PDBsum entry 1mbc

Oxygen storage

PDB id: 1mbc

Contents

Protein chain

153 a.a. *

Ligands

SO4

HEM-CMO

Waters ×137

* Residue conservation analysis

PDB id:

1mbc

Name:

Oxygen storage

Title:

X-ray structure and refinement of carbon-monoxy (fe ii)-myoglobin at 1.5 angstroms resolution

Structure:

Myoglobin. Chain: a. Engineered: yes

Source:

Physeter catodon. Sperm whale. Organism_taxid: 9755

Resolution:

1.50Å R-factor: 0.171

Authors:

J.Kuriyan,G.A.Petsko

Key ref:

J.Kuriyan et al. (1986). X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 A resolution. J Mol Biol, 192, 133-154. PubMed id: 3820301 DOI: 10.1016/0022-2836(86)90470-5

Date:

15-Sep-88 Release date: 09-Jan-89

Protein chain

P02185  (MYG_PHYMC) -  Myoglobin from Physeter macrocephalus

Seq: 154 a.a.

Struc: 153 a.a.

Enzyme reactions

• Enzyme class 2: E.C.1.11.1.- - ?????
• Enzyme class 3: E.C.1.7.-.-

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1016/0022-2836(86)90470-5

J Mol Biol 192:133-154 (1986)

PubMed id: 3820301

X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 A resolution.

J.Kuriyan, S.Wilz, M.Karplus, G.A.Petsko.

ABSTRACT

The structure of carbon-monoxy (Fe II) myoglobin at 260 K has been solved at a resolution of 1.5 A by X-ray diffraction and a model refined against the X-ray data by restrained least-squares. The CO ligand is disordered and distorted from the linear conformation seen in model compounds. At least two conformations, with Fe--C--O angles of 140 degrees and 120 degrees, are required to model the system. The heme pocket is significantly larger than in deoxy-myoglobin because the distal residues have relaxed around the ligand; the largest displacement occurs for the distal histidine side-chain, which moves more than 1.4 A on ligand binding. The side-chain of Arg45 (CD3) is disordered and apparently exists in two equally populated conformations. One of these does not block the motion of the distal histidine out of the binding pocket, suggesting a mechanism for ligand entry. The heme group is planar (root-mean-square deviation from planarity is 0.08 A) with no doming of the pyrrole groups. The Fe--N epsilon 2 (His93) bond length is 2.2 A and the Fe--C bond length in the CO complex is 1.9 A. The iron is the least-squares plane of the heme, and this leads to the proximal histidine moving by 0.4 A relative to its position in deoxy-myoglobin. This shift correlates with a global structural change, with the proximal part of the molecule translated towards the heme plane.

Selected figure(s)

Figure 2.
Figure 2. The eme group, and eviations rom planarity. The nomenclature used or he atoms f he heme is shown. The eviations of atoms that eviate by more han .1 A rom the plane of he 4 yrrole nitrogen atoms in O-Mb re ndicated. he igures in arenthees are he deviations for deoxy-Mb. The dihedral ngle q5 used to escribe the CO onformations is shown.

Figure 7.
Figure 7. xl-x2 energy map for is64 7. The total nergy s alculated as a functio of 1 and x2 with the of the protein kept fixed. There are 10 contour levels rom - 16 100.0 kcal/mol. (a) Arg45 CD3 is in onformation A. The X-ray conformation of is64 E7 is arked ith n X. b) Arg45 CD3 is in conformation B. he conformation of His64 E7 t was used in salculating the nergy map in Fig. 4(d) s mared with n X.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1986, 192, 133-154) copyright 1986.

Figures were selected by an automated process.