT_6G12 Apo (pdb code 7b07). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the TGOT_6G12 Apo, PDB code: 7b07:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the TGOT_6G12 Apo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of TGOT_6G12 Apo within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:85.5 occ:1.00 O A:THR5 2.5 96.4 1.0 OD1 A:ASP4 2.6 102.4 1.0 CG A:ASP4 3.4 102.2 1.0 OD2 A:ASP4 3.6 104.7 1.0 C A:THR5 3.7 96.2 1.0 OD2 A:ASP343 4.0 109.0 1.0 N A:THR5 4.2 95.9 1.0 CB A:ALA117 4.4 95.9 1.0 CA A:THR5 4.6 96.1 1.0 OG A:SER340 4.6 103.8 1.0 OG1 A:THR5 4.6 98.3 1.0 N A:ASP6 4.6 95.7 1.0 CB A:ASP6 4.7 98.0 1.0 CA A:ASP6 4.7 95.8 1.0 CB A:ASP4 4.8 97.9 1.0 OE1 A:GLU251 4.9 128.2 1.0

Calcium binding site 2 out of 4 in the TGOT_6G12 Apo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of TGOT_6G12 Apo within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:105.4 occ:1.00 OD1 A:ASP404 2.9 141.8 1.0 OD2 A:ASP404 3.0 143.0 1.0 CG A:ASP404 3.3 141.0 1.0 OE1 A:GLU578 3.6 148.8 1.0 O A:ASP404 4.6 133.3 1.0 O A:PHE405 4.6 128.5 1.0 CG A:GLU580 4.6 148.5 1.0 CB A:ASP404 4.7 136.6 1.0 CB A:GLU578 4.7 138.3 1.0 CD A:GLU578 4.7 147.9 1.0 CB A:GLU580 4.8 143.2 1.0

Calcium binding site 3 out of 4 in the TGOT_6G12 Apo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of TGOT_6G12 Apo within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:124.0 occ:1.00 OD1 A:ASP455 2.5 114.7 1.0 OE1 A:GLU458 3.5 128.4 1.0 CG A:ASP455 3.7 114.0 1.0 OD2 A:ASP455 4.4 115.9 1.0 N A:ASP455 4.5 107.8 1.0 CA A:ASP455 4.6 108.5 1.0 C A:GLY454 4.7 107.7 1.0 CD A:GLU458 4.7 126.9 1.0 CB A:ASP455 4.7 110.0 1.0 O A:SER451 4.9 108.2 1.0 O A:GLY454 4.9 107.7 1.0

Calcium binding site 4 out of 4 in the TGOT_6G12 Apo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of TGOT_6G12 Apo within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca804 b:123.3 occ:1.00 O A:ASN568 2.5 138.2 1.0 O A:LEU571 2.9 134.8 1.0 C A:ASN568 3.8 138.1 1.0 C A:LEU571 4.0 134.7 1.0 O A:ALA569 4.2 137.2 1.0 C A:ALA569 4.3 137.0 1.0 CA A:ALA569 4.3 137.4 1.0 N A:LEU571 4.4 135.1 1.0 N A:ALA569 4.5 137.5 1.0 O A:GLY573 4.5 133.6 1.0 CA A:LEU571 4.6 134.9 1.0 CB A:LEU571 4.7 135.2 1.0 CA A:ASN568 4.8 138.4 1.0 O A:LEU575 4.8 132.8 1.0 N A:LYS570 4.9 136.3 1.0

C.Samson, P.Legrand, M.Tekpinar, J.Rozenski, M.Abramov, P.Holliger, V.B.Pinheiro, P.Herdwijn, M.Delarue. Structural Studies of Hna Substrate Specificity in Mutants of An Archaeal Dna Polymerase Obtained By Directed Evolution. Biomolecules V. 10 2020.
ISSN: ESSN 2218-273X
PubMed: 33302546
DOI: 10.3390/BIOM10121647