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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

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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

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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

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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

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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

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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

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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

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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: Thu Jul 10 08:33:16 2025

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