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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Dec 14 09:04:41 2020

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