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Magnesium in PDB 4b4x: 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: 4b4x 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) 35.13 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.332, 92.113, 105.957, 90.00, 95.90, 90.00
R / Rfree (%) 21.736 / 26.849

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 4b4x). 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: 4b4x:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4b4x

Go back to Magnesium Binding Sites List in 4b4x
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:Mg1471

b:33.9
occ:1.00
 OE2 A:GLU251 1.6 58.9 1.0
O A:GLU188 2.1 56.8 1.0
NE2 A:HIS247 2.1 65.4 1.0
CD A:GLU251 2.7 61.1 1.0
CE1 A:HIS247 3.0 65.7 1.0
CD2 A:HIS247 3.1 64.6 1.0
C A:GLU188 3.3 56.8 1.0
OE1 A:GLU251 3.3 60.3 1.0
O A:ALA186 3.6 54.4 1.0
CG A:GLU251 4.0 61.1 1.0
CB A:GLU188 4.1 56.0 1.0
CA A:GLU188 4.1 56.4 1.0
ND1 A:HIS247 4.2 64.7 1.0
N A:GLY189 4.2 57.4 1.0
CG A:HIS247 4.2 63.3 1.0
N A:GLU188 4.3 56.2 1.0
CA A:GLY189 4.4 58.3 1.0
C A:ALA186 4.7 54.3 1.0
C A:ALA187 4.9 55.6 1.0
C A:GLY189 4.9 59.0 1.0
N A:TYR190 5.0 59.6 1.0

Magnesium binding site 2 out of 4 in 4b4x

Go back to Magnesium Binding Sites List in 4b4x
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:Mg1472

b:36.7
occ:1.00
 ND1 A:HIS462 2.2 73.0 1.0
CE1 A:HIS462 2.7 73.7 1.0
CG A:HIS462 3.3 72.7 1.0
CG2 A:VAL406 3.5 52.5 1.0
NE2 A:HIS462 3.8 73.5 1.0
CB A:HIS462 4.0 71.6 1.0
CD2 A:HIS462 4.1 73.1 1.0
O A:GLN463 4.5 72.2 1.0
CA A:HIS462 4.8 71.6 1.0
O A:GLU404 4.8 52.2 1.0
O A:ALA402 4.8 51.5 1.0
N A:GLN463 4.9 72.3 1.0

Magnesium binding site 3 out of 4 in 4b4x

Go back to Magnesium Binding Sites List in 4b4x
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:Mg1471

b:10.7
occ:1.00
 OE2 D:GLU251 1.9 37.9 1.0
O D:GLU188 2.2 37.7 1.0
NE2 D:HIS247 2.2 42.5 1.0
CD D:GLU251 2.8 38.2 1.0
OE1 D:GLU251 3.1 39.3 1.0
CD2 D:HIS247 3.1 43.0 1.0
CE1 D:HIS247 3.2 42.4 1.0
C D:GLU188 3.4 37.3 1.0
O D:ALA186 4.1 33.6 1.0
CA D:GLY189 4.2 37.8 1.0
N D:GLY189 4.2 37.5 1.0
CG D:GLU251 4.2 37.1 1.0
CG D:HIS247 4.3 40.6 1.0
ND1 D:HIS247 4.3 41.6 1.0
CA D:GLU188 4.4 36.6 1.0
CB D:GLU188 4.6 36.5 1.0
N D:GLU188 4.7 35.0 1.0
C D:GLY189 4.8 38.0 1.0

Magnesium binding site 4 out of 4 in 4b4x

Go back to Magnesium Binding Sites List in 4b4x
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:Mg1472

b:2.0
occ:1.00
 ND1 D:HIS462 2.2 40.9 1.0
CG D:HIS462 3.1 43.0 1.0
CE1 D:HIS462 3.2 42.8 1.0
CB D:HIS462 3.4 43.5 1.0
CG2 D:VAL406 3.9 28.4 1.0
CA D:HIS462 4.2 44.0 1.0
NE2 D:HIS462 4.3 39.9 1.0
O D:ALA402 4.3 32.7 1.0
CD2 D:HIS462 4.3 40.9 1.0
N D:GLN463 4.7 44.1 1.0
O D:GLN463 4.7 44.2 1.0
C D:HIS462 4.9 44.0 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 Aug 11 06:47:36 2025

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