Atomistry » Fluorine » PDB 6e69-6elo » 6ee6
Atomistry »
  Fluorine »
    PDB 6e69-6elo »
      6ee6 »

Fluorine in PDB 6ee6: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion

Protein crystallography data

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion, PDB code: 6ee6 was solved by N.Drinkwater, S.Mcgowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.78 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.550, 108.610, 117.790, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 18.8

Other elements in 6ee6:

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion (pdb code 6ee6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion, PDB code: 6ee6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6ee6

Go back to Fluorine Binding Sites List in 6ee6
Fluorine binding site 1 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:12.6
occ:1.00
FAD A:J4P1102 0.0 12.6 1.0
CAV A:J4P1102 1.4 9.2 1.0
CBA A:J4P1102 2.4 11.9 1.0
CAK A:J4P1102 2.5 9.5 1.0
FAF A:J4P1102 2.7 14.3 1.0
CG A:GLN317 3.3 10.1 1.0
CG2 A:THR305 3.4 11.5 1.0
O A:HOH2235 3.5 12.1 1.0
ND2 A:ASN458 3.5 12.1 1.0
CAW A:J4P1102 3.7 10.5 1.0
SD A:MET1034 3.7 14.1 1.0
CAY A:J4P1102 3.7 10.9 1.0
O A:HOH1695 3.9 13.9 1.0
O A:GLU319 4.0 10.5 1.0
O A:LEU304 4.1 11.4 1.0
CD A:GLN317 4.2 9.3 1.0
CAL A:J4P1102 4.2 11.3 1.0
NE2 A:GLN317 4.2 9.1 1.0
CB A:ASN458 4.2 9.7 1.0
CG A:ASN458 4.4 8.9 1.0
CE A:MET1034 4.4 14.9 1.0
O A:HOH1693 4.4 11.0 1.0
CB A:GLN317 4.5 10.2 1.0
CB A:THR305 4.6 10.6 1.0
FAE A:J4P1102 4.7 14.1 1.0
CAX A:J4P1102 4.8 11.9 1.0
CA A:THR305 4.9 10.0 1.0

Fluorine binding site 2 out of 3 in 6ee6

Go back to Fluorine Binding Sites List in 6ee6
Fluorine binding site 2 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:14.1
occ:1.00
FAE A:J4P1102 0.0 14.1 1.0
CAW A:J4P1102 1.3 10.5 1.0
CBA A:J4P1102 2.3 11.9 1.0
CAL A:J4P1102 2.3 11.3 1.0
FAF A:J4P1102 2.7 14.3 1.0
O A:HOH1848 3.2 12.5 1.0
N A:ALA320 3.4 9.5 1.0
CA A:GLU572 3.5 16.6 1.0
CAV A:J4P1102 3.6 9.2 1.0
CAY A:J4P1102 3.6 10.9 1.0
CG A:GLU572 3.6 18.6 1.0
O A:MET571 3.7 17.7 1.0
CE2 A:TYR575 3.7 9.9 1.0
O A:GLU319 3.8 10.5 1.0
N A:GLU572 3.9 16.0 1.0
C A:GLU319 4.0 8.6 1.0
C A:MET571 4.0 13.3 1.0
CB A:GLU572 4.0 15.8 1.0
CAK A:J4P1102 4.0 9.5 1.0
CD2 A:TYR575 4.1 11.8 1.0
CB A:ALA320 4.2 11.6 1.0
CE A:MET1034 4.4 14.9 1.0
CA A:ALA320 4.4 10.3 1.0
CZ A:TYR575 4.4 9.1 1.0
C A:GLU572 4.5 20.5 1.0
FAD A:J4P1102 4.7 12.6 1.0
O A:GLU572 4.7 22.4 1.0
SD A:MET1034 4.7 14.1 1.0
O A:HOH1613 4.7 13.9 1.0
OH A:TYR575 4.8 11.0 1.0
CB A:MET571 4.8 16.7 1.0
CAX A:J4P1102 4.8 11.9 1.0
CD A:GLU572 4.8 22.9 1.0

Fluorine binding site 3 out of 3 in 6ee6

Go back to Fluorine Binding Sites List in 6ee6
Fluorine binding site 3 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:14.3
occ:1.00
FAF A:J4P1102 0.0 14.3 1.0
CBA A:J4P1102 1.4 11.9 1.0
CAW A:J4P1102 2.4 10.5 1.0
CAV A:J4P1102 2.4 9.2 1.0
FAE A:J4P1102 2.7 14.1 1.0
FAD A:J4P1102 2.7 12.6 1.0
O A:HOH1613 3.2 13.9 1.0
CG A:GLU572 3.2 18.6 1.0
O A:HOH1695 3.4 13.9 1.0
OE2 A:GLU572 3.4 19.0 1.0
CG2 A:THR305 3.5 11.5 1.0
O A:GLU319 3.5 10.5 1.0
O A:HOH1848 3.6 12.5 1.0
CD A:GLU572 3.6 22.9 1.0
CAK A:J4P1102 3.6 9.5 1.0
CAL A:J4P1102 3.7 11.3 1.0
SD A:MET1034 3.7 14.1 1.0
CAY A:J4P1102 4.2 10.9 1.0
CB A:GLU572 4.2 15.8 1.0
CE A:MET1034 4.4 14.9 1.0
N A:ALA320 4.4 9.5 1.0
C A:GLU319 4.4 8.6 1.0
CB A:THR305 4.6 10.6 1.0
OE1 A:GLU572 4.6 18.7 1.0
CA A:GLU572 4.6 16.6 1.0

Reference:

N.B.Vinh, N.Drinkwater, T.R.Malcolm, M.Kassiou, L.Lucantoni, P.M.Grin, G.S.Butler, S.Duffy, C.M.Overall, V.M.Avery, P.J.Scammells, S.Mcgowan. Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J. Med. Chem. V. 62 622 2019.
ISSN: ISSN 1520-4804
PubMed: 30537832
DOI: 10.1021/ACS.JMEDCHEM.8B01310
Page generated: Thu Aug 1 19:31:41 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy