Calcium in PDB 6s30: Crystal Structure of Seryl-Trna Synthetase From Klebsiella Pneumoniae

All present enzymatic activity of Crystal Structure of Seryl-Trna Synthetase From Klebsiella Pneumoniae:
6.1.1.11;

The structure of Crystal Structure of Seryl-Trna Synthetase From Klebsiella Pneumoniae, PDB code: 6s30 was solved by L.Pang, S.De Graef, S.D.Weeks, S.V.Strelkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.28 / 2.41
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.342, 83.342, 229.999, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 23.6

The binding sites of Calcium atom in the Crystal Structure of Seryl-Trna Synthetase From Klebsiella Pneumoniae (pdb code 6s30). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Seryl-Trna Synthetase From Klebsiella Pneumoniae, PDB code: 6s30:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Seryl-Trna Synthetase From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Seryl-Trna Synthetase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:0.1 occ:1.00 OD2 A:ASP342 3.4 71.6 1.0 CD1 A:LEU328 3.5 67.1 1.0 O A:ASP332 3.8 77.2 1.0 OE1 A:GLU355 4.1 91.4 1.0 OG A:SER358 4.1 71.8 1.0 CG A:ASP342 4.3 69.4 1.0 OD1 A:ASP342 4.3 71.2 1.0 CD A:GLU355 4.7 83.7 1.0 OD1 A:ASP332 4.7 80.5 1.0 CG A:LEU328 4.8 68.2 1.0 OD2 A:ASP332 4.9 81.7 1.0 OE2 A:GLU355 5.0 76.9 1.0 CG A:ASP332 5.0 79.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Seryl-Trna Synthetase From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Seryl-Trna Synthetase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:0.5 occ:1.00 O A:HOH641 3.8 59.3 1.0 ND2 A:ASN389 3.9 56.6 1.0 OG A:SER360 4.1 66.4 1.0 CB A:SER336 4.1 60.3 1.0 OD1 A:ASN389 4.1 53.0 1.0 CB A:SER360 4.2 58.1 1.0 OE2 A:GLU239 4.2 75.4 1.0 N A:ALA337 4.2 56.7 1.0 CB A:ALA337 4.3 56.8 1.0 CG2 A:VAL362 4.5 60.5 1.0 CG A:ASN389 4.5 63.2 1.0 OE1 A:GLU239 4.6 96.6 1.0 C A:SER336 4.6 62.1 1.0 N A:SER336 4.6 60.1 1.0 CD A:GLU239 4.7 83.5 1.0 CA A:SER336 4.7 58.4 1.0 CA A:ALA337 4.7 56.7 1.0 OG A:SER336 4.9 75.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Seryl-Trna Synthetase From Klebsiella Pneumoniae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Seryl-Trna Synthetase From Klebsiella Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:70.4 occ:1.00 O A:ASP254 2.3 68.5 1.0 O A:HOH678 2.4 87.2 1.0 O A:HOH636 2.7 76.8 1.0 C A:ASP254 3.5 67.5 1.0 N A:ASP255 4.3 61.9 1.0 CA A:ASP255 4.4 60.3 1.0 CA A:ASP254 4.4 64.9 1.0 CB A:ASP254 4.7 66.8 1.0 O A:LEU256 4.9 62.8 1.0 C A:ASP255 4.9 63.2 1.0 OD1 A:ASP255 5.0 67.6 1.0

L.Pang, M.Nautiyal, S.De Graef, B.Gadakh, V.Zorzini, A.Economou, S.V.Strelkov, A.Van Aerschot, S.D.Weeks. Structural Insights Into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-Trna Synthetases. Acs Chem.Biol. 2019.
ISSN: ESSN 1554-8937
PubMed: 31869198
DOI: 10.1021/ACSCHEMBIO.9B00887