Atomistry » Magnesium » PDB 4nlz-4nxm » 4no1
Atomistry »
  Magnesium »
    PDB 4nlz-4nxm »
      4no1 »

Magnesium in PDB 4no1: Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2

Enzymatic activity of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2

All present enzymatic activity of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2:
3.4.25.1;

Protein crystallography data

The structure of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2, PDB code: 4no1 was solved by M.L.Stein, H.Cui, P.Beck, C.Dubiella, C.Voss, A.Krueger, B.Schmidt, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.440, 301.330, 144.910, 90.00, 113.06, 90.00
R / Rfree (%) 19 / 21.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2 (pdb code 4no1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2, PDB code: 4no1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4no1

Go back to Magnesium Binding Sites List in 4no1
Magnesium binding site 1 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:44.4
occ:1.00
 O G:ARG122 2.2 41.3 1.0
O G:MET125 2.3 37.6 1.0
O G:HOH441 2.4 40.9 1.0
O G:TYR119 2.6 36.8 1.0
OG1 G:THR8 2.7 33.9 1.0
O G:ALA123 3.4 42.3 1.0
C G:ARG122 3.4 38.9 1.0
CG2 G:THR8 3.4 36.8 1.0
C G:MET125 3.4 39.4 1.0
C G:ALA123 3.6 40.4 1.0
CB G:THR8 3.6 36.4 1.0
CA G:ALA123 3.6 39.2 1.0
C G:TYR119 3.7 34.4 1.0
N G:ALA123 4.0 38.1 1.0
N G:MET125 4.1 43.8 1.0
CA G:MET125 4.3 43.7 1.0
N G:ARG126 4.3 37.1 1.0
N G:THR8 4.4 38.0 1.0
CA G:ARG126 4.4 34.8 1.0
CA G:TYR119 4.5 33.8 1.0
N G:TYR124 4.5 42.8 1.0
CA G:ARG122 4.6 40.5 1.0
CD G:PRO127 4.6 29.8 1.0
N G:ARG122 4.6 38.8 1.0
CA G:THR8 4.6 38.1 1.0
N G:THR120 4.7 31.8 1.0
CB G:MET125 4.8 49.4 1.0
CA G:THR120 4.9 30.9 1.0
C G:TYR124 4.9 43.8 1.0
C G:ARG126 5.0 32.9 1.0
CB G:TYR119 5.0 31.8 1.0

Magnesium binding site 2 out of 8 in 4no1

Go back to Magnesium Binding Sites List in 4no1
Magnesium binding site 2 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:60.7
occ:1.00
 O N:HOH335 2.0 36.5 1.0
O N:HOH337 2.2 47.7 1.0
OE1 H:GLN91 2.2 42.2 1.0
CD H:GLN91 3.4 40.9 1.0
O N:ASN92 3.8 44.1 1.0
OD1 N:ASP51 3.9 37.2 1.0
NE2 H:GLN91 3.9 37.7 1.0
O H:HOH406 3.9 31.2 1.0
OD2 N:ASP51 4.3 34.8 1.0
CG N:ASP51 4.6 34.4 1.0
O N:HOH323 4.6 38.0 1.0
CG H:GLN91 4.6 38.8 1.0
C N:ASN92 4.7 42.7 1.0
CB H:GLN91 4.9 36.9 1.0
ND1 H:HIS116 5.0 40.9 1.0

Magnesium binding site 3 out of 8 in 4no1

Go back to Magnesium Binding Sites List in 4no1
Magnesium binding site 3 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:65.6
occ:1.00
 O I:SER180 2.6 34.5 1.0
O I:ASP177 2.6 38.3 1.0
O I:ALA174 2.6 40.7 1.0
C I:ALA174 3.6 40.9 1.0
C I:SER180 3.7 35.0 1.0
C I:ASP177 3.8 38.8 1.0
O I:HOH408 3.8 41.3 1.0
CA I:ASP175 3.9 40.8 1.0
OXT I:ASP204 4.1 41.0 1.0
N I:ASP175 4.2 41.0 1.0
C I:ASP175 4.4 39.2 1.0
OD1 I:ASP175 4.5 44.3 1.0
N I:ASP177 4.5 39.7 1.0
O I:ALA178 4.5 37.6 1.0
O I:ASP175 4.6 36.8 1.0
CA I:GLY181 4.6 34.0 1.0
N I:SER180 4.6 36.5 1.0
N I:GLY181 4.6 32.7 1.0
N I:ALA178 4.6 36.6 1.0
CA I:ALA178 4.6 35.6 1.0
C I:ALA178 4.6 35.4 1.0
CA I:ASP177 4.7 39.8 1.0
CA I:SER180 4.7 36.8 1.0
CA I:ALA174 4.8 40.4 1.0
NH2 Y:ARG19 4.9 45.4 1.0
NH1 Y:ARG19 4.9 43.3 1.0
C I:ASP204 5.0 41.1 1.0
CB I:ALA174 5.0 40.3 1.0

Magnesium binding site 4 out of 8 in 4no1

Go back to Magnesium Binding Sites List in 4no1
Magnesium binding site 4 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:42.5
occ:1.00
 O K:ASP168 2.2 39.7 1.0
O K:ALA165 2.3 35.6 1.0
O W:ASP204 2.4 36.3 1.0
O K:SER171 2.4 39.7 1.0
O K:HOH428 2.5 52.0 1.0
C K:ASP168 3.2 38.5 1.0
C W:ASP204 3.2 36.3 1.0
C K:ALA165 3.4 36.5 1.0
C K:SER171 3.6 39.6 1.0
CA K:ALA169 3.6 39.8 1.0
CA W:ASP204 3.8 37.1 1.0
N K:ALA169 3.8 40.5 1.0
C K:ALA169 3.9 39.3 1.0
NH1 K:ARG19 3.9 46.0 1.0
O K:ALA169 3.9 39.8 1.0
OXT W:ASP204 4.1 35.1 1.0
O K:HIS166 4.1 41.5 1.0
CB W:ASP204 4.1 37.3 1.0
N K:SER171 4.1 40.2 1.0
CA K:ALA165 4.2 37.5 1.0
C K:HIS166 4.3 39.0 1.0
N K:ASP168 4.3 37.4 1.0
CA K:ASP168 4.3 37.1 1.0
CA K:SER171 4.4 38.1 1.0
N K:HIS166 4.4 37.3 1.0
O K:ALA164 4.4 37.9 1.0
CZ K:ARG19 4.5 44.8 1.0
N K:TYR170 4.6 38.9 1.0
CA K:HIS166 4.6 37.8 1.0
N K:GLY172 4.6 39.7 1.0
CA K:GLY172 4.7 38.5 1.0
NH2 K:ARG19 4.8 45.7 1.0
CB K:SER171 4.8 35.9 1.0
C K:ARG167 4.8 38.2 1.0
N K:ARG167 4.9 38.3 1.0

Magnesium binding site 5 out of 8 in 4no1

Go back to Magnesium Binding Sites List in 4no1
Magnesium binding site 5 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:42.0
occ:1.00
 O N:SER169 2.5 31.1 1.0
O N:ILE163 2.6 35.3 1.0
O N:ASP166 2.7 35.2 1.0
NH1 N:ARG19 3.5 40.4 1.0
CD1 a:LEU34 3.5 33.6 1.0
C N:SER169 3.7 32.0 1.0
C N:ILE163 3.7 36.2 1.0
C N:ASP166 3.8 35.3 1.0
CG2 N:ILE163 4.0 36.2 1.0
CA N:GLY167 4.2 35.2 1.0
CZ N:ARG19 4.3 38.9 1.0
O N:GLY167 4.3 34.3 1.0
CA N:ILE163 4.4 36.4 1.0
N N:GLY167 4.4 35.6 1.0
C N:GLY167 4.5 33.7 1.0
CA N:GLY170 4.5 32.0 1.0
N N:GLY170 4.5 31.7 1.0
NH2 N:ARG19 4.6 39.0 1.0
N N:SER169 4.6 32.5 1.0
CA N:SER169 4.7 31.2 1.0
N N:LYS164 4.8 38.1 1.0
CB N:ILE163 4.8 37.5 1.0
CG a:LEU34 4.9 33.3 1.0
O N:LYS164 4.9 43.2 1.0
N N:ASP166 4.9 35.9 1.0
C N:LYS164 4.9 41.2 1.0
CA N:ASP166 4.9 35.7 1.0

Magnesium binding site 6 out of 8 in 4no1

Go back to Magnesium Binding Sites List in 4no1
Magnesium binding site 6 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:48.9
occ:1.00
 O V:ASP166 2.2 35.6 1.0
O V:ILE163 2.2 40.7 1.0
OXT L:ASP222 2.3 45.1 1.0
O V:SER169 2.4 45.0 1.0
C L:ASP222 3.1 47.4 1.0
C V:ASP166 3.2 36.2 1.0
C V:ILE163 3.3 41.5 1.0
C V:SER169 3.5 42.3 1.0
O V:GLY162 3.7 32.4 1.0
CA L:ASP222 3.8 47.1 1.0
O L:ASP222 3.9 51.1 1.0
N V:LEU167 3.9 35.9 1.0
CA V:LEU167 3.9 35.8 1.0
NH1 V:ARG19 4.0 41.3 1.0
N V:ASP166 4.0 41.3 1.0
CA V:ILE163 4.0 42.9 1.0
C V:TRP164 4.1 46.0 1.0
N V:TRP164 4.2 42.8 1.0
O V:TRP164 4.2 48.0 1.0
CA V:ASP166 4.2 37.8 1.0
CB L:ASP222 4.3 46.4 1.0
N V:SER169 4.3 37.5 1.0
CA V:TRP164 4.4 44.7 1.0
C V:LEU167 4.4 36.0 1.0
CA V:SER169 4.4 38.7 1.0
N V:GLY170 4.4 44.5 1.0
CA V:GLY170 4.5 46.8 1.0
N V:ASN165 4.5 45.0 1.0
CZ V:ARG19 4.5 41.8 1.0
O V:LEU167 4.6 37.6 1.0
NH2 V:ARG19 4.7 41.5 1.0
C V:GLY162 4.7 38.7 1.0
C V:ASN165 4.7 42.5 1.0
CB V:SER169 4.7 37.9 1.0
N V:ILE163 4.9 40.9 1.0
CB V:ASP166 5.0 36.8 1.0

Magnesium binding site 7 out of 8 in 4no1

Go back to Magnesium Binding Sites List in 4no1
Magnesium binding site 7 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:42.7
occ:1.00
 O Y:ASP168 2.2 36.9 1.0
O Y:SER171 2.3 41.7 1.0
O Y:ALA165 2.4 32.8 1.0
O I:ASP204 2.4 41.9 1.0
O Y:HOH402 2.5 33.6 1.0
C Y:ASP168 3.2 33.5 1.0
C I:ASP204 3.3 41.1 1.0
C Y:ALA165 3.5 33.0 1.0
C Y:SER171 3.5 38.6 1.0
CA Y:ALA169 3.6 35.0 1.0
C Y:ALA169 3.8 36.6 1.0
NH1 Y:ARG19 3.8 43.3 1.0
N Y:ALA169 3.8 34.1 1.0
CA I:ASP204 3.8 40.9 1.0
O Y:ALA169 3.9 38.5 1.0
N Y:SER171 4.0 37.7 1.0
CB I:ASP204 4.1 41.2 1.0
OXT I:ASP204 4.1 41.0 1.0
O Y:HIS166 4.2 33.0 1.0
CA Y:ALA165 4.2 34.5 1.0
CA Y:SER171 4.3 36.4 1.0
CZ Y:ARG19 4.4 43.5 1.0
CA Y:ASP168 4.4 30.7 1.0
N Y:ASP168 4.4 26.6 1.0
C Y:HIS166 4.4 32.5 1.0
O Y:ALA164 4.5 32.4 1.0
N Y:TYR170 4.5 38.2 1.0
N Y:HIS166 4.5 31.1 1.0
N Y:GLY172 4.5 37.9 1.0
CA Y:GLY172 4.6 36.5 1.0
NH2 Y:ARG19 4.7 45.4 1.0
CA Y:HIS166 4.7 29.9 1.0
CB Y:SER171 4.7 33.7 1.0
C Y:ARG167 4.9 32.4 1.0

Magnesium binding site 8 out of 8 in 4no1

Go back to Magnesium Binding Sites List in 4no1
Magnesium binding site 8 out of 8 in the Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ycp in Complex with Z-Leu-Leu-Leu-B(Oh)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:68.3
occ:1.00
 O Z:VAL198 2.4 38.6 1.0
O Z:THR192 2.7 42.3 1.0
O Z:HIS195 2.9 36.8 1.0
NH2 Z:ARG28 3.6 47.0 1.0
CG2 Z:THR192 3.6 40.9 1.0
C Z:VAL198 3.6 38.4 1.0
C Z:THR192 3.6 43.1 1.0
CA Z:THR192 3.9 44.2 1.0
O Z:ASP222 3.9 53.5 1.0
C Z:HIS195 4.0 35.9 1.0
O Z:ILE196 4.1 41.2 1.0
CA Z:ILE196 4.2 37.2 1.0
C Z:ILE196 4.3 37.2 1.0
OD1 Z:ASP222 4.3 42.0 1.0
CB Z:THR192 4.4 42.5 1.0
N Z:VAL198 4.4 34.9 1.0
NH2 H:ARG19 4.4 48.7 1.0
N Z:GLY199 4.5 38.2 1.0
CA Z:GLY199 4.5 39.5 1.0
CA Z:VAL198 4.5 35.4 1.0
N Z:ILE196 4.6 35.9 1.0
CZ Z:ARG28 4.6 49.6 1.0
C Z:ASP222 4.7 49.5 1.0
NH1 Z:ARG28 4.9 51.3 1.0
N Z:GLU193 4.9 41.9 1.0
O Z:LYS220 4.9 43.5 1.0

Reference:

M.L.Stein, H.Cui, P.Beck, C.Dubiella, C.Voss, A.Kruger, B.Schmidt, M.Groll. Systematic Comparison of Peptidic Proteasome Inhibitors Highlights the Alpha-Ketoamide Electrophile As An Auspicious Reversible Lead Motif. Angew.Chem.Int.Ed.Engl. V. 53 1679 2014.
ISSN: ISSN 1433-7851
PubMed: 24403024
DOI: 10.1002/ANIE.201308984
Page generated: Mon Aug 19 23:44:19 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy