wwPDB validation report of PDB entry 1HUG

THE RESIDUES DEFINING THE CAT SITE CONSTITUTE THE CATALYTIC ACTIVE SITE OF THE ENZYME. INHIBITOR GOLD CYANIDE ANION BINDS IN THE POCKET DEFINED BY THESE RESIDUES AND ACCEPTS A H-BOND FROM THE ACTIVITY LINKED HYDROXYL GROUP BOUND TO THE ZINC ION. THE CONFORMATIONAL REORIENTATION IN THE HYDROXYL GROUP DUE TO H-BOND WITH THE INHIBITOR ANION, RENDERS THE ENZYME INACTIVE.

ON THE BASIS OF HUMAN CARBONIC ANHYDRASE - BICARBONATE
COMPLEX STRUCTURE (VINAY KUMAR AND K.K. KANNAN,
UNPUBLISHED RESULTS) AND REFINED STRUCTURE OF THE TITLE
COMPOUND, THE FOLLOWING SEQUENCE MODIFICATION IN THE
NATIVE HUMAN CARBONIC ANHYDRASE ATOMIC MODEL (PDB IDENT
CODE 2CAB, VERSION OF 10/84) HAVE BEEN MADE IN THE
SUBMITTED ATOMIC MODEL.

SEQUENCE NUMBER 74 75
RESIDUE TYPE ASP ASN
THESE CHANGES ARE CONSISTENT WITH THE KNOWN CHEMICAL
SEQUENCE OF HUMAN CARBONIC ANHYDRASE I ENZYME.

THE POTENTIAL SOLVENT SITES WERE IDENTIFIED FROM FO-FC MAP IF THE PEAK HEIGHT WERE MORE THAN 3 TIMES THE S.D OF THE MAP AND WERE WITHIN THE H-BONDING DISTANCE TO A DONOR/ACCEPTOR ATOM. SOLVENTS WERE ADDED TO THE COORDINATE LIST IF ELECTRON DENSITY WAS ALSO OBSERVED IN (2FO - FC) MAP. IN ADDITION TO POSITIONAL AND ISOTROPIC THERMAL PARAMETER, OCCUPANCY WAS ALSO REFINED FOR THE SOLVENT MOLECULES. SOLVENTS WHICH REFINED TO HIGH B-VALUE (>58A2), LOW OCCUPANCY (<30 PER CENT) WERE NOT INCLUDED IN THE MODEL DURING SUBSEQUENT STAGES OF REFINEMENT. THE SUBMITTED MODEL HAS 231 SOLVENT MOLECULES OUT OF WHICH 70 SOLVENTS ARE WITH PARTIAL OXYGEN OCCUPANCY.

THE SIDE CHAINS OF RESIDUES ASP 9, LYS 10, ARG 173 AND GLU 221 SHOW VERY POOR ELECTRON DENSITY IN THE FOURIER MAPS.

ATOM AU 501 IS THE PARTIAL OVERLAPPING BINDING SITE OF THE HET AUC 500 GROUP.

CARBONIC ANHYDRASE I (E.C.4.2.1.1) COMPLEXED WITH GOLD CYANIDE INHIBITOR
Differences in anionic inhibition of Human Carbonic Anhydrase I revealed from the structures of iodide and gold cyanide inhibitor complexes

The largest off-origin peak in the Patterson function is 6.43% of the height of the origin peak. No significant pseudotranslation is detected.

20191225.v01 (using entries in the PDB archive December 25th 2019)

structure factor analysis and validation

geometric validation package for ligand chemistry in protein x-ray structures