Is the active-site drawing the measurement itself?
Diffraction intensities constrain a crystallographic model of atomic arrangement. Deposited coordinates and validation information allow a viewer to reconstruct and inspect that model. They are not a time-resolved recording of a catalytic cycle.
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EXPLORE THE MODEL
A deposited zinc site
Select a site to identify its entry, residue and atom. In the overlay, smaller purple wireframes represent the apo record; larger chemical-color wireframes show the native record. Click repeatedly to cycle overlapping sites, or use the site selector.
What this representation means
Coordinates are refined crystallographic models, not direct photographs or trajectories. PDB HOH oxygen has no modeled hydrogen atoms here; water/hydroxide protonation is not established from these coordinates alone. Protein side-chain bonds may be inferred by standard HIS connectivity, but only the four explicitly listed Zn contacts are coordination evidence. No metal atom is constructed for the apo record. A reference-location marker, if used, must be labeled ghost/reference. Native and aligned apo coordinates share one fixed display frame. Overlaying the records does not show motion, a reaction path or a time sequence. Purple apo atoms are deposited atoms; no apo zinc is constructed.
- Selected entries
- 2CBA
- Alignment
- 258 matched Cα atoms · RMSD 0.098 Å
- Zn contacts in 2CBA
- His94 NE2 2.101 Å · His96 NE2 2.116 Å · His119 ND1 2.107 Å
- Water O → Zn in 2CBA
- 2.052 Å
- 2CBE water O displacement after alignment
- 0.869 Å from native water O; not a trajectory
- Resolution
- 2CBA 1.54 Å · 2CBE 1.82 Å
Select an atom or residue site in the model. Native coordinates include zinc and its nearby ligands. The apo record is independently deposited and aligned on matched backbone atoms; removing the zinc from a picture would not generate those observations.
What this model can establish
Selected histidine residues and a water oxygen from deposited crystal structures. Connectors mark coordination or residue bonds, not a reaction movie. Hydrogen positions, motion and catalytic rates are not inferred.
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MAKE THE CONNECTION
Which observation directly belongs to the structural evidence?
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HISTORY THROUGH EVIDENCE
The speed problem before the structure
In 1933, Meldrum and Roughton framed carbon dioxide release from blood as a kinetic problem.
Explore how the evidence changed the explanation →