Fluorine in PDB 1xud: Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor

The structure of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor, PDB code: 1xud was solved by C.K.Engel, K.U.Wendt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.022, 36.475, 95.060, 90.00, 130.41, 90.00
R / Rfree (%)	16.8 / 20.3

The structure of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Zinc	(Zn)	4 atoms

The binding sites of Fluorine atom in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor (pdb code 1xud). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor, PDB code: 1xud:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:8.7 occ:1.00 F1 A:PB42001 0.0 8.7 1.0 C21 A:PB42001 1.5 6.6 1.0 C20 A:PB42001 2.5 6.3 1.0 C4 A:PB42001 2.6 7.5 1.0 C7 A:PB42001 3.0 8.1 1.0 CG1 A:VAL219 3.3 5.3 1.0 CA A:VAL219 3.4 5.0 1.0 CG2 A:VAL219 3.4 5.0 1.0 CB A:VAL219 3.6 5.0 1.0 CD1 A:LEU185 3.7 11.3 1.0 C19 A:PB42001 3.8 5.3 1.0 CB A:HIS222 3.9 5.3 1.0 C22 A:PB42001 3.9 7.2 1.0 CG A:HIS222 3.9 6.9 1.0 CD2 A:HIS222 4.0 9.2 1.0 O A:VAL219 4.0 5.0 1.0 C A:VAL219 4.2 5.4 1.0 OE2 A:GLU223 4.3 11.2 1.0 CD1 A:TYR244 4.4 8.8 1.0 C11 A:PB42001 4.4 5.0 1.0 N A:VAL219 4.5 6.4 1.0 ND1 A:HIS222 4.6 6.8 1.0 NE2 A:HIS222 4.7 8.2 1.0 CG A:LEU185 4.8 12.0 1.0 O A:LEU218 4.8 5.0 1.0 C A:LEU218 5.0 5.0 1.0

Fluorine binding site 2 out of 4 in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:22.6 occ:1.00 F2 A:PB42001 0.0 22.6 1.0 C16 A:PB42001 1.4 22.3 1.0 C17 A:PB42001 2.5 21.4 1.0 C6 A:PB42001 2.5 22.6 1.0 C8 A:PB42001 2.9 25.4 1.0 O A:HOH2004 3.5 31.2 1.0 CD2 A:PHE217 3.5 10.5 1.0 O A:HOH2003 3.5 33.7 1.0 C18 A:PB42001 3.8 20.4 1.0 NZ A:LYS140 3.8 24.5 1.0 ND2 A:ASN215 3.8 10.8 1.0 C15 A:PB42001 3.8 22.3 1.0 OD1 A:ASN215 3.9 10.0 1.0 CE2 A:PHE217 4.0 12.0 1.0 CG A:ASN215 4.2 9.6 1.0 C14 A:PB42001 4.3 19.7 1.0 O A:HOH2002 4.4 36.1 1.0 CG A:PHE217 4.4 9.1 1.0 CB A:PHE217 4.8 7.7 1.0 CE A:LYS140 5.0 21.6 1.0

Fluorine binding site 3 out of 4 in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F3001 b:16.0 occ:1.00 F1 B:PB43001 0.0 16.0 1.0 C21 B:PB43001 1.5 15.2 1.0 C20 B:PB43001 2.5 14.2 1.0 C4 B:PB43001 2.6 14.8 1.0 C7 B:PB43001 3.0 15.9 1.0 CG1 B:VAL219 3.4 9.1 1.0 CA B:VAL219 3.5 8.7 1.0 CG2 B:VAL219 3.6 9.6 1.0 CB B:VAL219 3.7 9.4 1.0 C19 B:PB43001 3.8 14.1 1.0 CD2 B:HIS222 3.9 11.3 1.0 C22 B:PB43001 3.9 14.8 1.0 CG B:HIS222 3.9 11.0 1.0 CB B:HIS222 4.0 9.8 1.0 O B:VAL219 4.1 8.9 1.0 OE2 B:GLU223 4.2 16.9 1.0 C B:VAL219 4.3 9.2 1.0 C11 B:PB43001 4.4 14.3 1.0 CD1 B:TYR244 4.5 15.5 1.0 CD1 B:LEU185 4.5 16.4 1.0 N B:VAL219 4.6 8.8 1.0 NE2 B:HIS222 4.6 11.3 1.0 ND1 B:HIS222 4.7 9.4 1.0 O B:LEU218 4.9 9.6 1.0

Fluorine binding site 4 out of 4 in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F3001 b:23.6 occ:1.00 F2 B:PB43001 0.0 23.6 1.0 C16 B:PB43001 1.4 21.7 1.0 C17 B:PB43001 2.5 20.7 1.0 C6 B:PB43001 2.5 21.9 1.0 C8 B:PB43001 2.9 23.3 1.0 O B:HOH3204 3.1 33.4 1.0 CD2 B:PHE217 3.2 11.7 1.0 ND2 B:ASN215 3.5 11.0 1.0 O B:HOH3002 3.6 35.4 1.0 OD1 B:ASN215 3.7 11.3 1.0 C18 B:PB43001 3.8 20.7 1.0 O B:HOH3192 3.8 27.3 1.0 C15 B:PB43001 3.8 21.2 1.0 CE2 B:PHE217 3.8 13.9 1.0 CG B:ASN215 3.9 10.3 1.0 CG B:PHE217 4.1 11.9 1.0 C14 B:PB43001 4.3 20.1 1.0 CB B:PHE217 4.4 10.5 1.0 CE B:LYS140 4.4 25.6 1.0

C.K.Engel, B.Pirard, S.Schimanski, R.Kirsch, J.Habermann, O.Klingler, V.Schlotte, K.U.Weithmann, K.U.Wendt. Structural Basis For the Highly Selective Inhibition of Mmp-13. Chem.Biol. V. 12 181 2005.
ISSN: ISSN 1074-5521
PubMed: 15734640
DOI: 10.1016/J.CHEMBIOL.2004.11.014