Magnesium in PDB 4hxg: Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form)

All present enzymatic activity of Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form):
3.4.19.1;

The structure of Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form), PDB code: 4hxg was solved by A.Kiss-Szeman, D.K.Menyhard, E.Tichy-Racs, B.Hornung, K.Radi, Z.Szeltner, K.Domokos, I.Szamosi, G.Naray-Szabo, L.Polgar, V.Harmat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	183.310, 183.800, 275.740, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 24.1

The structure of Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Magnesium atom in the Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form) (pdb code 4hxg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form), PDB code: 4hxg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in the Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:36.1 occ:1.00 O A:LYS99 2.3 53.1 1.0 O A:HOH938 2.4 39.0 1.0 O C:HOH858 2.5 70.3 1.0 O A:HOH949 2.5 39.9 1.0 O C:HOH841 2.5 46.5 1.0 OE1 A:GLU162 2.5 56.6 1.0 C A:LYS99 3.4 54.6 1.0 OE1 C:GLU42 3.5 50.0 1.0 CD A:GLU162 3.7 56.1 1.0 OE2 A:GLU162 4.1 58.0 1.0 O A:VAL100 4.2 66.0 1.0 CB A:LYS99 4.3 56.9 1.0 N A:VAL100 4.3 55.5 1.0 CA A:LYS99 4.3 55.1 1.0 OE1 C:GLU59 4.3 47.7 1.0 CA A:VAL100 4.4 57.2 1.0 CD C:GLU42 4.4 50.5 1.0 O C:HOH827 4.4 39.1 1.0 C A:VAL100 4.6 61.6 1.0 N A:LYS99 4.6 54.3 1.0 OG1 C:THR44 4.7 41.2 1.0 CD A:LYS99 4.8 60.2 1.0 CB C:GLU42 4.9 48.6 1.0 CG A:GLU162 4.9 53.2 1.0

Magnesium binding site 2 out of 21 in the Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:60.6 occ:1.00 O A:HOH947 2.4 64.1 1.0 O A:HOH812 2.5 42.2 1.0 OD2 A:ASP244 2.7 48.0 1.0 OE2 A:GLU263 2.9 52.0 1.0 CD A:GLU263 3.5 51.8 1.0 OE1 A:GLU263 3.5 52.5 1.0 CG A:ASP244 3.9 48.4 1.0 O A:HOH886 4.0 48.4 1.0 OD1 A:ASP244 4.6 46.2 1.0 OH A:TYR232 4.6 46.7 1.0 CG A:GLU263 4.7 49.5 1.0 CB A:ASP244 4.8 50.3 1.0 NZ A:LYS389 4.9 37.2 1.0 O A:VAL240 4.9 48.9 1.0 O A:GLU242 5.0 56.0 1.0

Magnesium binding site 3 out of 21 in the Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:37.9 occ:1.00 O A:HOH854 2.3 38.9 1.0 O B:LYS99 2.4 52.0 1.0 OE1 B:GLU162 2.4 48.0 1.0 O A:HOH853 2.6 35.1 0.5 O B:HOH828 2.6 29.0 1.0 OE1 A:GLU42 3.3 44.5 1.0 CD B:GLU162 3.3 50.4 1.0 OE2 B:GLU162 3.6 50.6 1.0 C B:LYS99 3.6 51.0 1.0 O A:HOH853 3.7 35.2 0.5 O A:HOH850 3.7 55.7 1.0 CD A:GLU42 4.4 43.6 1.0 CG B:GLU162 4.5 51.7 1.0 CA B:LYS99 4.5 46.3 1.0 OE1 A:GLU59 4.5 39.2 1.0 N B:VAL100 4.5 53.1 1.0 CB B:LYS99 4.6 44.7 1.0 O B:VAL100 4.6 55.2 1.0 CA B:VAL100 4.6 52.4 1.0 N B:LYS99 4.6 45.7 1.0 OG1 A:THR44 4.7 40.5 1.0 C B:VAL100 4.7 53.8 1.0 CB B:GLU162 4.8 50.8 1.0 CB A:GLU42 4.9 37.9 1.0

Magnesium binding site 4 out of 21 in the Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:60.7 occ:1.00 O C:HOH801 2.3 44.4 1.0 OE1 C:GLU162 2.5 56.3 1.0 O B:HOH829 2.5 47.8 1.0 O C:LYS99 2.7 56.5 1.0 OE1 B:GLU42 2.9 58.9 1.0 CD C:GLU162 3.5 58.7 1.0 OE2 C:GLU162 3.9 58.9 1.0 C C:LYS99 3.9 58.9 1.0 CD B:GLU42 4.1 56.9 1.0 O C:VAL100 4.3 66.0 1.0 CB B:GLU42 4.5 51.0 1.0 CA C:VAL100 4.7 59.2 1.0 OG1 B:THR44 4.7 50.9 1.0 N C:VAL100 4.7 60.1 1.0 CG C:GLU162 4.7 60.0 1.0 C C:VAL100 4.8 62.6 1.0 CB C:LYS99 4.8 60.9 1.0 CG B:LYS33 4.8 47.0 1.0 OE2 B:GLU42 4.8 57.8 1.0 CB C:GLU162 4.8 58.9 1.0 CA C:LYS99 4.9 59.5 1.0 OE1 B:GLU59 4.9 54.6 1.0 CG B:GLU42 4.9 52.1 1.0

Magnesium binding site 5 out of 21 in the Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:93.6 occ:1.00 OE2 C:GLU263 2.4 79.8 1.0 O C:HOH802 2.5 58.2 1.0 O C:HOH810 2.5 69.7 1.0 O C:HOH859 2.5 0.8 1.0 OD2 C:ASP244 2.6 83.5 1.0 O C:HOH857 2.6 69.7 1.0 CD C:GLU263 3.2 80.0 1.0 OE1 C:GLU263 3.3 81.3 1.0 CG C:ASP244 3.6 82.3 1.0 CB C:ASP244 4.1 80.4 1.0 NZ C:LYS389 4.2 81.5 1.0 OH C:TYR232 4.5 68.1 1.0 O C:GLU242 4.5 80.8 1.0 CG C:GLU263 4.6 78.7 1.0 OD1 C:ASP244 4.6 81.8 1.0 N C:ASP244 4.7 74.3 1.0 O C:VAL240 4.7 80.2 1.0 NZ C:LYS237 4.9 66.5 1.0 CD C:LYS389 5.0 81.2 1.0

Magnesium binding site 6 out of 21 in the Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg709 b:63.6 occ:1.00 O D:HOH802 2.4 41.2 1.0 OD2 D:ASP244 2.4 52.7 1.0 O D:HOH936 2.7 64.1 1.0 O D:HOH935 2.7 41.4 1.0 OE1 D:GLU263 2.9 45.3 1.0 OE2 D:GLU263 3.0 48.0 1.0 CD D:GLU263 3.1 45.6 1.0 O D:HOH975 3.5 46.5 1.0 CG D:ASP244 3.5 48.4 1.0 O D:HOH920 3.7 50.7 1.0 O D:HOH1014 4.3 45.8 1.0 CB D:ASP244 4.3 44.0 1.0 CG D:GLU263 4.4 41.6 1.0 OD1 D:ASP244 4.4 47.0 1.0 OH D:TYR232 4.4 40.3 1.0 O1 D:HEZ708 4.5 69.2 1.0 C1 D:HEZ708 4.5 68.0 1.0 N D:ASP244 4.8 37.4 1.0 NZ D:LYS389 4.8 34.4 1.0 O D:GLU242 4.8 37.1 1.0 O D:VAL240 4.9 41.2 1.0

Magnesium binding site 7 out of 21 in the Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg710 b:42.2 occ:1.00 OE1 D:GLU162 2.3 29.3 1.0 O D:HOH1021 2.4 34.5 1.0 O E:HOH902 2.6 40.0 1.0 O E:HOH832 2.9 25.6 1.0 O D:LYS99 3.0 42.4 1.0 OE1 E:GLU42 3.3 32.6 1.0 CD D:GLU162 3.3 30.8 1.0 OE2 D:GLU162 3.6 28.9 1.0 OG1 E:THR44 3.9 35.3 1.0 C D:LYS99 4.3 39.0 1.0 CD E:GLU42 4.3 31.7 1.0 CB E:GLU42 4.3 31.2 1.0 CG E:LYS33 4.6 26.6 1.0 OE1 E:GLU59 4.6 32.9 1.0 O E:HOH850 4.6 49.3 1.0 CG D:GLU162 4.6 29.6 1.0 OE2 E:GLU59 4.9 34.9 1.0 CB E:LYS33 4.9 24.1 1.0 CG E:GLU42 4.9 30.1 1.0 CB D:GLU162 4.9 26.2 1.0 O E:HOH828 4.9 42.6 1.0

Magnesium binding site 8 out of 21 in the Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg704 b:58.1 occ:1.00 OD2 E:ASP244 2.5 52.3 1.0 O E:HOH987 2.6 46.9 1.0 O E:HOH842 2.7 37.2 1.0 OE2 E:GLU263 2.7 42.8 1.0 CD E:GLU263 2.9 40.9 1.0 OE1 E:GLU263 2.9 42.4 1.0 O E:HOH801 2.9 52.0 1.0 CG E:ASP244 3.5 48.8 1.0 O E:HOH917 3.6 74.3 1.0 OH E:TYR232 3.6 40.8 1.0 CB E:ASP244 3.8 43.9 1.0 CG E:GLU263 4.0 38.2 1.0 OD1 E:ASP244 4.6 49.1 1.0 CZ E:TYR232 4.6 40.0 1.0 N E:ASP244 4.6 44.6 1.0 CE2 E:TYR232 4.9 34.9 1.0 O E:HOH868 4.9 42.3 1.0 CA E:ASP244 4.9 43.2 1.0 NZ E:LYS389 4.9 31.1 1.0 O E:VAL264 5.0 32.3 1.0

Magnesium binding site 9 out of 21 in the Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg705 b:29.7 occ:1.00 O F:HOH872 2.3 51.6 1.0 O E:HOH919 2.4 37.8 1.0 OE1 E:GLU162 2.4 36.1 1.0 O E:LYS99 2.5 38.6 1.0 O F:HOH871 2.6 49.0 1.0 O F:HOH873 2.6 60.2 1.0 OE1 F:GLU42 3.2 36.4 1.0 CD E:GLU162 3.5 36.4 1.0 C E:LYS99 3.7 34.6 1.0 OE2 E:GLU162 4.0 33.0 1.0 CD F:GLU42 4.3 38.3 1.0 OG1 F:THR44 4.4 33.5 1.0 OE1 F:GLU59 4.5 37.8 1.0 CA E:LYS99 4.6 33.2 1.0 N E:LYS99 4.6 28.7 1.0 N E:VAL100 4.7 36.0 1.0 CA E:VAL100 4.7 39.0 1.0 O E:VAL100 4.7 49.6 1.0 CB F:GLU42 4.7 35.1 1.0 CB E:LYS99 4.7 37.3 1.0 CG E:GLU162 4.8 37.5 1.0 O E:HOH853 4.9 44.0 1.0 C E:VAL100 4.9 43.9 1.0 CB E:GLU162 5.0 36.9 1.0

Magnesium binding site 10 out of 21 in the Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Pyrococcus Horikoshii Acylaminoacyl Peptidase (Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg706 b:44.3 occ:1.00 O E:HOH946 2.5 35.9 1.0 O E:HOH901 2.5 48.6 1.0 O E:HOH896 2.6 69.9 1.0 O D:HOH915 2.7 33.5 1.0 O D:HOH1006 2.7 63.0 1.0 O E:HOH828 3.7 42.6 1.0 OE2 D:GLU163 3.8 46.4 1.0 OE1 E:GLU37 4.0 59.4 1.0 O D:HOH913 4.0 56.8 1.0 O D:HOH1000 4.6 35.1 1.0 O E:ALA34 4.6 34.3 1.0 CD D:GLU163 4.7 43.2 1.0 CG E:ASN35 4.7 43.2 1.0 CA E:ASN35 4.7 39.2 1.0 OD1 E:ASN35 4.7 43.6 1.0 OE1 D:GLU163 4.8 44.7 1.0 CD E:GLU37 4.9 58.7 1.0

D.K.Menyhard, A.Kiss-Szeman, E.Tichy-Racs, B.Hornung, K.Radi, Z.Szeltner, K.Domokos, I.Szamosi, G.Naray-Szabo, L.Polgar, V.Harmat. A Self-Compartmentalizing Hexamer Serine Protease From Pyrococcus Horikoshii: Substrate Selection Achieved Through Multimerization. J.Biol.Chem. V. 288 17884 2013.
ISSN: ISSN 0021-9258
PubMed: 23632025
DOI: 10.1074/JBC.M113.451534