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Calcium in PDB 6h9x: Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine

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

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

Protein crystallography data

The structure of Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine, PDB code: 6h9x 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) 68.03 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.407, 84.407, 229.874, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine (pdb code 6h9x). 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 the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine, PDB code: 6h9x:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6h9x

Go back to Calcium Binding Sites List in 6h9x
Calcium binding site 1 out of 3 in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine


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 the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:0.3
occ:1.00
 OE2 A:GLU355 3.2 56.1 1.0
O2S A:SSA501 3.5 48.7 1.0
OE1 A:GLU355 3.5 57.9 1.0
CD A:GLU355 3.7 68.1 1.0
O A:HOH760 3.7 69.7 1.0
OG A:SER358 3.8 62.0 1.0
OD2 A:ASP342 3.8 67.2 1.0
CB A:SER358 4.2 52.2 1.0
OD1 A:ASP342 4.3 59.6 1.0
CG A:ASP342 4.4 59.6 1.0
CD1 A:LEU328 4.6 51.4 1.0
S1 A:SSA501 4.7 46.6 1.0
O A:HOH644 5.0 86.3 1.0

Calcium binding site 2 out of 3 in 6h9x

Go back to Calcium Binding Sites List in 6h9x
Calcium binding site 2 out of 3 in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine


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 the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:0.4
occ:1.00
 ND2 A:ASN389 3.0 45.5 1.0
OD1 A:ASN389 3.6 43.5 1.0
CG2 A:VAL362 3.6 44.7 1.0
OE2 A:GLU239 3.7 50.5 1.0
CG A:ASN389 3.7 55.3 1.0
CB A:SER336 3.9 54.9 1.0
O A:HOH602 3.9 62.1 1.0
OE1 A:GLU239 3.9 48.5 1.0
CD A:GLU239 4.1 58.8 1.0
O A:HOH639 4.1 43.5 1.0
CB A:SER360 4.2 44.7 1.0
OG A:SER360 4.3 47.0 1.0
N A:ALA337 4.4 49.1 1.0
O2 A:EDO504 4.5 84.1 1.0
NE2 A:GLN366 4.5 44.8 1.0
C A:SER336 4.7 53.7 1.0
CB A:ALA337 4.8 48.8 1.0
CA A:SER336 4.8 51.0 1.0
CA A:ALA337 4.9 48.6 1.0
OG A:SER336 4.9 68.3 1.0

Calcium binding site 3 out of 3 in 6h9x

Go back to Calcium Binding Sites List in 6h9x
Calcium binding site 3 out of 3 in the Klebsiella Pneumoniae Seryl-Trna Synthetase in Complex with the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine


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 the Intermediate Analog 5'-O-(N-(L-Seryl)-Sulfamoyl)Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:57.8
occ:1.00
 O A:ASP254 2.4 53.3 1.0
O A:HOH709 2.5 55.8 1.0
O A:HOH784 2.6 64.4 1.0
C A:ASP254 3.5 54.1 1.0
N A:ASP255 4.4 49.1 1.0
CA A:ASP255 4.4 49.8 1.0
O A:HOH742 4.4 57.8 1.0
CA A:ASP254 4.4 52.8 1.0
CB A:ASP254 4.6 55.3 1.0
OD1 A:ASP255 4.7 58.2 1.0
O A:LEU256 4.9 54.1 1.0
C A:ASP255 5.0 54.1 1.0

Reference:

D.De Ruysscher, L.Pang, S.De Graef, M.Nautiyal, W.M.De Borggraeve, J.Rozenski, S.V.Strelkov, S.D.Weeks, A.Van Aerschot. Acylated Sulfonamide Adenosines As Potent Inhibitors of the Adenylate-Forming Enzyme Superfamily. Eur.J.Med.Chem. V. 174 252 2019.
ISSN: ISSN 0223-5234
PubMed: 31048140
DOI: 10.1016/J.EJMECH.2019.04.045
Page generated: Wed Jul 9 14:33:35 2025

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