lmnature · Molecular biology · Page 2

Two hemoglobin chains, two measured oxygen pockets

Media on this page: text, diagram, video and live animation are available.

Hemoglobin carries oxygen in red blood cells. Adult hemoglobin contains two alpha chains and two beta chains; each chain has a heme group (Shaanan 1983, J. Mol. Biol. 171, 31–59). The RCSB PDB 1HHO entry is human oxyhaemoglobin, determined by X-ray diffraction at 2.10 Å resolution.

This page compares alpha chain A (UniProt accession P69905, 141 residues) with beta chain B (UniProt accession P68871, 146 residues). Chain identities and residue counts come from the entry’s DBREF and SEQRES records.

Two pockets in one coordinate set

Every value here is a heavy-atom distance computed from deposited coordinates. Fe in HEM 143 is 1.94 Å from proximal His87 NE2, 1.66 Å from O1 and 2.79 Å from O2; O1 and O2 are 1.22 Å apart. Distal His58 NE2 is 2.99 Å from O1 and 2.57 Å from O2. Fe in HEM 147 is 2.07 Å from proximal His92 NE2, 1.86 Å from O1 and 3.05 Å from O2; O1 and O2 are 1.24 Å apart. Distal His63 NE2 is 3.20 Å from O1 and 3.49 Å from O2.

Measured projected distances in chain A: Fe to proximal His87 NE2 1.94 angstrom; Fe to O1 1.66; Fe to O2 2.79; O1 to O2 1.22; distal His58 NE2 to O1 2.99 and to O2 2.57 angstrom.
Alpha chain A. Dashed labels are full 3D distances. The footer reports the computed projection depth and all drawn-length ratios.
Measured projected distances in chain B: Fe to proximal His92 NE2 2.07 angstrom; Fe to O1 1.86; Fe to O2 3.05; O1 to O2 1.24; distal His63 NE2 to O1 3.20 and to O2 3.49 angstrom.
Beta chain B. Dashed labels are full 3D distances. The footer reports the computed projection depth and all drawn-length ratios.

Video: a turn around the two-chain structure

Heavy-atom distances are geometric measurements, not inferred bonds. Only the camera turns; no atom moves. At 4.0 Å, only four of the twelve measured pairs appear as distance-contact lines: distal His58 NE2 to O1 and O2 in chain A, and distal His63 NE2 to O1 and O2 in chain B. Five pairs appear only as PDB CONECT sticks: chain A Fe–O1, Fe–O2 and O1–O2; chain B Fe–O1 and O1–O2. Not drawn in the video are chain A Fe–His87 NE2, chain B Fe–His92 NE2, and chain B Fe–O2 (3.05 Å). Both SVG panels show all twelve measured pairs.

Rendered with public lmvideo v0.1.126 from videos/mb02.lms and the same pinned 1HHO file.

What a distance comparison can say

The two modeled pockets have different coordinate distances. That describes this deposited snapshot; the measurements do not explain why the values differ or establish what caused them. The file’s LINK records list each heme iron with its proximal histidine NE2 and O1; chain A also lists O2. Its CONECT records list each iron with the four heme nitrogens, proximal His NE2 and O1, and list O2 for chain A. These are records in the source file, separate from the distances recomputed here.

Precision: the structure was solved at 2.10 Šresolution. Oxygen B-factors are 17.77 and 33.84 Ų in alpha chain A, and 42.12 and 37.44 Ų in beta chain B. The coordinate file contains no hydrogen atoms; the second decimal is arithmetic formatting, not measurement certainty.

The coordinate file also records phosphate group PO4 A 142 at occupancy 0.50. Its phosphorus atom is identified separately in the video legend; the group is not among the twelve selected measurements.

Not shown: the coordinate file’s asymmetric unit contains chains A and B. REMARK 350 describes a tetrameric biological assembly and a crystallographic twofold operator that generates a second alpha-beta pair. This page measures only the deposited asymmetric-unit chains; it does not show motion or oxygen arriving or leaving.

Live: orbit it yourself

Interactive viewer unavailable

See the measured diagram or video.

Heavy-atom distances are geometric measurements, not inferred bonds. A single static snapshot; no atom moves.

Papers the corpus links to this protein

The corpus links 243 papers across 2 UniProt entries (P68871, P69905); per-protein counts: P68871: 137; P69905: 116. These papers are cross-referenced by the corpus and are not necessarily about this structure.

Titles, journal and year load from Europe PMC when JavaScript is available.