Chlorine in PDB 2dqt: High Resolution Crystal Structure of the Complex of the Hydrolytic Antibody Fab 6D9 and A Transition-State Analog

The structure of High Resolution Crystal Structure of the Complex of the Hydrolytic Antibody Fab 6D9 and A Transition-State Analog, PDB code: 2dqt 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)	6.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.906, 61.662, 66.673, 90.00, 104.68, 90.00
R / Rfree (%)	18.7 / 24.6

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

Fluorine

(F)

3 atoms

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

Chlorine binding site 1 out of 2 in the 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 Chlorine with other atoms in the Cl binding site number 1 of 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:Cl501 b:26.9 occ:1.00 CL1 H:CPD501 0.0 26.9 1.0 C1 H:CPD501 1.8 15.1 1.0 C2 H:CPD501 2.7 16.1 1.0 CL2 H:CPD501 2.9 21.3 1.0 O1 H:CPD501 3.1 14.2 1.0 N H:GLY100 3.3 17.4 1.0 N1 H:CPD501 3.7 15.7 1.0 CA H:GLY100 3.9 16.1 1.0 C H:ASP99 4.1 18.9 1.0 CB H:ASP99 4.2 10.8 1.0 CA H:ASP99 4.2 18.6 1.0 CG H:ASP99 4.5 17.0 1.0 OD2 H:ASP99 4.8 20.1 1.0 C3 H:CPD501 5.0 17.5 1.0

Chlorine binding site 2 out of 2 in the 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 Chlorine with other atoms in the Cl binding site number 2 of 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:Cl501 b:21.3 occ:1.00 CL2 H:CPD501 0.0 21.3 1.0 C1 H:CPD501 1.8 15.1 1.0 C2 H:CPD501 2.7 16.1 1.0 CL1 H:CPD501 2.9 26.9 1.0 O1 H:CPD501 3.3 14.2 1.0 OD1 H:ASP99 3.4 16.2 1.0 CG H:ASP99 3.5 17.0 1.0 N1 H:CPD501 3.6 15.7 1.0 OD2 H:ASP99 3.9 20.1 1.0 OG H:SER52 4.0 9.8 1.0 CA H:ASP99 4.1 18.6 1.0 OG H:SER56 4.1 23.0 1.0 C7 H:CPD501 4.1 7.2 1.0 CB H:ASP99 4.1 10.8 1.0 CB H:SER52 4.1 7.4 1.0 CE1 H:HIS97 4.3 17.1 1.0 O H:HOH527 4.3 21.0 1.0 C9 H:CPD501 4.4 14.4 1.0 CB H:SER56 4.4 12.0 1.0 N H:GLY100 4.5 17.4 1.0 OH H:TYR58 4.7 22.8 1.0 C H:ASP99 4.9 18.9 1.0 C3 H:CPD501 4.9 17.5 1.0 C6 H:CPD501 4.9 11.3 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