Calcium in PDB 8yku: Pathil in Complex with Amp-Pnp and Tmp

Enzymatic activity of Pathil in Complex with Amp-Pnp and Tmp

All present enzymatic activity of Pathil in Complex with Amp-Pnp and Tmp:
2.7.4.16;

Protein crystallography data

The structure of Pathil in Complex with Amp-Pnp and Tmp, PDB code: 8yku was solved by J.Q.Lin, Z.Chung, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.35 / 2.17
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 118.59, 118.59, 131.87, 90, 90, 120
R / Rfree (%) 16.9 / 17.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Pathil in Complex with Amp-Pnp and Tmp (pdb code 8yku). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Pathil in Complex with Amp-Pnp and Tmp, PDB code: 8yku:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8yku

Go back to Calcium Binding Sites List in 8yku
Calcium binding site 1 out of 8 in the Pathil in Complex with Amp-Pnp and Tmp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pathil in Complex with Amp-Pnp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:26.4
occ:1.00
 OE2 A:GLU180 2.4 26.5 1.0
OE2 A:GLU183 2.5 30.4 1.0
OE1 A:GLU180 2.6 25.6 1.0
OE1 A:GLU183 2.6 29.5 1.0
CD A:GLU180 2.8 26.5 1.0
CD A:GLU183 2.9 30.3 1.0
CG A:GLU180 4.4 22.2 1.0
CG A:GLU183 4.4 27.7 1.0
O A:HOH530 4.6 32.3 1.0
O A:HOH506 4.8 43.8 1.0

Calcium binding site 2 out of 8 in 8yku

Go back to Calcium Binding Sites List in 8yku
Calcium binding site 2 out of 8 in the Pathil in Complex with Amp-Pnp and Tmp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pathil in Complex with Amp-Pnp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:15.9
occ:1.00
 O2B A:ANP411 2.2 20.0 1.0
O A:HOH566 2.4 15.9 1.0
OD1 A:ASP75 2.4 16.7 1.0
OG A:SER45 2.4 16.1 1.0
CG A:ASP75 3.3 15.4 1.0
CB A:SER45 3.5 13.1 1.0
PB A:ANP411 3.7 19.4 1.0
OD2 A:ASP75 4.0 14.7 1.0
CB A:ASP75 4.0 12.7 1.0
CA A:CA405 4.1 16.1 1.0
O1B A:ANP411 4.2 20.0 1.0
CA A:SER45 4.3 15.6 1.0
O A:THR46 4.3 17.0 1.0
O A:HOH622 4.4 16.5 1.0
N A:THR46 4.4 16.2 1.0
O A:HOH509 4.5 14.5 1.0
O2' A:ANP411 4.5 16.3 1.0
O3A A:ANP411 4.6 22.8 1.0
O2G A:ANP411 4.6 18.1 1.0
N3B A:ANP411 4.7 19.9 1.0
O1G A:ANP411 4.7 17.9 1.0
OD1 A:ASP47 4.8 16.0 1.0
C A:SER45 4.9 16.5 1.0
C2' A:ANP411 4.9 18.3 1.0
PG A:ANP411 4.9 18.5 1.0
CA A:CA406 5.0 14.6 1.0

Calcium binding site 3 out of 8 in 8yku

Go back to Calcium Binding Sites List in 8yku
Calcium binding site 3 out of 8 in the Pathil in Complex with Amp-Pnp and Tmp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pathil in Complex with Amp-Pnp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:17.5
occ:1.00
 OD2 A:ASP47 2.3 15.6 1.0
O1G A:ANP411 2.4 17.9 1.0
O A:HOH513 2.4 21.2 1.0
O A:HOH504 2.4 19.9 1.0
O A:HOH654 2.7 30.7 1.0
CG A:ASP47 3.6 16.7 1.0
O A:HOH681 3.6 36.8 1.0
PG A:ANP411 3.7 18.5 1.0
CA A:CA405 3.9 16.1 1.0
O A:HOH641 3.9 20.6 1.0
O A:HOH566 4.0 15.9 1.0
O3G A:ANP411 4.1 19.5 1.0
O3 A:TPS410 4.3 30.1 1.0
CB A:ASP47 4.3 15.2 1.0
CA A:ASP47 4.5 17.6 1.0
OD1 A:ASP47 4.5 16.0 1.0
N3B A:ANP411 4.6 19.9 1.0
N A:THR48 4.7 15.3 1.0
O2G A:ANP411 4.7 18.1 1.0
O A:THR48 4.8 16.2 1.0
O A:THR46 4.9 17.0 1.0

Calcium binding site 4 out of 8 in 8yku

Go back to Calcium Binding Sites List in 8yku
Calcium binding site 4 out of 8 in the Pathil in Complex with Amp-Pnp and Tmp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pathil in Complex with Amp-Pnp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:16.1
occ:1.00
 O1G A:ANP411 2.4 17.9 1.0
OD1 A:ASP47 2.4 16.0 1.0
OD1 A:ASP75 2.4 16.7 1.0
O A:HOH641 2.5 20.6 1.0
O2G A:ANP411 2.5 18.1 1.0
OD2 A:ASP47 2.5 15.6 1.0
O A:HOH543 2.6 13.4 1.0
O A:HOH566 2.7 15.9 1.0
CG A:ASP47 2.8 16.7 1.0
PG A:ANP411 3.0 18.5 1.0
CG A:ASP75 3.3 15.4 1.0
OD2 A:ASP75 3.7 14.7 1.0
CA A:CA404 3.9 17.5 1.0
CA A:CA403 4.1 15.9 1.0
O2B A:ANP411 4.2 20.0 1.0
O3G A:ANP411 4.2 19.5 1.0
CA A:CA406 4.2 14.6 1.0
N3B A:ANP411 4.2 19.9 1.0
O A:HOH509 4.3 14.5 1.0
CB A:ASP75 4.3 12.7 1.0
O A:VAL71 4.3 16.0 1.0
CB A:ASP47 4.4 15.2 1.0
PB A:ANP411 4.6 19.4 1.0
OG A:SER45 4.6 16.1 1.0
O A:HOH654 4.8 30.7 1.0
O A:THR46 4.8 17.0 1.0
O1B A:ANP411 4.9 20.0 1.0

Calcium binding site 5 out of 8 in 8yku

Go back to Calcium Binding Sites List in 8yku
Calcium binding site 5 out of 8 in the Pathil in Complex with Amp-Pnp and Tmp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Pathil in Complex with Amp-Pnp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:14.6
occ:1.00
 OD2 A:ASP75 2.3 14.7 1.0
OD1 A:ASP211 2.3 14.2 1.0
O1B A:ANP411 2.3 20.0 1.0
O2G A:ANP411 2.3 18.1 1.0
O A:HOH516 2.5 17.0 1.0
CG A:ASP75 3.3 15.4 1.0
CG A:ASP211 3.4 16.5 1.0
PB A:ANP411 3.5 19.4 1.0
PG A:ANP411 3.6 18.5 1.0
OD1 A:ASP75 3.7 16.7 1.0
OD2 A:ASP211 3.9 16.4 1.0
N3B A:ANP411 3.9 19.9 1.0
NH2 A:ARG146 4.0 17.0 1.0
O2B A:ANP411 4.0 20.0 1.0
O A:HOH543 4.2 13.4 1.0
CA A:CA405 4.2 16.1 1.0
O A:ASP211 4.3 18.1 1.0
OG A:SER213 4.4 21.3 1.0
O3G A:ANP411 4.4 19.5 1.0
O A:HOH522 4.4 26.4 1.0
N A:ASP211 4.4 16.0 1.0
CB A:ASP75 4.7 12.7 1.0
CB A:ASP211 4.7 13.7 1.0
O1G A:ANP411 4.7 17.9 1.0
O3A A:ANP411 4.8 22.8 1.0
CA A:ASP211 4.9 15.1 1.0
C A:ASP211 4.9 19.9 1.0
CA A:ASP75 4.9 14.9 1.0
CA A:CA403 5.0 15.9 1.0
CB A:ALA78 5.0 13.2 1.0

Calcium binding site 6 out of 8 in 8yku

Go back to Calcium Binding Sites List in 8yku
Calcium binding site 6 out of 8 in the Pathil in Complex with Amp-Pnp and Tmp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Pathil in Complex with Amp-Pnp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:31.0
occ:1.00
 O A:HOH675 2.2 28.3 1.0
O3 A:TPS410 2.3 30.1 1.0
OD2 A:ASP214 2.3 32.4 1.0
O A:HOH676 2.6 42.4 1.0
O A:HOH539 2.7 33.7 1.0
O2 A:TPS410 2.7 36.6 1.0
P1 A:TPS410 3.1 31.1 1.0
CG A:ASP214 3.2 28.6 1.0
OD1 A:ASP214 3.4 28.8 1.0
O A:HOH504 4.0 19.9 1.0
O1 A:TPS410 4.2 29.7 1.0
O7 A:TPS410 4.2 31.5 1.0
C7 A:TPS410 4.3 25.0 1.0
O A:HOH571 4.4 24.8 1.0
O A:HOH653 4.5 47.1 1.0
O A:HOH665 4.5 46.9 1.0
CB A:ASP214 4.6 23.0 1.0
O A:HOH518 4.8 42.9 1.0
O3G A:ANP411 4.8 19.5 1.0
C6 A:TPS410 4.8 26.4 1.0

Calcium binding site 7 out of 8 in 8yku

Go back to Calcium Binding Sites List in 8yku
Calcium binding site 7 out of 8 in the Pathil in Complex with Amp-Pnp and Tmp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Pathil in Complex with Amp-Pnp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:39.9
occ:1.00
 O A:HOH571 2.3 24.8 1.0
OD1 A:ASP214 2.3 28.8 1.0
OD1 A:ASP219 2.3 23.0 1.0
O A:HOH670 2.3 32.8 1.0
NE2 A:HIS222 2.5 27.9 1.0
O A:HOH522 2.5 26.4 1.0
CD2 A:HIS222 3.2 20.9 1.0
CG A:ASP214 3.3 28.6 1.0
CE1 A:HIS222 3.6 30.1 1.0
CG A:ASP219 3.6 21.1 1.0
CB A:ASP214 3.8 23.0 1.0
O A:HOH539 3.9 33.7 1.0
O A:HOH675 4.2 28.3 1.0
OD2 A:ASP219 4.3 20.8 1.0
OD2 A:ASP214 4.3 32.4 1.0
O2A A:ANP411 4.4 22.3 1.0
O1A A:ANP411 4.4 23.5 1.0
CG A:HIS222 4.5 27.1 1.0
CA A:ASP219 4.5 17.3 1.0
ND1 A:HIS222 4.6 30.3 1.0
CB A:ASP219 4.6 17.8 1.0
O A:HOH537 4.7 37.1 1.0
OG A:SER213 4.7 21.3 1.0
O A:HOH516 4.7 17.0 1.0
N A:ASP214 4.8 21.3 1.0
N A:ASP219 4.9 19.6 1.0
O A:ALA218 4.9 22.4 1.0
O3G A:ANP411 4.9 19.5 1.0
CA A:ASP214 4.9 22.1 1.0
C A:ALA218 5.0 22.1 1.0

Calcium binding site 8 out of 8 in 8yku

Go back to Calcium Binding Sites List in 8yku
Calcium binding site 8 out of 8 in the Pathil in Complex with Amp-Pnp and Tmp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Pathil in Complex with Amp-Pnp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca409

b:34.9
occ:1.00
 O A:LEU144 2.5 23.7 1.0
O A:ALA209 2.5 16.6 1.0
O A:ALA78 2.6 17.0 1.0
SD A:MET79 3.2 19.3 1.0
C A:ALA209 3.6 19.8 1.0
C A:LEU144 3.6 21.8 1.0
C A:ALA78 3.6 17.8 1.0
CA A:LEU210 4.1 17.1 1.0
CA A:THR145 4.1 22.3 1.0
CG A:ARG146 4.2 23.1 1.0
N A:THR145 4.3 20.3 1.0
N A:LEU210 4.3 16.2 1.0
C A:THR145 4.3 26.2 1.0
CE A:MET79 4.3 18.9 1.0
CA A:MET79 4.3 17.8 1.0
N A:MET79 4.3 17.3 1.0
CB A:LEU210 4.4 17.1 1.0
NE A:ARG146 4.5 21.1 1.0
CG A:MET79 4.5 17.6 1.0
O A:THR145 4.5 22.1 1.0
CB A:ALA78 4.5 13.2 1.0
CB A:LEU144 4.5 16.9 1.0
CA A:ALA209 4.6 18.7 1.0
CA A:ALA78 4.6 15.2 1.0
CA A:LEU144 4.6 20.1 1.0
N A:ARG146 4.8 24.0 1.0
N A:ALA209 4.8 15.0 1.0
CB A:ALA209 4.9 15.2 1.0
CD A:ARG146 4.9 21.9 1.0
CB A:MET79 5.0 14.6 1.0

Reference:

J.Q.Lin, J.Lescar. Thil in Complex with Amp-Pnp To Be Published.
Page generated: Sat Sep 28 09:25:19 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy