Atomistry » Magnesium » PDB 4hlq-4hyt » 4hxf
Atomistry »
  Magnesium »
    PDB 4hlq-4hyt »
      4hxf »

Magnesium in PDB 4hxf: Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone

Enzymatic activity of Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone

All present enzymatic activity of Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone:
3.4.19.1;

Protein crystallography data

The structure of Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone, PDB code: 4hxf 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) 19.74 / 1.60
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.057, 184.057, 145.529, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 18.6

Other elements in 4hxf:

The structure of Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone (pdb code 4hxf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone, PDB code: 4hxf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4hxf

Go back to Magnesium Binding Sites List in 4hxf
Magnesium binding site 1 out of 5 in the Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:18.7
occ:1.00
 O B:HOH980 2.1 16.9 1.0
O B:HOH891 2.1 20.4 1.0
OD1 B:ASP424 2.1 19.7 1.0
CG B:ASP424 3.1 18.4 1.0
OD2 B:ASP424 3.4 19.4 1.0
O1 B:HEZ707 3.9 35.1 1.0
OE1 B:GLU423 4.2 19.3 1.0
O B:HOH808 4.3 14.1 1.0
CB B:ASP424 4.4 16.5 1.0
CA B:ASP424 4.7 15.4 1.0
N B:ASP424 4.7 15.0 1.0
C1 B:HEZ707 4.7 32.3 1.0

Magnesium binding site 2 out of 5 in 4hxf

Go back to Magnesium Binding Sites List in 4hxf
Magnesium binding site 2 out of 5 in the Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:19.6
occ:1.00
 O B:HOH975 2.1 18.9 1.0
O B:HOH978 2.1 16.5 1.0
OD2 B:ASP244 2.1 21.1 1.0
OE2 B:GLU263 2.1 16.2 1.0
O B:HOH865 2.2 20.3 1.0
O B:HOH862 2.2 22.2 1.0
CD B:GLU263 3.0 17.4 1.0
CG B:ASP244 3.3 19.8 1.0
OE1 B:GLU263 3.3 20.0 1.0
CB B:ASP244 3.9 14.8 1.0
N B:ASP244 4.1 15.6 1.0
O B:GLU242 4.1 15.9 1.0
OD1 B:ASP244 4.2 22.8 1.0
CG B:GLU263 4.2 14.2 1.0
NZ B:LYS389 4.4 13.7 1.0
NZ B:LYS237 4.4 19.1 1.0
O1 B:HEZ715 4.4 58.6 1.0
OH B:TYR232 4.4 15.7 1.0
O B:HOH967 4.5 30.6 1.0
O B:VAL240 4.5 16.1 1.0
O B:HOH1148 4.6 29.9 0.5
O B:HOH1416 4.6 46.3 1.0
CA B:ASP244 4.7 15.0 1.0

Magnesium binding site 3 out of 5 in 4hxf

Go back to Magnesium Binding Sites List in 4hxf
Magnesium binding site 3 out of 5 in the Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:27.8
occ:1.00
 O B:HOH956 2.1 29.2 1.0
O B:HOH1229 2.1 28.9 1.0
O B:HOH915 2.2 21.7 1.0
O B:HOH901 2.3 22.3 1.0
O B:HOH1069 3.9 29.9 1.0
OE1 B:GLU37 4.0 37.3 1.0
O B:HOH1019 4.1 32.7 1.0
O B:ALA34 4.3 17.2 1.0
O B:THR12 4.5 18.1 1.0
CA B:ASN35 4.7 17.4 1.0
O B:HOH1217 4.9 24.9 1.0
N B:LEU36 4.9 18.6 1.0

Magnesium binding site 4 out of 5 in 4hxf

Go back to Magnesium Binding Sites List in 4hxf
Magnesium binding site 4 out of 5 in the Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:14.3
occ:1.00
 OE1 B:GLU162 2.0 14.4 1.0
O B:HOH876 2.1 16.3 1.0
O B:LYS99 2.2 16.3 1.0
CD B:GLU162 3.0 13.9 1.0
C B:LYS99 3.3 15.7 1.0
OE2 B:GLU162 3.4 17.1 1.0
N B:VAL100 4.2 15.3 1.0
CA B:VAL100 4.2 14.9 1.0
CA B:LYS99 4.3 16.2 1.0
CG B:GLU162 4.4 14.4 1.0
N B:LYS99 4.4 15.0 1.0
CB B:LYS99 4.5 19.2 1.0
O B:VAL100 4.7 22.2 1.0
C B:VAL100 4.7 18.0 1.0
CB B:GLU162 4.8 14.5 1.0

Magnesium binding site 5 out of 5 in 4hxf

Go back to Magnesium Binding Sites List in 4hxf
Magnesium binding site 5 out of 5 in the Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Acylaminoacyl Peptidase in Complex with Z-Gly-Gly-Phe-Chloromethyl Ketone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg706

b:43.9
occ:1.00
 O B:HOH926 2.0 22.5 1.0
O B:HOH1106 2.1 35.7 1.0
OE1 B:GLU127 2.1 36.2 1.0
O B:HOH1135 2.2 36.2 1.0
O B:HOH1349 2.3 43.3 1.0
O B:HOH1272 2.3 40.2 1.0
CD B:GLU127 3.1 40.4 1.0
OE2 B:GLU127 3.5 46.4 1.0
O B:HOH1003 3.8 31.6 1.0
CA B:GLU127 4.3 23.7 1.0
CG B:GLU127 4.4 33.6 1.0
OD2 B:ASP148 4.5 20.4 1.0
O B:HOH924 4.5 26.3 1.0
O B:HOH1158 4.5 42.9 1.0
O B:HOH1431 4.5 46.8 1.0
CD B:ARG125 4.6 18.1 1.0
CB B:GLU127 4.6 32.9 1.0
O B:HOH1248 4.7 34.6 1.0
NH1 B:ARG125 4.8 20.8 1.0
N B:GLU127 4.9 25.4 1.0
CB B:ARG125 4.9 19.4 1.0

Reference:

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
Page generated: Fri Aug 16 16:26:30 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy