lmnature · Molecular biology · Page 7

Insulin zinc sites: two distances, an incomplete assembly

Media: text, diagram, video and live animation.

Two zinc positions and two nearby histidines are present in the deposited 4INS insulin coordinates. Here we measure only the atom pairs that exist in that file. The whole hexamer is not shown.

What was measured

The pinned pig insulin entry reports 1.50 Å X-ray resolution. Each number below is a Euclidean heavy-atom separation from its first coordinate model, retaining blank/A alternate locations. Second decimals are arithmetic rounding, not experimental precision.

• Zn B 101 ZN to His B 10 NE2: 2.11 Å. B-factors (Zn / His NE2): 10.40 / 9.41 Ų. Occupancies: 0.33 / 1.00.
• Zn D 101 ZN to His D 10 NE2: 2.08 Å. B-factors (Zn / His NE2): 11.00 / 11.60 Ų. Occupancies: 0.33 / 1.00.

What the deposited file records

The coordinate file contains chains A and C with 21 residues each and B and D with 30 each: four peptide chains, representing two insulin molecules. There are two Zn coordinate rows, B 101 and D 101. Their listed occupancy is 0.33; this is the deposited model field, not a claim that a zinc atom is fractionally present. The selected His NE2 atoms have occupancy 1.00. Source: pinned 4INS records.

The file has 830 ATOM rows, 352 HETATM rows and 350 water rows. Its 48 nonblank alternate-location rows comprise A and B alternatives; only blank/A coordinates enter our measurements. There are 0 hydrogen/deuterium/tritium coordinate rows. Both protein components are marked ENGINEERED in COMPND. DBREF maps the deposited chains to pig insulin P01315; the labels here retain PDB chain and residue numbering. The renderer omits water.

There are 7 LINK rows, 17 CONECT rows and 14 SITE rows. Each measured Zn–His pair has an identity-coordinate LINK and a CONECT entry: serials 247–835 for B and 664–836 for D. Further LINK rows repeat His B 10 NE2 or His D 10 NE2 using symmetry codes 2555 and 3555, while the Zn remains at 1555. A remaining LINK records Zn B 101 to water B 213. These are deposited connection annotations, separate from our distance arithmetic; they do not establish bond order or biological function. 4INS connection records.

What is not expanded

REMARK 350 does not describe a single assembly: author-designated assemblies 1 and 2 use A+B and C+D with identity transforms. Software-defined assembly 3 applies three transforms to A–D and calls the resulting twelve peptide chains DODECAMERIC. In insulin-molecule terminology those chains form six two-chain molecules. This page, video and live view show only the deposited four peptide chains, not that symmetry-expanded hexamer. Only one of the symmetry-related His partners for each Zn is shown. No missing histidine copies are invented.

Interpretation from the cited source

Baker and colleagues describe three insulin dimers forming a hexamer around two zinc ions. That is the paper's structural interpretation, not a conclusion from our two distances. Their crystal analysis includes symmetry-related molecules that are absent from this displayed asymmetric unit. Baker et al., 1988, The structure of 2Zn pig insulin crystals at 1.5 A resolution (PMID 2905485).

A static coordinate model does not show an assembly process, atom motion or changes over time. A measured distance alone is not evidence of chemical bonding, affinity or a reaction mechanism.

Video and live view: only the deposited coordinates

Legend: gray-blue protein trace; gold lines are explicit measurements. Public lmvideo v0.1.127 renders the same source used by the live view. Orbiting is a presentation change; it does not expand symmetry.