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

Enzymatic activity of Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine

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

Protein crystallography data

The structure of Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine, PDB code: 6hhz 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) 43.00 / 2.15
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.351, 83.351, 229.329, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.6

Other elements in 6hhz:

The structure of Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine (pdb code 6hhz). 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)Cytidine, PDB code: 6hhz:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6hhz

Go back to Calcium Binding Sites List in 6hhz
Calcium binding site 1 out of 3 in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine


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)Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:55.0
occ:1.00
 O A:ASP254 2.3 49.5 1.0
O A:HOH671 2.5 49.3 1.0
O A:HOH779 2.7 65.4 1.0
O A:HOH646 2.7 61.5 1.0
C A:ASP254 3.5 50.2 1.0
N A:ASP255 4.3 45.3 1.0
CA A:ASP255 4.3 45.0 1.0
CA A:ASP254 4.4 48.6 1.0
O A:HOH699 4.5 55.0 1.0
CB A:ASP254 4.6 50.6 1.0
OD1 A:ASP255 4.8 50.4 1.0
C A:ASP255 4.9 49.4 1.0
O A:LEU256 4.9 48.8 1.0

Calcium binding site 2 out of 3 in 6hhz

Go back to Calcium Binding Sites List in 6hhz
Calcium binding site 2 out of 3 in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine


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)Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:0.3
occ:1.00
 OD2 A:ASP342 3.6 57.1 1.0
CD1 A:LEU328 3.7 51.5 1.0
OE2 A:GLU355 3.8 58.9 1.0
OG A:SER358 3.8 58.5 1.0
OD1 A:ASP342 4.1 53.0 1.0
OE1 A:GLU355 4.1 66.2 1.0
CG A:ASP342 4.2 54.0 1.0
CD A:GLU355 4.3 67.4 1.0
O2S A:FZQ504 4.3 48.4 1.0
O A:ASP332 4.4 57.7 1.0
O A:HOH734 4.5 63.0 1.0
CB A:SER358 4.6 50.1 1.0
O A:HOH680 4.6 54.6 1.0

Calcium binding site 3 out of 3 in 6hhz

Go back to Calcium Binding Sites List in 6hhz
Calcium binding site 3 out of 3 in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine


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)Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:98.8
occ:1.00
 O A:HOH764 2.3 67.2 1.0
ND2 A:ASN389 3.5 43.5 1.0
OE2 A:GLU239 3.7 55.5 1.0
OD1 A:ASN389 3.8 44.4 1.0
CB A:SER336 3.8 47.9 1.0
OE1 A:GLU239 3.9 48.2 1.0
CG2 A:VAL362 4.0 43.2 1.0
CG A:ASN389 4.0 51.7 1.0
CD A:GLU239 4.1 63.2 1.0
O1 A:EDO503 4.2 73.6 1.0
O A:HOH679 4.3 68.9 1.0
O A:HOH632 4.4 43.6 1.0
CB A:SER360 4.5 42.5 1.0
N A:ALA337 4.5 44.1 1.0
O A:HOH734 4.5 63.0 1.0
OG A:SER360 4.5 46.8 1.0
NE2 A:GLN366 4.6 42.7 1.0
OG A:SER336 4.7 58.8 1.0
CA A:SER336 4.7 45.2 1.0
C A:SER336 4.7 48.0 1.0
CB A:ALA337 4.9 44.7 1.0
N A:SER336 4.9 45.8 1.0

Reference:

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.
Page generated: Wed Jul 9 14:36:48 2025

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