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Magnesium in PDB 4b4z: Crystal Structure of A Complex Between Actinomadura R39 Dd-Peptidase and A Sulfonamide Boronate Inhibitor

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

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

Protein crystallography data

The structure of Crystal Structure of A Complex Between Actinomadura R39 Dd-Peptidase and A Sulfonamide Boronate Inhibitor, PDB code: 4b4z was solved by S.E.Cannella, 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) 35.25 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.123, 90.692, 105.729, 90.00, 94.52, 90.00
R / Rfree (%) 20.631 / 26.035

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Complex Between Actinomadura R39 Dd-Peptidase and A Sulfonamide Boronate Inhibitor (pdb code 4b4z). 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 Sulfonamide Boronate Inhibitor, PDB code: 4b4z:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4b4z

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Magnesium binding site 1 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd-Peptidase and A Sulfonamide Boronate 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 Sulfonamide Boronate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:37.1
occ:1.00
 O A:GLU188 2.1 26.6 1.0
NE2 A:HIS247 2.1 31.3 1.0
OE2 A:GLU251 2.1 37.7 1.0
CD A:GLU251 2.9 37.8 1.0
CE1 A:HIS247 2.9 31.5 1.0
OE1 A:GLU251 3.1 38.8 1.0
CD2 A:HIS247 3.2 30.3 1.0
C A:GLU188 3.2 26.2 1.0
O A:ALA186 3.8 26.0 1.0
ND1 A:HIS247 4.1 30.7 1.0
N A:GLY189 4.1 26.4 1.0
CA A:GLU188 4.2 26.2 1.0
CB A:GLU188 4.2 26.0 1.0
CA A:GLY189 4.2 26.5 1.0
CG A:GLU251 4.3 35.4 1.0
CG A:HIS247 4.3 28.8 1.0
N A:GLU188 4.4 25.8 1.0
O A:HOH2153 4.8 41.1 1.0
C A:ALA186 4.8 25.6 1.0
C A:GLY189 4.8 26.8 1.0
C A:ALA187 4.9 25.7 1.0
N A:TYR190 4.9 26.7 1.0
CD2 A:LEU248 5.0 24.6 1.0

Magnesium binding site 2 out of 4 in 4b4z

Go back to Magnesium Binding Sites List in 4b4z
Magnesium binding site 2 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd-Peptidase and A Sulfonamide Boronate 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 Sulfonamide Boronate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg611

b:54.9
occ:1.00
 O A:GLU404 3.2 35.4 1.0
ND1 A:HIS462 3.9 49.2 1.0
CG2 A:VAL406 3.9 34.6 1.0
O A:GLN463 4.2 46.3 1.0
O A:ALA402 4.3 36.2 1.0
CE1 A:HIS462 4.3 49.1 1.0
C A:GLU404 4.5 35.2 1.0
CD A:PRO465 4.6 47.5 1.0
CB A:VAL406 4.6 33.4 1.0
CG A:HIS462 4.8 47.7 1.0

Magnesium binding site 3 out of 4 in 4b4z

Go back to Magnesium Binding Sites List in 4b4z
Magnesium binding site 3 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd-Peptidase and A Sulfonamide Boronate 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 Sulfonamide Boronate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg610

b:40.7
occ:1.00
 OE2 D:GLU251 2.1 46.2 1.0
O D:GLU188 2.2 31.6 1.0
NE2 D:HIS247 2.3 37.7 1.0
CD D:GLU251 3.1 46.0 1.0
CD2 D:HIS247 3.1 36.0 1.0
CE1 D:HIS247 3.3 37.8 1.0
OE1 D:GLU251 3.3 46.6 1.0
C D:GLU188 3.4 31.4 1.0
O D:ALA186 3.7 32.2 1.0
N D:GLY189 4.3 31.2 1.0
CA D:GLU188 4.3 32.3 1.0
CG D:HIS247 4.3 36.6 1.0
ND1 D:HIS247 4.3 37.4 1.0
CA D:GLY189 4.4 30.6 1.0
N D:GLU188 4.4 31.6 1.0
CG D:GLU251 4.4 45.9 1.0
CB D:GLU188 4.5 33.1 1.0
C D:ALA186 4.7 31.4 1.0
CD2 D:LEU248 4.8 33.9 1.0
C D:GLY189 4.8 30.8 1.0
C D:ALA187 4.9 31.2 1.0

Magnesium binding site 4 out of 4 in 4b4z

Go back to Magnesium Binding Sites List in 4b4z
Magnesium binding site 4 out of 4 in the Crystal Structure of A Complex Between Actinomadura R39 Dd-Peptidase and A Sulfonamide Boronate 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 Sulfonamide Boronate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg611

b:42.1
occ:1.00
 ND1 D:HIS462 2.6 69.2 1.0
CE1 D:HIS462 3.5 69.8 1.0
CG D:HIS462 3.6 69.2 1.0
CG2 D:VAL406 3.6 42.3 1.0
CB D:HIS462 3.8 68.8 1.0
CA D:HIS462 4.5 68.9 1.0
O D:ALA402 4.6 48.1 1.0
NE2 D:HIS462 4.6 69.6 1.0
CD2 D:HIS462 4.7 69.1 1.0
N D:GLN463 4.9 69.7 1.0
O D:GLN463 4.9 70.6 1.0

Reference:

E.Sauvage, S.E.Cannella, E.Sauvage, R.Herman, F.Kerff, M.Rocaboy, P.Charlier. N/A N/A.
Page generated: Mon Dec 14 09:11:00 2020

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