Calcium in PDB 6hi0: Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Uridine

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

The structure of Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Uridine, PDB code: 6hi0 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)	59.62 / 2.25
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.321, 84.321, 229.998, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 22.3

The binding sites of Calcium atom in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Uridine (pdb code 6hi0). 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)Uridine, PDB code: 6hi0:
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)Uridine


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)Uridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:67.5 occ:1.00 O A:ASP254 2.3 59.7 1.0 O A:HOH635 2.7 67.2 1.0 O A:HOH672 2.7 74.1 1.0 C A:ASP254 3.5 60.4 1.0 N A:ASP255 4.3 56.2 1.0 CA A:ASP254 4.4 59.2 1.0 CA A:ASP255 4.4 55.8 1.0 CB A:ASP254 4.6 61.6 1.0 O A:LEU256 4.9 55.7 1.0 OD1 A:ASP255 4.9 65.4 1.0 C A:ASP255 4.9 59.4 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)Uridine


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)Uridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:0.9 occ:1.00 ND2 A:ASN389 3.4 52.1 1.0 OD1 A:ASN389 3.8 52.7 1.0 CB A:SER336 3.8 60.0 1.0 OE2 A:GLU239 3.8 61.4 1.0 CG2 A:VAL362 3.8 53.4 1.0 CG A:ASN389 4.0 63.5 1.0 OE1 A:GLU239 4.0 62.5 1.0 CD A:GLU239 4.2 65.9 1.0 O A:HOH619 4.2 49.0 1.0 O A:HOH654 4.3 66.4 1.0 CB A:SER360 4.3 54.3 1.0 N A:ALA337 4.3 57.4 1.0 OG A:SER360 4.4 61.9 1.0 NE2 A:GLN366 4.6 50.7 1.0 C A:SER336 4.6 60.9 1.0 CA A:SER336 4.7 57.6 1.0 CB A:ALA337 4.8 57.6 1.0 OG A:SER336 4.8 75.0 1.0 CA A:ALA337 4.9 57.3 1.0 N A:SER336 4.9 58.1 1.0 O1 A:EDO503 5.0 81.9 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)Uridine


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)Uridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:0.0 occ:1.00 OD2 A:ASP342 3.7 68.4 1.0 CD1 A:LEU328 3.9 59.6 1.0 OE2 A:GLU355 3.9 62.3 1.0 OG A:SER358 4.0 64.8 1.0 O A:ASP332 4.1 73.8 1.0 OE1 A:GLU355 4.1 72.2 1.0 OD1 A:ASP342 4.3 66.5 1.0 O1S A:FZK504 4.3 56.7 1.0 CD A:GLU355 4.3 74.9 1.0 CG A:ASP342 4.4 66.2 1.0 O A:HOH670 4.6 72.5 1.0 CB A:SER358 4.8 57.6 1.0 O A:HOH663 4.8 85.9 1.0 O A:HOH613 4.8 61.7 1.0 OD1 A:ASP332 5.0 76.4 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.