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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

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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

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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: Mon Dec 14 18:50:55 2020

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