Atomistry » Magnesium » PDB 3zi8-3zwk » 3zvw
Atomistry »
  Magnesium »
    PDB 3zi8-3zwk »
      3zvw »

Magnesium in PDB 3zvw: 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: 3zvw 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) 34.59 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.748, 91.365, 107.332, 90.00, 94.63, 90.00
R / Rfree (%) 17.898 / 22.712

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

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 3zvw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 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: 3zvw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 3zvw

Go back to Magnesium Binding Sites List in 3zvw
Magnesium binding site 1 out of 14 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:52.5
occ:1.00
 O A:GLU188 2.7 21.7 1.0
O A:ALA186 2.7 21.8 1.0
NE2 A:HIS247 2.8 26.8 1.0
OE1 A:GLU251 2.9 34.3 1.0
OE2 A:GLU251 3.1 35.6 1.0
O A:HOH2276 3.3 43.1 1.0
CD A:GLU251 3.4 33.7 1.0
CD2 A:HIS247 3.4 25.8 1.0
C A:ALA186 3.7 21.2 1.0
C A:GLU188 3.7 21.7 1.0
CD2 A:LEU248 3.9 19.0 1.0
CE1 A:HIS247 3.9 26.0 1.0
N A:GLU188 4.0 21.1 1.0
CB A:GLU188 4.2 21.9 1.0
CA A:GLU188 4.2 21.7 1.0
O A:HOH2331 4.3 38.9 1.0
O A:HOH2074 4.3 47.4 1.0
CA A:ALA186 4.4 20.9 1.0
O A:GLY185 4.5 21.4 1.0
C A:ALA187 4.6 21.0 1.0
CG A:HIS247 4.6 24.4 1.0
N A:ALA187 4.6 20.5 1.0
CA A:ALA187 4.8 20.6 1.0
ND1 A:HIS247 4.9 26.6 1.0
CG A:GLU251 4.9 31.1 1.0
N A:GLY189 4.9 22.0 1.0

Magnesium binding site 2 out of 14 in 3zvw

Go back to Magnesium Binding Sites List in 3zvw
Magnesium binding site 2 out of 14 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:37.7
occ:1.00
 O A:HOH2441 2.6 28.5 1.0
O A:ALA402 2.8 28.4 1.0
O A:GLN463 3.0 34.4 1.0
CG2 A:VAL406 3.4 29.3 1.0
ND1 A:HIS462 3.4 34.6 1.0
O A:HOH2468 3.6 28.3 1.0
C A:ALA402 3.6 28.5 1.0
CB A:HIS462 3.7 33.4 1.0
CG A:HIS462 3.7 34.0 1.0
O A:GLU404 3.8 27.2 1.0
N A:GLN463 4.0 35.0 1.0
C A:GLN463 4.0 35.0 1.0
CA A:ALA402 4.0 29.4 1.0
CE1 A:HIS462 4.3 35.3 1.0
CB A:VAL406 4.5 27.6 1.0
CD A:PRO465 4.6 35.8 1.0
CA A:HIS462 4.6 34.8 1.0
CA A:GLN463 4.6 36.1 1.0
C A:HIS462 4.6 34.9 1.0
CB A:ALA402 4.7 29.7 1.0
O A:THR401 4.7 29.9 1.0
N A:ALA403 4.8 28.2 1.0
CD2 A:HIS462 4.8 34.0 1.0
C A:GLU404 4.8 27.3 1.0
N A:ALA464 4.9 35.4 1.0
N A:GLU404 4.9 27.5 1.0

Magnesium binding site 3 out of 14 in 3zvw

Go back to Magnesium Binding Sites List in 3zvw
Magnesium binding site 3 out of 14 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
A:Mg1469

b:37.8
occ:1.00
 O A:HOH2080 3.0 15.9 1.0
CD A:ARG93 3.8 30.3 1.0
N A:GLY70 3.9 15.9 1.0
CA A:GLY70 4.1 15.6 1.0
CB A:ARG93 4.2 21.0 1.0
O A:HOH2023 4.4 22.4 1.0
O A:HOH2073 4.5 18.6 1.0
O A:HOH2118 4.6 35.1 1.0
CG A:ARG93 4.6 23.7 1.0
O A:HOH2076 4.8 38.4 1.0
C A:GLY70 4.8 15.9 1.0
O A:GLY70 4.8 15.3 1.0
C A:PHE69 4.9 15.7 1.0
NE A:ARG93 5.0 34.8 1.0

Magnesium binding site 4 out of 14 in 3zvw

Go back to Magnesium Binding Sites List in 3zvw
Magnesium binding site 4 out of 14 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
B:Mg1467

b:40.8
occ:1.00
 O B:HOH2481 3.1 64.0 1.0
N B:VAL214 3.7 22.6 1.0
CG1 B:VAL214 3.7 22.8 1.0
CA B:PRO213 4.1 22.7 1.0
O B:HOH2323 4.1 25.6 1.0
O B:HOH2321 4.2 20.9 1.0
O B:HOH2226 4.3 33.7 1.0
CB B:VAL214 4.3 22.6 1.0
CB B:PRO213 4.4 23.3 1.0
C B:PRO213 4.4 22.4 1.0
CA B:VAL214 4.6 22.9 1.0
OD2 B:ASP211 5.0 26.3 1.0

Magnesium binding site 5 out of 14 in 3zvw

Go back to Magnesium Binding Sites List in 3zvw
Magnesium binding site 5 out of 14 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 5 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
B:Mg3001

b:48.5
occ:1.00
 O B:HOH2058 3.5 35.4 1.0
N B:ASP40 3.5 32.2 1.0
CA B:ASP40 4.3 31.5 1.0
O B:HOH2062 4.3 32.7 1.0
CA B:ARG39 4.3 34.0 1.0
O B:SER38 4.4 36.7 1.0
C B:ARG39 4.5 32.8 1.0
OD1 B:ASP40 4.8 32.8 1.0
O B:HOH2061 4.9 44.8 1.0

Magnesium binding site 6 out of 14 in 3zvw

Go back to Magnesium Binding Sites List in 3zvw
Magnesium binding site 6 out of 14 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 6 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
B:Mg3002

b:38.0
occ:1.00
 O B:HOH2464 3.7 49.9 1.0
N D:ARG1 3.8 51.6 1.0
CD2 B:TYR459 4.0 40.0 1.0
NH2 B:ARG455 4.1 35.5 1.0
N D:LEU2 4.1 49.1 1.0
NH1 B:ARG455 4.2 31.9 1.0
CB D:LEU2 4.2 48.2 1.0
CA B:TYR459 4.5 39.2 1.0
N B:ARG1 4.5 0.3 1.0
CE2 B:TYR459 4.6 42.2 1.0
CZ B:ARG455 4.6 34.2 1.0
O B:HOH2001 4.6 79.8 1.0
O B:HOH2467 4.7 48.5 1.0
CG B:TYR459 4.7 39.6 1.0
CA D:LEU2 4.8 48.0 1.0
CB B:TYR459 4.9 38.5 1.0
CA D:ARG1 5.0 50.9 1.0

Magnesium binding site 7 out of 14 in 3zvw

Go back to Magnesium Binding Sites List in 3zvw
Magnesium binding site 7 out of 14 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 7 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
C:Mg1467

b:54.7
occ:1.00
 NH2 C:ARG455 3.7 32.6 1.0
CD1 C:TYR459 3.7 30.4 1.0
NH1 C:ARG455 3.9 29.0 1.0
O C:HOH2001 3.9 96.7 1.0
CZ C:ARG455 4.2 30.9 1.0
CE1 C:TYR459 4.2 32.4 1.0
O C:HOH2512 4.3 41.7 1.0
OE1 C:GLU4 4.4 67.2 1.0
O C:HOH2515 4.4 42.5 1.0
CA C:TYR459 4.5 28.6 1.0
O C:ARG1 4.7 60.0 1.0
CG C:TYR459 4.7 29.8 1.0
CB C:TYR459 4.9 28.4 1.0

Magnesium binding site 8 out of 14 in 3zvw

Go back to Magnesium Binding Sites List in 3zvw
Magnesium binding site 8 out of 14 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 8 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
C:Mg1468

b:40.7
occ:1.00
 N C:VAL214 3.3 23.9 1.0
O C:HOH2341 3.5 22.2 1.0
CA C:PRO213 3.8 22.7 1.0
CG1 C:VAL214 3.9 26.3 1.0
O C:HOH2076 4.0 31.9 1.0
C C:PRO213 4.0 23.4 1.0
O C:HOH2079 4.0 43.4 1.0
CB C:VAL214 4.1 24.6 1.0
O C:HOH2347 4.1 25.5 1.0
O C:HOH2342 4.2 43.4 1.0
CB C:PRO213 4.2 23.0 1.0
CA C:VAL214 4.3 24.4 1.0
OD2 C:ASP211 4.5 28.1 1.0
O C:HOH2236 4.8 24.5 1.0
N C:PRO213 5.0 21.9 1.0

Magnesium binding site 9 out of 14 in 3zvw

Go back to Magnesium Binding Sites List in 3zvw
Magnesium binding site 9 out of 14 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 9 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
C:Mg1469

b:38.7
occ:1.00
 OE1 C:GLN312 2.9 21.5 1.0
CA C:GLY316 3.7 23.6 1.0
O C:HOH2188 3.8 47.8 1.0
O C:HOH2417 3.9 39.5 1.0
CD C:GLN312 4.0 21.8 1.0
CZ3 C:TRP128 4.2 23.8 1.0
CH2 C:TRP128 4.3 21.7 1.0
O C:GLN312 4.3 20.2 1.0
C C:GLY316 4.3 23.1 1.0
O C:GLY316 4.4 22.6 1.0
NE2 C:GLN312 4.5 19.8 1.0
O C:HOH2064 4.6 42.7 1.0
N C:GLY316 4.9 24.4 1.0

Magnesium binding site 10 out of 14 in 3zvw

Go back to Magnesium Binding Sites List in 3zvw
Magnesium binding site 10 out of 14 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 10 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
C:Mg3001

b:38.0
occ:1.00
 O C:HOH2055 3.6 26.0 1.0
N C:ASP40 3.6 24.5 1.0
CA C:ASP40 4.3 24.4 1.0
O C:HOH2058 4.4 21.2 1.0
CA C:ARG39 4.6 25.7 1.0
C C:ARG39 4.6 24.9 1.0
OD1 C:ASP40 4.7 26.8 1.0
O C:SER38 4.8 26.1 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: Thu Aug 15 14:06:49 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