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Fluorine in PDB 6zgm: Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681

Protein crystallography data

The structure of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681, PDB code: 6zgm was solved by J.D.Docquier, C.Pozzi, F.Marcoccia, F.De Luca, M.Benvenuti, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.75 / 1.65
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 67.960, 78.178, 79.659, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.5

Other elements in 6zgm:

The structure of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681 also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681 (pdb code 6zgm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681, PDB code: 6zgm:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6zgm

Go back to Fluorine Binding Sites List in 6zgm
Fluorine binding site 1 out of 2 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:55.3
occ:0.70
F A:QKK406 0.0 55.3 0.7
C3 A:QKK406 1.3 51.5 0.7
C4 A:QKK406 2.4 43.9 0.7
C2 A:QKK406 2.5 53.9 0.7
N3 A:QKK406 2.9 58.0 0.7
CZ A:PHE61 3.4 57.3 0.7
CE1 A:PHE61 3.6 55.0 0.7
C5 A:QKK406 3.7 42.9 0.7
C7 A:QKK406 3.8 48.8 0.7
C1 A:QKK406 4.1 58.7 0.7
CE2 A:PHE61 4.1 59.6 0.7
C6 A:QKK406 4.2 46.4 0.7
CG A:ASN233 4.5 43.7 1.0
CD1 A:PHE61 4.5 56.2 0.7
ND2 A:ASN233 4.5 45.3 1.0
CB A:ASN233 4.6 38.2 1.0
O A:QKK406 4.7 62.1 0.7
OD1 A:ASN233 4.9 45.1 1.0
CD2 A:PHE61 4.9 55.8 0.7
S1 A:QKK406 4.9 31.9 0.7
N2 A:QKK406 5.0 56.5 0.7
F1 A:QKK406 5.0 51.3 0.7

Fluorine binding site 2 out of 2 in 6zgm

Go back to Fluorine Binding Sites List in 6zgm
Fluorine binding site 2 out of 2 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:51.3
occ:0.70
F1 A:QKK406 0.0 51.3 0.7
C7 A:QKK406 1.3 48.8 0.7
N2 A:QKK406 2.1 56.5 0.7
C6 A:QKK406 2.3 46.4 0.7
C2 A:QKK406 2.5 53.9 0.7
N6 A:QKK406 2.8 49.0 0.7
C1 A:QKK406 2.9 58.7 0.7
N3 A:QKK406 3.0 58.0 0.7
N1 A:QKK406 3.1 55.3 0.7
C A:QKK406 3.3 50.0 0.7
C5 A:QKK406 3.6 42.9 0.7
CA A:ASN233 3.6 35.4 1.0
C3 A:QKK406 3.8 51.5 0.7
O A:GLY232 3.9 40.0 1.0
N A:ASN233 4.0 34.0 1.0
O A:QKK406 4.1 62.1 0.7
C A:GLY232 4.2 38.6 1.0
C4 A:QKK406 4.2 43.9 0.7
CB A:ASN233 4.2 38.2 1.0
OD1 A:ASN233 4.4 45.1 1.0
N A:QKK406 4.6 62.4 0.7
O1 A:QKK406 4.7 39.2 0.7
CG A:ASN233 4.7 43.7 1.0
S A:QKK406 4.8 42.1 0.7
C A:ASN233 4.8 34.4 1.0
N A:VAL234 4.9 30.6 1.0
F A:QKK406 5.0 55.3 0.7

Reference:

D.T.Davies, S.Leiris, N.Sprynski, J.Castandet, C.Lozano, J.Bousquet, M.Zalacain, S.Vasa, P.K.Dasari, R.Pattipati, N.Vempala, S.Gujjewar, S.Godi, R.Jallala, R.R.Sathyap, N.A.Darshanoju, V.R.Ravu, R.R.Juventhala, N.Pottabathini, S.Sharma, S.Pothukanuri, K.Holden, P.Warn, F.Marcoccia, M.Benvenuti, C.Pozzi, S.Mangani, J.D.Docquier, M.Lemonnier, M.Everett. ANT2681: Sar Studies Leading to the Identification of A Metallo-Beta-Lactamase Inhibitor with Potential For Clinical Use in Combination with Meropenem For the Treatment of Infections Caused By Ndm-Producingenterobacteriaceae. Acs Infect Dis. V. 6 2419 2020.
ISSN: ESSN 2373-8227
PubMed: 32786279
DOI: 10.1021/ACSINFECDIS.0C00207
Page generated: Fri Aug 2 05:13:18 2024

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