3G53

Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloropropyl benzene bound to the XE4 cavity

Summary for 3G53

• Entry DOI: 10.2210/pdb3g53/pdb
• Related: 3G46 3G4Q 3G4R 3G4U 3G4V 3G4W 3G4Y 3G52 3SDH 4SDH
• Descriptor: Globin-1, PROTOPORPHYRIN IX CONTAINING FE, CARBON MONOXIDE, ... (5 entities in total)
• Functional Keywords: oxygen transport, allostery, oxygen affinity, cytoplasm, heme, iron, metal-binding, oxygen storage/transport, oxygen binding
• Biological source: Anadara inaequivalvis (Inequivalve ark)
• Total number of polymer chains: 2
• Total formula weight: 33378.24

Authors

Knapp, J.E.,Pahl, R.,Cohen, J.,Nichols, J.C.,Schulten, K.,Gibson, Q.H.,Srajer, V.,Royer Jr., W.E. (deposition date: 2009-02-04, release date: 2009-12-01, Last modification date: 2023-09-06)

Primary citation

Knapp, J.E.,Pahl, R.,Cohen, J.,Nichols, J.C.,Schulten, K.,Gibson, Q.H.,Srajer, V.,Royer, W.E.
Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis.
Structure, 17:1494-1504, 2009

PubMed Abstract: As in many other hemoglobins, no direct route for migration of ligands between solvent and active site is evident from crystal structures of Scapharca inaequivalvis dimeric HbI. Xenon (Xe) and organic halide binding experiments, along with computational analysis presented here, reveal protein cavities as potential ligand migration routes. Time-resolved crystallographic experiments show that photodissociated carbon monoxide (CO) docks within 5 ns at the distal pocket B site and at more remote Xe4 and Xe2 cavities. CO rebinding is not affected by the presence of dichloroethane within the major Xe4 protein cavity, demonstrating that this cavity is not on the major exit pathway. The crystal lattice has a substantial influence on ligand migration, suggesting that significant conformational rearrangements may be required for ligand exit. Taken together, these results are consistent with a distal histidine gate as one important ligand entry and exit route, despite its participation in the dimeric interface.

PubMed: 19913484
DOI: 10.1016/j.str.2009.09.004

Experimental method

X-RAY DIFFRACTION (1.64 Å)