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Magnesium in PDB 3zcz: Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor

Enzymatic activity of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor

All present enzymatic activity of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor:
3.4.16.4;

Protein crystallography data

The structure of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor, PDB code: 3zcz was solved by E.Sauvage, R.Herman, F.Kerff, M.Rocaboy, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.9 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.653, 91.727, 106.882, 90.00, 94.30, 90.00
R / Rfree (%) 19.3 / 23.7

Other elements in 3zcz:

The structure of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor also contains other interesting chemical elements:

Fluorine (F) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor (pdb code 3zcz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor, PDB code: 3zcz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3zcz

Go back to Magnesium Binding Sites List in 3zcz
Magnesium binding site 1 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:35.6
occ:1.00
 O A:GLU188 2.0 48.9 1.0
NE2 A:HIS247 2.1 48.8 1.0
OE2 A:GLU251 2.1 55.7 1.0
CE1 A:HIS247 2.9 48.7 1.0
CD A:GLU251 3.0 55.4 1.0
CD2 A:HIS247 3.2 47.5 1.0
C A:GLU188 3.2 49.1 1.0
OE1 A:GLU251 3.4 56.0 1.0
ND1 A:HIS247 4.1 48.6 1.0
O A:ALA186 4.1 48.0 1.0
N A:GLY189 4.1 49.2 1.0
CA A:GLU188 4.1 48.9 1.0
CB A:GLU188 4.2 49.2 1.0
CA A:GLY189 4.2 49.5 1.0
CG A:HIS247 4.2 47.0 1.0
CG A:GLU251 4.3 54.8 1.0
N A:GLU188 4.4 48.3 1.0
C A:GLY189 4.5 49.1 1.0
N A:TYR190 4.8 48.6 1.0
C A:ALA187 5.0 48.1 1.0

Magnesium binding site 2 out of 4 in 3zcz

Go back to Magnesium Binding Sites List in 3zcz
Magnesium binding site 2 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg611

b:56.4
occ:1.00
 OE2 A:GLU168 2.6 50.3 1.0
NE2 A:HIS158 2.9 43.0 1.0
O3 A:SO4604 3.3 96.0 1.0
CD A:GLU168 3.4 48.1 1.0
OE1 A:GLU168 3.6 49.4 1.0
CE1 A:HIS158 3.6 42.4 1.0
CD2 A:HIS158 4.0 42.0 1.0
S A:SO4604 4.6 96.2 1.0
CG A:GLU168 4.7 44.5 1.0
ND1 A:HIS158 4.8 41.6 1.0

Magnesium binding site 3 out of 4 in 3zcz

Go back to Magnesium Binding Sites List in 3zcz
Magnesium binding site 3 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg610

b:39.7
occ:1.00
 O D:HOH2051 2.0 48.0 1.0
O D:GLU188 2.1 61.6 1.0
OE2 D:GLU251 2.1 69.9 1.0
NE2 D:HIS247 2.3 62.7 1.0
CD D:GLU251 3.0 70.5 1.0
CE1 D:HIS247 3.3 64.0 1.0
C D:GLU188 3.3 61.5 1.0
CD2 D:HIS247 3.3 62.3 1.0
OE1 D:GLU251 3.4 69.9 1.0
CA D:GLY189 4.1 61.8 1.0
O D:ALA186 4.1 61.5 1.0
N D:GLY189 4.1 61.4 1.0
CA D:GLU188 4.3 61.5 1.0
ND1 D:HIS247 4.4 63.5 1.0
CG D:GLU251 4.4 71.3 1.0
CG D:HIS247 4.4 62.1 1.0
C D:GLY189 4.5 61.3 1.0
N D:GLU188 4.5 60.9 1.0
CB D:GLU188 4.5 62.5 1.0
N D:TYR190 4.9 60.4 1.0
O D:GLY189 4.9 61.8 1.0
C D:ALA187 4.9 60.3 1.0

Magnesium binding site 4 out of 4 in 3zcz

Go back to Magnesium Binding Sites List in 3zcz
Magnesium binding site 4 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Complex Between Actinomadura R39 Dd- Peptidase and A Trifluoroketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg611

b:63.0
occ:1.00
 ND1 D:HIS462 2.9 1.0 1.0
CG2 D:VAL406 3.5 78.8 1.0
CE1 D:HIS462 3.8 0.0 1.0
CG D:HIS462 3.9 1.0 1.0
CB D:HIS462 4.1 0.4 1.0
O D:ALA402 4.7 83.2 1.0
CA D:HIS462 4.8 0.8 1.0
NE2 D:HIS462 4.9 0.6 1.0
CD2 D:HIS462 5.0 0.4 1.0

Reference:

L.Dzhekieva, S.A.Adediran, R.Herman, F.Kerff, C.Duez, P.Charlier, E.Sauvage, R.F.Pratt. Inhibition of Dd-Peptidases By A Specific Trifluoroketone: Crystal Structure of A Complex with the Actinomadura R39 Dd-Peptidase. Biochemistry V. 52 2128 2013.
ISSN: ISSN 0006-2960
PubMed: 23484909
DOI: 10.1021/BI400048S
Page generated: Mon Aug 11 05:11:07 2025

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