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Magnesium in PDB 8yks: Pathil in Complex with Amp-Pnp

Enzymatic activity of Pathil in Complex with Amp-Pnp

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

Protein crystallography data

The structure of Pathil in Complex with Amp-Pnp, PDB code: 8yks 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) 43.54 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 113.19, 115.46, 132.62, 90, 90, 90
R / Rfree (%) 18.2 / 19.8

Other elements in 8yks:

The structure of Pathil in Complex with Amp-Pnp also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 8yks

Go back to Magnesium Binding Sites List in 8yks
Magnesium binding site 1 out of 6 in the Pathil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pathil in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:20.4
occ:1.00
 OD1 B:ASP75 2.1 20.9 1.0
OD1 B:ASP211 2.1 19.9 1.0
O B:HOH539 2.1 18.5 1.0
O B:HOH519 2.2 20.2 1.0
O B:HOH566 2.3 22.1 1.0
CG B:ASP211 3.1 21.8 1.0
CG B:ASP75 3.2 20.8 1.0
OD2 B:ASP211 3.4 20.4 1.0
OD2 B:ASP75 3.7 21.1 1.0
NH2 B:ARG146 3.9 22.3 1.0
O3G B:ANP406 4.0 33.0 1.0
O B:ASP211 4.1 19.8 1.0
N B:ASP211 4.4 19.6 1.0
CB B:ASP75 4.4 16.7 1.0
CB B:ASP211 4.4 19.5 1.0
O B:HOH523 4.5 30.9 1.0
MG B:MG402 4.5 25.6 1.0
O B:HOH696 4.6 28.6 1.0
CA B:ASP75 4.6 20.7 1.0
O B:HOH506 4.6 33.7 1.0
N3B B:ANP406 4.7 31.3 1.0
CB B:ALA78 4.7 19.4 1.0
CA B:ASP211 4.8 17.9 1.0
C B:ASP211 4.8 25.0 1.0
O B:HOH618 4.8 26.0 1.0
OG B:SER213 4.9 30.5 1.0

Magnesium binding site 2 out of 6 in 8yks

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Magnesium binding site 2 out of 6 in the Pathil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pathil in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:25.6
occ:1.00
 O3G B:ANP406 1.9 33.0 1.0
OD2 B:ASP75 2.0 21.1 1.0
O B:HOH618 2.0 26.0 1.0
OD2 B:ASP47 2.1 26.0 1.0
OD1 B:ASP47 2.3 27.0 1.0
O B:HOH559 2.3 27.3 1.0
CG B:ASP47 2.5 24.6 1.0
CG B:ASP75 3.2 20.8 1.0
PG B:ANP406 3.3 26.9 1.0
O B:HOH519 3.5 20.2 1.0
NA B:NA405 3.7 25.1 1.0
O2G B:ANP406 3.7 39.6 1.0
O1G B:ANP406 3.8 31.5 1.0
OD1 B:ASP75 3.8 20.9 1.0
O B:HOH566 3.9 22.1 1.0
O B:HOH502 3.9 22.0 1.0
CB B:ASP47 4.0 20.7 1.0
O B:HOH501 4.0 28.1 1.0
OG B:SER45 4.2 16.1 1.0
O B:HOH534 4.3 27.9 1.0
CB B:ASP75 4.3 16.7 1.0
O B:HOH696 4.3 28.6 1.0
NA B:NA404 4.4 30.1 1.0
O B:THR46 4.4 17.4 1.0
O B:VAL71 4.5 19.5 1.0
N3B B:ANP406 4.5 31.3 1.0
MG B:MG401 4.5 20.4 1.0
CA B:ASP47 4.9 18.7 1.0

Magnesium binding site 3 out of 6 in 8yks

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Magnesium binding site 3 out of 6 in the Pathil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pathil in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:64.9
occ:1.00
 O2A B:ANP406 2.0 44.8 1.0
O B:HOH617 2.0 34.6 1.0
O1B B:ANP406 2.1 44.8 1.0
O1G B:ANP406 2.2 31.5 1.0
PB B:ANP406 3.2 44.8 1.0
PA B:ANP406 3.2 33.8 1.0
NA B:NA404 3.4 30.1 1.0
PG B:ANP406 3.4 26.9 1.0
O3A B:ANP406 3.5 29.8 1.0
O B:HOH534 3.8 27.9 1.0
O1A B:ANP406 3.8 33.5 1.0
N3B B:ANP406 3.8 31.3 1.0
O B:HOH537 4.0 34.9 1.0
O2G B:ANP406 4.2 39.6 1.0
O B:HOH540 4.3 41.6 1.0
O B:HOH616 4.4 37.6 1.0
O2B B:ANP406 4.5 44.8 1.0
O B:HOH656 4.5 38.6 1.0
O5' B:ANP406 4.5 22.4 1.0
O3G B:ANP406 4.5 33.0 1.0
OD1 B:ASP47 4.8 27.0 1.0

Magnesium binding site 4 out of 6 in 8yks

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Magnesium binding site 4 out of 6 in the Pathil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pathil in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:19.7
occ:1.00
 OD2 A:ASP75 2.0 19.0 1.0
O2G A:ANP406 2.0 21.2 1.0
O A:HOH554 2.1 17.9 1.0
O A:HOH564 2.2 20.7 1.0
OD1 A:ASP47 2.2 20.4 1.0
OD2 A:ASP47 2.2 20.6 1.0
CG A:ASP47 2.5 18.8 1.0
CG A:ASP75 3.2 20.4 1.0
PG A:ANP406 3.2 23.8 1.0
NA A:NA405 3.5 19.5 1.0
O1G A:ANP406 3.7 23.0 1.0
O A:HOH523 3.8 21.0 1.0
O3G A:ANP406 3.8 23.1 1.0
OD1 A:ASP75 3.8 20.4 1.0
O A:HOH542 3.9 20.5 1.0
CB A:ASP47 4.0 20.2 1.0
OG A:SER45 4.1 18.9 1.0
O A:HOH505 4.1 24.6 1.0
NA A:NA404 4.1 24.4 1.0
O A:HOH512 4.1 17.9 1.0
O A:THR46 4.3 16.2 1.0
CB A:ASP75 4.3 17.7 1.0
O A:VAL71 4.5 19.2 1.0
N3B A:ANP406 4.6 24.7 1.0
MG A:MG402 4.7 18.6 1.0
CA A:ASP47 4.8 18.7 1.0
C A:THR46 4.9 16.6 1.0

Magnesium binding site 5 out of 6 in 8yks

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Magnesium binding site 5 out of 6 in the Pathil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pathil in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:18.6
occ:1.00
 O A:HOH523 2.0 21.0 1.0
O A:HOH521 2.0 21.7 1.0
O A:HOH542 2.1 20.5 1.0
OD1 A:ASP211 2.1 18.5 1.0
OD1 A:ASP75 2.1 20.4 1.0
CG A:ASP211 3.1 20.4 1.0
CG A:ASP75 3.3 20.4 1.0
OD2 A:ASP211 3.5 21.2 1.0
OD2 A:ASP75 3.8 19.0 1.0
NH2 A:ARG146 4.0 25.2 1.0
O2G A:ANP406 4.1 21.2 1.0
O A:ASP211 4.1 20.3 1.0
O A:HOH614 4.3 31.6 1.0
N A:ASP211 4.5 19.4 1.0
CB A:ASP211 4.5 19.9 1.0
CB A:ASP75 4.5 17.7 1.0
OG A:SER213 4.6 33.1 1.0
CA A:ASP75 4.6 18.6 1.0
O A:HOH522 4.6 34.0 1.0
O A:HOH564 4.7 20.7 1.0
CB A:ALA78 4.7 19.4 1.0
MG A:MG401 4.7 19.7 1.0
C A:ASP211 4.8 21.4 1.0
CA A:ASP211 4.8 18.7 1.0
N3B A:ANP406 4.9 24.7 1.0
CB A:SER213 5.0 29.2 1.0

Magnesium binding site 6 out of 6 in 8yks

Go back to Magnesium Binding Sites List in 8yks
Magnesium binding site 6 out of 6 in the Pathil in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pathil in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:29.8
occ:1.00
 O2A A:ANP406 2.0 23.6 1.0
O1G A:ANP406 2.1 23.0 1.0
O A:HOH613 2.1 26.3 1.0
O1B A:ANP406 2.2 29.3 1.0
PB A:ANP406 3.2 29.4 1.0
PA A:ANP406 3.2 24.3 1.0
PG A:ANP406 3.3 23.8 1.0
NA A:NA404 3.4 24.4 1.0
O3A A:ANP406 3.5 23.8 1.0
N3B A:ANP406 3.8 24.7 1.0
O A:HOH502 3.9 43.2 1.0
O3G A:ANP406 3.9 23.1 1.0
O1A A:ANP406 4.0 26.9 1.0
O A:HOH578 4.2 28.4 1.0
O A:HOH548 4.3 42.0 1.0
O5' A:ANP406 4.5 20.4 1.0
O2B A:ANP406 4.6 26.5 1.0
O2G A:ANP406 4.6 21.2 1.0

Reference:

J.Q.Lin, J.Lescar. Thil in Complex with Amp-Pnp To Be Published.
Page generated: Fri Aug 15 21:31:27 2025

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