Fluorine in PDB 3fa3: Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form

All present enzymatic activity of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form:
4.1.3.32;

The structure of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form, PDB code: 3fa3 was solved by B.C.Narayanan, O.Herzberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.60
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	160.570, 160.570, 161.410, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 25.5

The structure of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form also contains other interesting chemical elements:

Manganese

(Mn)

16 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form (pdb code 3fa3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 28 binding sites of Fluorine where determined in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form, PDB code: 3fa3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 28 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form


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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:35.3 occ:1.00 F1 A:OAF501 0.0 35.3 1.0 C3 A:OAF501 1.3 35.5 1.0 F2 A:OAF501 2.1 37.0 1.0 C4 A:OAF501 2.3 36.4 1.0 C2 A:OAF501 2.3 34.9 1.0 C1 A:OAF501 2.6 34.9 1.0 O5 A:OAF501 2.7 36.7 1.0 O3 A:OAF501 3.0 33.8 1.0 O1 A:OAF501 3.0 33.4 1.0 OD1 A:ASP59 3.1 38.9 1.0 O2 A:OAF501 3.2 34.5 1.0 O A:HOH306 3.3 31.8 1.0 O6 A:OAF501 3.3 36.8 1.0 CB A:ALA48 3.5 35.9 1.0 O4 A:OAF501 3.5 35.3 1.0 MN A:MN401 3.6 34.0 1.0 SG A:CYS124 3.8 40.8 1.0 CB A:CYS124 4.0 38.4 1.0 CG A:ASP59 4.2 38.9 1.0 CA A:CYS124 4.3 38.9 1.0 N A:ALA48 4.5 36.8 1.0 CA A:ALA48 4.6 36.7 1.0 N A:GLY125 4.6 37.8 1.0 CZ A:PHE241 4.7 38.3 1.0 O A:HOH304 4.8 31.8 1.0 OD2 A:ASP59 4.9 40.1 1.0 OG1 A:THR46 4.9 36.7 1.0 CZ B:PHE276 5.0 32.5 1.0 C A:CYS124 5.0 38.5 1.0

Fluorine binding site 2 out of 28 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form


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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:37.0 occ:1.00 F2 A:OAF501 0.0 37.0 1.0 C3 A:OAF501 1.3 35.5 1.0 F1 A:OAF501 2.1 35.3 1.0 C4 A:OAF501 2.3 36.4 1.0 C2 A:OAF501 2.4 34.9 1.0 O6 A:OAF501 2.5 36.8 1.0 O4 A:OAF501 2.7 35.3 1.0 O2 A:OAF501 2.9 34.5 1.0 C1 A:OAF501 2.9 34.9 1.0 O5 A:OAF501 3.4 36.7 1.0 CG2 A:VAL216 3.5 34.2 1.0 CG A:PRO240 3.6 37.5 1.0 O3 A:OAF501 3.6 33.8 1.0 CB A:PRO240 3.7 37.5 1.0 O1 A:OAF501 4.0 33.4 1.0 ND2 A:ASN214 4.2 34.0 1.0 CZ A:PHE241 4.3 38.3 1.0 SG A:CYS124 4.6 40.8 1.0 CB A:ALA48 4.6 35.9 1.0 CE1 A:PHE241 4.7 37.8 1.0 CB A:VAL216 4.8 37.0 1.0 OD1 A:ASN214 4.9 33.5 1.0 MN A:MN401 4.9 34.0 1.0 OG1 A:THR46 4.9 36.7 1.0 OE2 A:GLU191 4.9 37.3 1.0 CE2 A:PHE241 4.9 39.8 1.0 CD A:PRO240 4.9 37.9 1.0 CD2 A:HIS126 4.9 39.1 1.0

Fluorine binding site 3 out of 28 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:36.2 occ:1.00 F1 B:OAF501 0.0 36.2 1.0 C3 B:OAF501 1.3 33.5 1.0 C4 B:OAF501 2.3 32.6 1.0 F2 B:OAF501 2.3 32.9 1.0 C2 B:OAF501 2.4 32.4 1.0 O5 B:OAF501 2.6 28.9 1.0 C1 B:OAF501 2.7 34.0 1.0 O1 B:OAF501 3.0 32.6 1.0 O B:HOH306 3.0 29.9 1.0 OD1 B:ASP59 3.0 39.9 1.0 O3 B:OAF501 3.0 30.8 1.0 O6 B:OAF501 3.2 35.6 1.0 O2 B:OAF501 3.5 36.6 1.0 O4 B:OAF501 3.5 32.6 1.0 MN B:MN401 3.6 37.4 1.0 SG B:CYS124 3.6 36.7 1.0 CB B:ALA48 3.9 35.8 1.0 CB B:CYS124 4.1 39.8 1.0 CA B:CYS124 4.2 39.7 1.0 CG B:ASP59 4.3 39.1 1.0 N B:GLY125 4.6 40.7 1.0 N B:ALA48 4.6 36.1 1.0 CZ B:PHE241 4.6 43.2 1.0 CA B:ALA48 4.8 35.9 1.0 O B:HOH308 4.9 26.0 1.0 C B:CYS124 4.9 40.9 1.0

Fluorine binding site 4 out of 28 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:32.9 occ:1.00 F2 B:OAF501 0.0 32.9 1.0 C3 B:OAF501 1.4 33.5 1.0 F1 B:OAF501 2.3 36.2 1.0 C2 B:OAF501 2.3 32.4 1.0 O4 B:OAF501 2.4 32.6 1.0 C4 B:OAF501 2.4 32.6 1.0 O6 B:OAF501 2.6 35.6 1.0 C1 B:OAF501 3.0 34.0 1.0 O2 B:OAF501 3.1 36.6 1.0 CG2 B:VAL216 3.5 34.3 1.0 O3 B:OAF501 3.6 30.8 1.0 O5 B:OAF501 3.6 28.9 1.0 CB B:PRO240 3.6 36.4 1.0 ND2 B:ASN214 3.7 39.2 1.0 CG B:PRO240 3.7 34.9 1.0 O1 B:OAF501 4.0 32.6 1.0 CZ B:PHE241 4.4 43.2 1.0 OD1 B:ASN214 4.5 40.9 1.0 CG B:ASN214 4.6 40.4 1.0 CE2 B:PHE241 4.7 40.8 1.0 CB B:VAL216 4.7 35.8 1.0 SG B:CYS124 4.7 36.7 1.0 CG1 B:VAL216 4.8 34.6 1.0 CD B:PRO240 4.8 35.1 1.0 MN B:MN401 5.0 37.4 1.0

Fluorine binding site 5 out of 28 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:36.9 occ:1.00 F1 C:OAF501 0.0 36.9 1.0 C3 C:OAF501 1.3 34.7 1.0 F2 C:OAF501 2.1 34.0 1.0 C4 C:OAF501 2.2 35.3 1.0 C2 C:OAF501 2.3 34.4 1.0 C1 C:OAF501 2.5 33.6 1.0 O5 C:OAF501 2.6 35.0 1.0 O3 C:OAF501 2.9 35.1 1.0 O1 C:OAF501 3.0 32.4 1.0 O C:HOH309 3.0 33.0 1.0 O2 C:OAF501 3.1 33.7 1.0 O6 C:OAF501 3.2 35.2 1.0 OD1 C:ASP59 3.2 37.2 1.0 SG C:CYS124 3.4 40.2 1.0 O4 C:OAF501 3.5 34.7 1.0 MN C:MN401 3.6 35.7 1.0 CB C:ALA48 3.9 36.8 1.0 CB C:CYS124 4.2 38.4 1.0 CG C:ASP59 4.4 36.3 1.0 CA C:CYS124 4.4 38.3 1.0 CZ C:PHE241 4.6 38.0 1.0 N C:GLY125 4.7 37.5 1.0 N C:ALA48 4.7 36.0 1.0 O C:HOH310 4.8 32.4 1.0 OG1 C:THR46 4.9 35.5 1.0 CA C:ALA48 4.9 36.3 1.0

Fluorine binding site 6 out of 28 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:34.0 occ:1.00 F2 C:OAF501 0.0 34.0 1.0 C3 C:OAF501 1.3 34.7 1.0 F1 C:OAF501 2.1 36.9 1.0 C2 C:OAF501 2.3 34.4 1.0 C4 C:OAF501 2.4 35.3 1.0 O4 C:OAF501 2.6 34.7 1.0 O6 C:OAF501 2.7 35.2 1.0 O2 C:OAF501 2.8 33.7 1.0 C1 C:OAF501 2.9 33.6 1.0 CG C:PRO240 3.5 37.3 1.0 O3 C:OAF501 3.5 35.1 1.0 O5 C:OAF501 3.5 35.0 1.0 CB C:PRO240 3.6 37.1 1.0 CG2 C:VAL216 3.8 37.4 1.0 O1 C:OAF501 4.0 32.4 1.0 ND2 C:ASN214 4.0 40.6 1.0 CE1 C:PHE241 4.4 38.5 1.0 SG C:CYS124 4.4 40.2 1.0 CZ C:PHE241 4.4 38.0 1.0 OD1 C:ASN214 4.6 39.9 1.0 CG C:ASN214 4.7 37.4 1.0 O C:HOH309 4.8 33.0 1.0 CD C:PRO240 4.9 35.9 1.0 MN C:MN401 5.0 35.7 1.0

Fluorine binding site 7 out of 28 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ D:F501 b:33.0 occ:1.00 F1 D:OAF501 0.0 33.0 1.0 C3 D:OAF501 1.3 32.8 1.0 C4 D:OAF501 2.2 31.6 1.0 F2 D:OAF501 2.2 33.6 1.0 O5 D:OAF501 2.4 30.5 1.0 C2 D:OAF501 2.4 32.5 1.0 C1 D:OAF501 2.8 31.9 1.0 O3 D:OAF501 3.1 31.4 1.0 OD1 D:ASP59 3.2 37.4 1.0 O6 D:OAF501 3.2 31.0 1.0 O1 D:OAF501 3.2 31.7 1.0 O2 D:OAF501 3.5 32.3 1.0 SG D:CYS124 3.6 37.7 1.0 O D:HOH314 3.6 32.5 1.0 O4 D:OAF501 3.6 34.1 1.0 MN D:MN401 3.6 36.2 1.0 CB D:ALA48 3.9 36.4 1.0 CB D:CYS124 4.1 36.1 1.0 CG D:ASP59 4.2 37.9 1.0 CA D:CYS124 4.3 36.5 1.0 N D:GLY125 4.4 36.3 1.0 N D:ALA48 4.7 38.0 1.0 CZ D:PHE241 4.7 39.1 1.0 C D:CYS124 4.9 35.9 1.0 CA D:ALA48 4.9 37.3 1.0 OD2 D:ASP59 4.9 38.0 1.0 NH2 D:ARG161 5.0 35.2 1.0

Fluorine binding site 8 out of 28 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ D:F501 b:33.6 occ:1.00 F2 D:OAF501 0.0 33.6 1.0 C3 D:OAF501 1.3 32.8 1.0 C2 D:OAF501 2.2 32.5 1.0 F1 D:OAF501 2.2 33.0 1.0 C4 D:OAF501 2.3 31.6 1.0 O4 D:OAF501 2.4 34.1 1.0 O6 D:OAF501 2.5 31.0 1.0 C1 D:OAF501 2.8 31.9 1.0 O2 D:OAF501 2.8 32.3 1.0 O5 D:OAF501 3.3 30.5 1.0 O3 D:OAF501 3.4 31.4 1.0 CG2 D:VAL216 3.6 39.6 1.0 CG D:PRO240 3.6 35.6 1.0 ND2 D:ASN214 3.7 42.5 1.0 CB D:PRO240 3.7 36.4 1.0 O1 D:OAF501 3.8 31.7 1.0 CG D:ASN214 4.5 41.4 1.0 OD1 D:ASN214 4.5 39.8 1.0 MN D:MN401 4.7 36.2 1.0 CZ D:PHE241 4.7 39.1 1.0 OE2 D:GLU191 4.8 34.5 1.0 CD D:PRO240 4.8 36.2 1.0 OH D:TYR44 4.8 39.7 1.0 NH2 D:ARG161 4.8 35.2 1.0 SG D:CYS124 4.8 37.7 1.0 CB D:VAL216 4.9 39.9 1.0

Fluorine binding site 9 out of 28 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ E:F501 b:34.8 occ:1.00 F1 E:OAF501 0.0 34.8 1.0 C3 E:OAF501 1.3 33.7 1.0 F2 E:OAF501 2.0 34.2 1.0 C2 E:OAF501 2.3 32.9 1.0 C4 E:OAF501 2.4 33.6 1.0 C1 E:OAF501 2.7 31.1 1.0 O5 E:OAF501 2.8 32.8 1.0 O3 E:OAF501 3.0 32.5 1.0 OD1 E:ASP59 3.1 39.7 1.0 O1 E:OAF501 3.2 28.4 1.0 O2 E:OAF501 3.2 31.3 1.0 CB E:ALA48 3.4 35.7 1.0 O6 E:OAF501 3.5 30.6 1.0 O4 E:OAF501 3.5 33.3 1.0 O E:HOH317 3.5 26.4 1.0 MN E:MN401 3.7 36.4 1.0 SG E:CYS124 3.8 41.4 1.0 CB E:CYS124 4.1 40.2 1.0 CG E:ASP59 4.3 39.5 1.0 CA E:ALA48 4.5 37.0 1.0 CA E:CYS124 4.5 40.1 1.0 N E:ALA48 4.5 37.6 1.0 CZ E:PHE241 4.6 39.2 1.0 N E:GLY125 4.9 39.8 1.0 OG1 E:THR46 4.9 37.8 1.0 CZ F:PHE276 4.9 34.5 1.0 O E:HOH315 5.0 30.3 1.0

Fluorine binding site 10 out of 28 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ E:F501 b:34.2 occ:1.00 F2 E:OAF501 0.0 34.2 1.0 C3 E:OAF501 1.3 33.7 1.0 F1 E:OAF501 2.0 34.8 1.0 C2 E:OAF501 2.3 32.9 1.0 C4 E:OAF501 2.3 33.6 1.0 O4 E:OAF501 2.6 33.3 1.0 O6 E:OAF501 2.6 30.6 1.0 C1 E:OAF501 3.0 31.1 1.0 O2 E:OAF501 3.0 31.3 1.0 CG2 E:VAL216 3.4 32.7 1.0 O5 E:OAF501 3.4 32.8 1.0 O3 E:OAF501 3.5 32.5 1.0 CG E:PRO240 3.8 38.0 1.0 CB E:PRO240 3.9 38.5 1.0 O1 E:OAF501 4.1 28.4 1.0 ND2 E:ASN214 4.2 32.7 1.0 CZ E:PHE241 4.4 39.2 1.0 CB E:ALA48 4.6 35.7 1.0 SG E:CYS124 4.6 41.4 1.0 CE2 E:PHE241 4.6 42.5 1.0 CB E:VAL216 4.7 35.4 1.0 OD1 E:ASN214 4.8 33.2 1.0 CG1 E:VAL216 4.9 35.5 1.0 MN E:MN401 4.9 36.4 1.0 CG E:ASN214 5.0 33.8 1.0 CE1 E:PHE241 5.0 39.4 1.0

B.Narayanan, W.Niu, H.J.Joosten, Z.Li, R.K.Kuipers, P.J.Schaap, D.Dunaway-Mariano, O.Herzberg. Structure and Function of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member. J.Mol.Biol. V. 386 486 2009.
ISSN: ISSN 0022-2836
PubMed: 19133276
DOI: 10.1016/J.JMB.2008.12.037