Calcium in PDB 7ap1: Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with Compound SERS7HMDDA

All present enzymatic activity of Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with Compound SERS7HMDDA:
6.1.1.11;

The structure of Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with Compound SERS7HMDDA, PDB code: 7ap1 was solved by L.Pang, S.De Graef, S.V.Strelkov, S.D.Weeks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.18
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.670, 84.670, 229.865, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22.6

The binding sites of Calcium atom in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with Compound SERS7HMDDA (pdb code 7ap1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with Compound SERS7HMDDA, PDB code: 7ap1:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with Compound SERS7HMDDA


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with Compound SERS7HMDDA within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:61.4 occ:1.00 O A:ASP254 2.3 55.5 1.0 O A:HOH679 2.5 61.2 1.0 O A:HOH677 2.5 52.2 1.0 O A:HOH718 2.6 64.7 1.0 O A:HOH619 2.6 61.3 1.0 O A:HOH608 2.8 63.5 1.0 C A:ASP254 3.5 55.2 1.0 N A:ASP255 4.3 54.1 1.0 CA A:ASP255 4.3 54.3 1.0 O A:HOH671 4.4 58.3 1.0 CA A:ASP254 4.4 56.1 1.0 CB A:ASP254 4.6 58.6 1.0 OD1 A:ASP255 4.8 59.7 1.0 O A:LEU256 4.9 54.2 1.0 C A:ASP255 4.9 54.5 1.0

Calcium binding site 2 out of 3 in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with Compound SERS7HMDDA


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with Compound SERS7HMDDA within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:0.6 occ:1.00 OG A:SER336 3.0 59.3 1.0 ND2 A:ASN389 3.1 43.8 1.0 OE2 A:GLU239 3.5 57.8 1.0 CG2 A:VAL362 3.6 47.8 1.0 OD1 A:ASN389 3.8 46.0 1.0 CG A:ASN389 3.8 46.3 1.0 OE1 A:GLU239 4.0 52.1 1.0 CD A:GLU239 4.1 54.8 1.0 CB A:SER336 4.3 56.4 1.0 CB A:SER360 4.4 49.9 1.0 N A:ALA337 4.4 54.8 1.0 O A:HOH611 4.4 43.1 1.0 NE2 A:GLN366 4.4 48.1 1.0 O A:HOH660 4.4 66.2 1.0 OG A:SER360 4.6 51.9 1.0 C A:SER336 4.6 55.4 1.0 CB A:ALA337 4.7 54.1 1.0 O1 A:EDO504 4.8 86.7 1.0 CA A:ALA337 4.8 54.9 1.0 CA A:SER336 4.9 55.7 1.0

Calcium binding site 3 out of 3 in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with Compound SERS7HMDDA


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with Compound SERS7HMDDA within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:1.0 occ:1.00 OD2 A:ASP342 3.3 65.4 1.0 OE2 A:GLU355 3.5 65.8 1.0 OE1 A:GLU355 3.7 71.7 1.0 OG A:SER358 3.7 59.3 1.0 OD1 A:ASP342 3.8 63.9 1.0 CD1 A:LEU328 3.8 59.1 1.0 CD A:GLU355 3.9 68.7 1.0 CG A:ASP342 4.0 62.9 1.0 O1S A:RUZ501 4.1 53.2 1.0 O A:HOH645 4.4 83.4 1.0 CB A:SER358 4.5 55.4 1.0 O A:ASP332 4.7 67.9 1.0

B.Zhang, L.Pang, M.Nautiyal, S.De Graef, B.Gadakh, E.Lescrinier, J.Rozenski, S.V.Strelkov, S.D.Weeks, A.Van Aerschot. Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues As Aminoacyl-Trna Synthetase Inhibitors. Molecules V. 25 2020.
ISSN: ESSN 1420-3049
PubMed: 33081246
DOI: 10.3390/MOLECULES25204751