Fluorine in PDB 2dqu: Crystal Form II: High Resolution Crystal Structure of the Complex of the Hydrolytic Antibody Fab 6D9 and A Transition-State Analog

The structure of Crystal Form II: High Resolution Crystal Structure of the Complex of the Hydrolytic Antibody Fab 6D9 and A Transition-State Analog, PDB code: 2dqu was solved by O.Kristensen, D.G.Vassylyev, F.Tanaka, N.Ito, K.Morikawa, I.Fujii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.700, 63.040, 56.560, 90.00, 98.75, 90.00
R / Rfree (%)	20.7 / 24.6

The structure of Crystal Form II: High Resolution Crystal Structure of the Complex of the Hydrolytic Antibody Fab 6D9 and A Transition-State Analog also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Form II: High Resolution Crystal Structure of the Complex of the Hydrolytic Antibody Fab 6D9 and A Transition-State Analog (pdb code 2dqu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Form II: High Resolution Crystal Structure of the Complex of the Hydrolytic Antibody Fab 6D9 and A Transition-State Analog, PDB code: 2dqu:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Form II: High Resolution Crystal Structure of the Complex of the Hydrolytic Antibody Fab 6D9 and A Transition-State Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Form II: High Resolution Crystal Structure of the Complex of the Hydrolytic Antibody Fab 6D9 and A Transition-State Analog within 5.0Å range: probe atom residue distance (Å) B Occ H:F501 b:16.8 occ:1.00 F1 H:CPD501 0.0 16.8 1.0 C20 H:CPD501 1.4 11.9 1.0 F3 H:CPD501 2.2 13.4 1.0 F2 H:CPD501 2.2 16.2 1.0 C19 H:CPD501 2.4 7.1 1.0 O8 H:CPD501 3.0 7.2 1.0 N3 H:CPD501 3.3 6.7 1.0 CG1 H:VAL95 3.4 5.2 1.0 CD1 H:TRP100I 3.7 2.5 1.0 O3 H:CPD501 3.8 12.7 1.0 CG2 H:VAL95 4.0 4.3 1.0 CE1 H:PHE100K 4.1 9.1 1.0 CG H:TRP100I 4.3 5.0 1.0 CB H:VAL95 4.3 1.1 1.0 CB H:TRP100I 4.4 2.4 1.0 OG H:SER50 4.4 5.7 1.0 CZ H:PHE100K 4.5 5.7 1.0 NE1 H:TRP100I 4.7 5.1 1.0 C18 H:CPD501 4.7 7.2 1.0 CD1 H:PHE100K 4.7 8.8 1.0 N2 H:CPD501 4.7 10.9 1.0 N H:TYR100J 4.8 2.6 1.0 C10 H:CPD501 4.8 8.2 1.0 C H:TRP100I 4.9 1.1 1.0

Fluorine binding site 2 out of 3 in the Crystal Form II: High Resolution Crystal Structure of the Complex of the Hydrolytic Antibody Fab 6D9 and A Transition-State Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Form II: High Resolution Crystal Structure of the Complex of the Hydrolytic Antibody Fab 6D9 and A Transition-State Analog within 5.0Å range: probe atom residue distance (Å) B Occ H:F501 b:16.2 occ:1.00 F2 H:CPD501 0.0 16.2 1.0 C20 H:CPD501 1.4 11.9 1.0 F3 H:CPD501 2.2 13.4 1.0 F1 H:CPD501 2.2 16.8 1.0 C19 H:CPD501 2.4 7.1 1.0 O8 H:CPD501 2.8 7.2 1.0 CZ H:PHE100K 3.3 5.7 1.0 CE1 H:PHE100K 3.4 9.1 1.0 N3 H:CPD501 3.5 6.7 1.0 OG H:SER50 3.5 5.7 1.0 CG L:PRO96 3.7 8.5 1.0 NE1 H:TRP47 3.8 3.8 1.0 CD1 H:TRP47 3.9 3.6 1.0 CZ L:PHE89 3.9 4.2 1.0 CB L:PRO96 4.1 6.0 1.0 CE2 H:PHE100K 4.3 7.1 1.0 CE2 L:PHE89 4.6 5.6 1.0 CD1 H:PHE100K 4.6 8.8 1.0 CE2 H:TRP47 4.7 3.6 1.0 CG H:TRP47 4.8 1.1 1.0 C18 H:CPD501 4.8 7.2 1.0 OG H:SER35 4.8 9.1 1.0 CB H:SER50 4.8 2.7 1.0 CE1 L:PHE89 4.9 4.1 1.0 CG2 H:VAL95 4.9 4.3 1.0 CD L:PRO96 5.0 7.4 1.0

Fluorine binding site 3 out of 3 in the Crystal Form II: High Resolution Crystal Structure of the Complex of the Hydrolytic Antibody Fab 6D9 and A Transition-State Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Form II: High Resolution Crystal Structure of the Complex of the Hydrolytic Antibody Fab 6D9 and A Transition-State Analog within 5.0Å range: probe atom residue distance (Å) B Occ H:F501 b:13.4 occ:1.00 F3 H:CPD501 0.0 13.4 1.0 C20 H:CPD501 1.4 11.9 1.0 F1 H:CPD501 2.2 16.8 1.0 F2 H:CPD501 2.2 16.2 1.0 C19 H:CPD501 2.4 7.1 1.0 N3 H:CPD501 2.7 6.7 1.0 O8 H:CPD501 3.5 7.2 1.0 CA L:GLY91 3.5 5.3 1.0 CD1 H:TRP100I 3.6 2.5 1.0 CZ L:PHE89 3.6 4.2 1.0 O L:GLY91 3.7 5.7 1.0 CE2 L:PHE89 3.7 5.6 1.0 CG L:PRO96 3.9 8.5 1.0 NE1 H:TRP100I 4.0 5.1 1.0 O L:HOH227 4.0 8.2 1.0 C18 H:CPD501 4.1 7.2 1.0 C L:GLY91 4.1 5.8 1.0 CB L:PRO96 4.2 6.0 1.0 CZ H:PHE100K 4.7 5.7 1.0 CG H:TRP100I 4.7 5.0 1.0 C16 H:CPD501 4.7 6.1 1.0 N L:GLY91 4.7 6.2 1.0 CE1 H:PHE100K 4.9 9.1 1.0 CE1 L:PHE89 4.9 4.1 1.0

M.Oda, N.Ito, T.Tsumuraya, K.Suzuki, M.Sakakura, I.Fujii. Thermodynamic and Structural Basis For Transition-State Stabilization in Antibody-Catalyzed Hydrolysis J.Mol.Biol. V. 369 198 2007.
ISSN: ISSN 0022-2836
PubMed: 17428500
DOI: 10.1016/J.JMB.2007.03.023