Calcium in PDB 6hhy: Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine

All present enzymatic activity of Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine:
6.1.1.11;

The structure of Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine, PDB code: 6hhy 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)	67.52 / 2.27
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.721, 83.721, 228.419, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 22.3

The binding sites of Calcium atom in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine (pdb code 6hhy). 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 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine, PDB code: 6hhy:
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 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine


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 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:58.8 occ:1.00 O A:ASP254 2.2 58.9 1.0 O A:HOH685 2.4 55.1 1.0 O A:HOH655 2.6 76.2 1.0 C A:ASP254 3.4 58.4 1.0 N A:ASP255 4.3 53.3 1.0 CA A:ASP255 4.3 51.9 1.0 CA A:ASP254 4.4 54.7 1.0 CB A:ASP254 4.7 56.7 1.0 O A:LEU256 4.8 54.4 1.0 C A:ASP255 4.8 55.5 1.0 OD1 A:ASP255 4.9 58.0 1.0

Calcium binding site 2 out of 3 in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine


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 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:99.2 occ:1.00 OD2 A:ASP342 3.7 60.8 1.0 CD1 A:LEU328 3.7 55.7 1.0 OE2 A:GLU355 4.0 63.5 1.0 OG A:SER358 4.0 65.9 1.0 OD1 A:ASP342 4.1 57.0 1.0 O A:ASP332 4.2 65.3 1.0 OE1 A:GLU355 4.3 62.6 1.0 CG A:ASP342 4.3 57.1 1.0 O2S A:FZT504 4.4 54.4 1.0 CD A:GLU355 4.5 66.3 1.0 O A:HOH650 4.6 51.6 1.0 CB A:SER358 4.7 52.8 1.0 OD1 A:ASP332 4.9 70.1 1.0

Calcium binding site 3 out of 3 in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine


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 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:0.1 occ:1.00 O A:HOH678 2.6 62.9 1.0 ND2 A:ASN389 3.4 44.5 1.0 OE2 A:GLU239 3.5 57.5 1.0 OE1 A:GLU239 3.8 55.3 1.0 OD1 A:ASN389 3.8 45.8 1.0 CB A:SER336 3.8 50.2 1.0 CD A:GLU239 3.9 63.2 1.0 CG A:ASN389 4.0 53.9 1.0 CG2 A:VAL362 4.1 47.9 1.0 O1 A:EDO503 4.2 78.4 1.0 O A:HOH611 4.4 47.8 1.0 NE2 A:GLN366 4.5 44.0 1.0 N A:ALA337 4.6 48.5 1.0 OG A:SER336 4.7 61.9 1.0 CB A:SER360 4.7 45.6 1.0 OG A:SER360 4.7 51.5 1.0 CA A:SER336 4.8 48.3 1.0 C A:SER336 4.9 51.6 1.0 N A:SER336 5.0 49.3 1.0

L.Pang, M.Nautiyal, S.De Graef, S.V.Strelkov, A.Van Aerschot, S.D.Weeks. Structural Insights Into the Binding of Natural Pyrimidine Based Inhibitors of Class II Aminoacyl-Trna Synthetase To Be Published.