BIOINORGANIC CHEMISTRY A Short Course Second Edition

208 GROUP I AND II METALS IN BIOLOGICAL SYSTEMS

Research Collaboratory for Structural Bioinformatics Protein Data Bank
(RCSB - PDB) website at http://www.rcsb.org/pdb/home/home.do contains a
wealth of information about each biomolecule whose structural data have
been deposited. Enter the PDB accession number in the search routine,
then click on the “ biology and chemistry, ” “ material and methods, ” “ sequence
details, ” and “ geometries ” tabs to obtain more information. A schematic
diagram of the membrane topology of the Shaker potassium ion channel is
shown in Figure 5.4. The diagram shows the S1 – S6 α - helices that surround the
potassium ion channel pore. More detail about S1 – S6 is given in the discussion
of X - ray crystallographic determinations and other methods for studying the
structure and function of the pore domain that follows.
The Shaker potassium channel did not yield crystals for the fi rst potassium
ion channel X - ray crystallographic structure. Rather, it was the prokaryote
bacteriumStreptomyces lividans , abbreviated as the KcsA K + channel, that
fi rst produced crystals suitable for crystallography. This structure, published in
1998 by MacKinnon ’ s group in Science magazine, was received with great
praise from the scientifi c community. It was known at that time that the amino
acid sequence of KcsA was similar to that of other K + channels, including
vertebrate and invertebrate voltage - dependent K + (K v ) channels (such as the

Figure 5.4 Membrane topology for the Shaker potassium ion channel with important
residues circled. (Adapted with permission from Figure 1A of reference 29. Copyright
2003, with permission from Elsevier.)

S2 S3 S4 S5 S6

NH 2 COOH

S1

228

-246

F416

A419

R362

S1-S2 linker

247-254

279

-300

S2-S3 linker

301-311

312

-332

S3-S4 linker

330-340

361

-380

S4-S5 linker

381-395

396 Pore

-415

457

-478

Shaker K+ Channel Protein
Residue numbers given inside each transmembrane segment S1 - S6
Pore contains selectivity filter residues 442 - 447
Shaker residue numbers from http://www.expasy.org/uniprot/P08510
N-terminal residues 1-227
C-terminal residues 479-616

Comparable KvAP residues (PDB: 1ORQ, 1ORS)

(differs from PDB residue numbering system)

from http://www.expasy.org/uniprot/Q9YDF8

S1 39-63 (PDB:26-50)

S2 68-92 (PDB:55-79)

S3a 97-105 (PDB:84-92)

S3b 109-125 (PDB:96-112)

S4 129-145 (PDB:116-132)

S5 160-184 (PDB:147-171)

S6 222-253 (PDB:209-240)

N-terminal 1-38

C-terminal 254-295

pore 196-208 (PDB:183-195)

selectivity filter 209-214 (PDB: 196-201)

outside (extracellular)

inside (intracellular)