Atomistry » Magnesium » PDB 3zia-3zx4 » 3zvt
Atomistry »
  Magnesium »
    PDB 3zia-3zx4 »
      3zvt »

Magnesium in PDB 3zvt: Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein

Enzymatic activity of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein

All present enzymatic activity of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein:
3.4.16.4;

Protein crystallography data

The structure of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein, PDB code: 3zvt was solved by E.Sauvage, A.Zervosen, 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) 35.83 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.993, 92.227, 107.044, 90.00, 94.43, 90.00
R / Rfree (%) 20.284 / 25.41

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein (pdb code 3zvt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein, PDB code: 3zvt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3zvt

Go back to Magnesium Binding Sites List in 3zvt
Magnesium binding site 1 out of 4 in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:60.5
occ:1.00
 O A:GLU188 2.2 53.9 1.0
OE2 A:GLU251 2.4 61.9 1.0
NE2 A:HIS247 2.5 54.3 1.0
OE1 A:GLU251 2.8 61.6 1.0
CD A:GLU251 2.9 61.6 1.0
O A:ALA186 3.1 53.1 1.0
C A:GLU188 3.2 53.3 1.0
CD2 A:HIS247 3.4 53.9 1.0
CE1 A:HIS247 3.5 55.0 1.0
CB A:GLU188 3.6 52.4 1.0
N A:GLU188 3.6 52.1 1.0
CA A:GLU188 3.6 52.3 1.0
C A:ALA186 4.2 52.7 1.0
C A:ALA187 4.4 52.2 1.0
N A:GLY189 4.4 53.6 1.0
CG A:GLU251 4.4 60.5 1.0
CD2 A:LEU248 4.6 51.7 1.0
CG A:HIS247 4.6 54.5 1.0
ND1 A:HIS247 4.6 55.6 1.0
O A:GLY185 4.8 53.3 1.0
N A:TYR190 4.9 54.6 1.0
CA A:GLY189 4.9 54.6 1.0
CA A:ALA187 5.0 52.2 1.0
N A:ALA187 5.0 52.2 1.0

Magnesium binding site 2 out of 4 in 3zvt

Go back to Magnesium Binding Sites List in 3zvt
Magnesium binding site 2 out of 4 in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg611

b:64.3
occ:1.00
 ND1 A:HIS462 3.0 82.4 1.0
CG2 A:VAL406 3.1 57.9 1.0
CE1 A:HIS462 3.7 83.1 1.0
O A:GLU404 3.8 56.3 1.0
O A:ALA402 3.9 56.1 1.0
CG A:HIS462 4.0 82.2 1.0
O A:GLN463 4.0 85.2 1.0
CB A:HIS462 4.3 81.9 1.0
CB A:VAL406 4.6 56.9 1.0
N A:GLN463 4.8 84.9 1.0
NE2 A:HIS462 4.8 82.8 1.0
C A:ALA402 4.9 56.1 1.0
CD2 A:HIS462 5.0 81.7 1.0
C A:GLU404 5.0 55.8 1.0

Magnesium binding site 3 out of 4 in 3zvt

Go back to Magnesium Binding Sites List in 3zvt
Magnesium binding site 3 out of 4 in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg610

b:69.1
occ:1.00
 O D:GLU188 1.9 68.1 1.0
OE2 D:GLU251 2.0 82.0 1.0
NE2 D:HIS247 2.6 77.2 1.0
CD D:GLU251 3.1 82.4 1.0
C D:GLU188 3.1 66.6 1.0
CD2 D:HIS247 3.6 75.1 1.0
OE1 D:GLU251 3.6 81.7 1.0
CE1 D:HIS247 3.6 77.0 1.0
N D:GLU188 3.9 64.3 1.0
CA D:GLU188 3.9 65.1 1.0
CB D:GLU188 4.1 66.1 1.0
N D:GLY189 4.2 66.3 1.0
CG D:GLU251 4.3 83.6 1.0
CA D:GLY189 4.4 67.8 1.0
C D:ALA187 4.6 63.1 1.0
N D:TYR190 4.7 65.7 1.0
C D:GLY189 4.7 67.2 1.0
CG D:HIS247 4.7 73.6 1.0
ND1 D:HIS247 4.7 75.5 1.0
CG D:GLU188 4.9 66.7 1.0

Magnesium binding site 4 out of 4 in 3zvt

Go back to Magnesium Binding Sites List in 3zvt
Magnesium binding site 4 out of 4 in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg611

b:35.9
occ:1.00
 ND1 D:HIS462 2.4 78.9 1.0
CE1 D:HIS462 3.1 79.1 1.0
CG D:HIS462 3.4 79.0 1.0
CG2 D:VAL406 3.7 65.8 1.0
CB D:HIS462 3.9 79.1 1.0
O D:ALA402 4.1 64.0 1.0
NE2 D:HIS462 4.2 79.2 1.0
CD2 D:HIS462 4.4 79.0 1.0
CA D:HIS462 4.6 80.7 1.0
O D:GLN463 4.8 80.4 1.0
N D:GLN463 4.8 80.7 1.0
O D:GLU404 4.9 64.9 1.0

Reference:

A.Zervosen, R.Herman, F.Kerff, A.Herman, A.Bouillez, F.Prati, R.F.Pratt, J.M.Frere, B.Joris, A.Luxen, P.Charlier, E.Sauvage. Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin- Binding Protein. J.Am.Chem.Soc. V. 133 10839 2011.
ISSN: ISSN 0002-7863
PubMed: 21574608
DOI: 10.1021/JA200696Y
Page generated: Mon Aug 11 05:22:29 2025

Last articles

Mg in 5D9B
Mg in 5D8N
Mg in 5D92
Mg in 5D91
Mg in 5D8G
Mg in 5D7R
Mg in 5D87
Mg in 5D5L
Mg in 5D86
Mg in 5D7D
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy