Chlorine 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:

Fluorine

(F)

3 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl501 b:16.8 occ:1.00 CL1 H:CPD501 0.0 16.8 1.0 C1 H:CPD501 1.8 9.4 1.0 C2 H:CPD501 2.7 10.1 1.0 CL2 H:CPD501 2.9 13.6 1.0 O1 H:CPD501 3.1 6.6 1.0 N H:GLY100 3.5 7.1 1.0 N1 H:CPD501 3.7 9.2 1.0 CA H:GLY100 4.1 10.7 1.0 C H:ASP99 4.1 6.9 1.0 CB H:ASP99 4.2 8.6 1.0 CA H:ASP99 4.3 6.9 1.0 CG H:ASP99 4.5 8.5 1.0 OD2 H:ASP99 4.6 10.2 1.0 O H:HOH517 4.9 24.9 1.0

Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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:Cl501 b:13.6 occ:1.00 CL2 H:CPD501 0.0 13.6 1.0 C1 H:CPD501 1.8 9.4 1.0 C2 H:CPD501 2.7 10.1 1.0 CL1 H:CPD501 2.9 16.8 1.0 O1 H:CPD501 3.1 6.6 1.0 OD1 H:ASP99 3.3 5.7 1.0 CG H:ASP99 3.4 8.5 1.0 N1 H:CPD501 3.6 9.2 1.0 OD2 H:ASP99 3.7 10.2 1.0 CA H:ASP99 3.9 6.9 1.0 OG H:SER52 3.9 8.6 1.0 CB H:ASP99 3.9 8.6 1.0 C7 H:CPD501 4.0 3.2 1.0 O H:HOH517 4.1 24.9 1.0 CB H:SER52 4.1 9.9 1.0 OG H:SER56 4.2 15.4 1.0 O H:HOH529 4.2 15.8 1.0 C9 H:CPD501 4.3 3.6 1.0 CE1 H:HIS97 4.3 6.3 1.0 CB H:SER56 4.4 13.0 1.0 N H:GLY100 4.4 7.1 1.0 OH H:TYR58 4.6 15.8 1.0 C H:ASP99 4.7 6.9 1.0 C3 H:CPD501 4.9 9.2 1.0 N H:ASP99 4.9 5.0 1.0 C6 H:CPD501 4.9 5.4 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