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

Enzymatic activity of 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;

Protein crystallography data

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

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)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 6hi0

Go back to Calcium Binding Sites List in 6hi0
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 6hi0

Go back to Calcium Binding Sites List in 6hi0
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 6hi0

Go back to Calcium Binding Sites List in 6hi0
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

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: Sat Dec 12 06:09:47 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy