Compare binding states

What changes when oxygen binds?

Compare deliberately identified oxygenated and deoxygenated hemoglobin states without treating a morph as measured dynamics.

Hemoglobin can bind oxygen reversibly at its heme sites. Switch between the deoxygenated 1A3N structure and oxygenated 1HHO structure, then inspect a heme group and its ligand labels. These are separately measured, separately centered views. Switching reveals distinct records; it does not show a protein moving through an oxygen-binding event.

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EXPLORE THE MODEL

Inspect deposited hemoglobin structures

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Cα traces, heme atoms and O₂ from deposited structures; biological assembly operators applied. Missing atoms remain missing. No morph or measured trajectory is asserted.

Deposited state

Representation

View angle20 °

StructureDeoxy · 1A3N

RepresentationProtein and hemes

SourceDeposited X-ray structure

Compare two separately measured structures. Their different preparation and resolution mean this is not a controlled movie of oxygen binding.

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HOW DO WE KNOW?

Evidence & limits

Deposited structure + original rendering

What this interaction establishes

Compare deliberately identified oxygenated and deoxygenated hemoglobin states without treating a morph as measured dynamics.

Cα traces, heme atoms and O₂ from deposited structures; biological assembly operators applied. Missing atoms remain missing. No morph or measured trajectory is asserted.

Source bindings for this explanation

Start here

Sources: S09, S08, SRC-1HHO.

Explore the science

The selected records are human deoxyhemoglobin 1A3N and oxyhemoglobin 1HHO. Their deposited heme and oxygen coordinates provide structural examples of different binding states. Oxygen binding can couple to changes within the protein assembly and influence other sites. These specific views are not aligned for quantitative displacement analysis. The familiar PDB-101 comparison uses a different deoxygenated entry, 2HHB, with 1HHO; that pairing should not be attributed to the present selection.

Sources: S09, S08, SRC-1HHO.

Go deeper

The reported diffraction resolutions are 1.80 Å for 1A3N and 2.10 Å for 1HHO. They come from separate experiments with different preparation, crystallographic environments and refinement. Separate centering does not establish equivalent orientation or align corresponding atoms. A visual difference can therefore include viewing geometry as well as structural differences. The viewer presents no intermediate coordinates or measured timing; establishing a binding pathway or kinetics requires additional evidence beyond switching between these two records.

Sources: S09, S08, SRC-1HHO.

Limitations

The two records come from separate experiments with their own preparation, resolution and refinement. Views are separately centered and not structurally aligned; apparent screen motion is not an atomic displacement measurement. The viewer does not present a morph, a measured trajectory or binding kinetics. Bound ligand identity remains explicit; deoxygenated and oxygenated metadata are not interchangeable.

Sources: S09, S08, SRC-1HHO.

Keep these boundaries in mind

The two records come from separate experiments with their own preparation, resolution and refinement.
Views are separately centered and not structurally aligned; apparent screen motion is not an atomic displacement measurement.
The viewer does not present a morph, a measured trajectory or binding kinetics.
Bound ligand identity remains explicit; deoxygenated and oxygenated metadata are not interchangeable.

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Supplemental primary reference ↗Supplemental primary reference ↗

Scientific explanations with linked references. Model calculations retain their stated assumptions and limits.

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recognition

Which selected object distinguishes an oxygen-bound heme site in the comparison?

A free carbon atom replacing ironA specifically labeled O₂ ligandThe entire red blood cell

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mechanism

Why can binding at one hemoglobin site affect the others?

All four sites are unrelated objectsA screen animation forces every real protein to move identicallyStructural coupling within the protein assembly can alter binding behavior

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evidence

You switch between the separately centered deoxy and oxy structures. What does a changed screen position establish about atomic motion?

No measured displacement or binding time without structural alignment and additional evidenceThe exact distance and speed each atom traveled during bindingThat both records are consecutive frames from one experiment

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transfer

A drug-binding animation uses two deposited protein structures. How should its middle frames be described?

As photographs taken between the two experimentsAs illustrative interpolations unless independently supportedAs proof that no other pathways are possible

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Find iron in a protein Next: Follow oxygen, not iron

EXPLORE THE MODEL

Inspect deposited hemoglobin structures

INTERACTIVE 3D744 visible sites

1A3N · hemoglobin in three dimensionsDrag to rotate · scroll or pinch to zoom

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Inspect

Four folded protein chains position four iron-containing hemes. Rotate the deposited coordinate model, then isolate a heme to examine the local environment.

What this representation means

RCSB PDB 1A3N, X-ray resolution 1.80 Å. Selected deposited coordinates and biological assembly operators; atom display sizes are exaggerated. Cα connectors indicate sequence continuity, not direct Cα–Cα bonds. Heme connectors use a distance heuristic, not a bond-order assignment. Missing residues are not reconstructed. Oxy/deoxy views are separately centered, not aligned or morphed.

Coordinate record: 1A3N
Experimental resolution: 1.80 Å
Assembly: Four chains · biological tetramer
Oxygen state: No OXY ligand deposited

Source: www.rcsb.org ↗

Deposited record 1A3N · revision 1.4, 2026-08-12. Archive coordinates: CC0. Original rendering.

Loading deposited structure data…

Cα traces, heme atoms and O₂ from deposited structures; biological assembly operators applied. Missing atoms remain missing. No morph or measured trajectory is asserted.

Deposited state

Representation

View angle20 °

StructureDeoxy · 1A3N

RepresentationProtein and hemes

SourceDeposited X-ray structure

Compare two separately measured structures. Their different preparation and resolution mean this is not a controlled movie of oxygen binding.

INTERACTIVE 3D744 visible sites

1A3N · hemoglobin in three dimensionsDrag to rotate · scroll or pinch to zoom

Turn slowlyConnectionsFocus

Inspect

Four folded protein chains position four iron-containing hemes. Rotate the deposited coordinate model, then isolate a heme to examine the local environment.

What this representation means

Coordinate record: 1A3N
Experimental resolution: 1.80 Å
Assembly: Four chains · biological tetramer
Oxygen state: No OXY ligand deposited

Source: www.rcsb.org ↗

Deposited record 1A3N · revision 1.4, 2026-08-12. Archive coordinates: CC0. Original rendering.