482 INDEX
SemiChem, 179
Serena Software, 164, 179
SpartanTM, 170, 175, 180
Tripos, 159, 175, 179
Wavefunction, Inc., 180
Windows, 158, 175–182
Computer software, mathematical:
Mathematica, 180 –181
MathType, 180
SigmaPlot, Deltagraph, 180
Computer software, nomenclature:
ACD / Name, 182
AutoNom Standard, 181
Computer software, visualization
resources:
Chime, 35, 181–182
ISIS/Draw, 181–182
projected stereo images, 183
Protein Explorer, 182
PyMOL, 176
RasMol, 182
Conformation
A-, B-, Z-DNA, 47, 50, 52f, 53, 53t, 66
Sugars in DNA and RNA, 33, 47, 48t,
240, 259, 289
Cooperativity
calcium in calmodulin, 308
calcium in Ca2+-ATPase, 331
dioxygen binding in hemoglobin, 346,
359
Coordination geometry
common transition metal, 14–16, 14f
ion size infl uence, 8
octahedral, 4t, 5t, 6t, 14f, 15f, 17–18,
17f, 18t, 21, 79, 81, 109, 126, 163,
167, 252, 258, 284, 379
square planar, 6t, 10, 14f, 15–17, 15f,
18t, 19, 81, 127, 163
square pyramid, 4t, 5t, 14f, 18t, 21, 82,
380, 451
tetrahedral, 4t, 5t, 6t, 14f, 15–18, 15f,
18t, 21, 63, 65– 66, 79, 81, 120,
135t
trigonal bipyramid, 16, 21, 257, 287,
296, 450
trigonal planar, 5t
trigonal prism, 21
Coordination number, 4t, 5t, 6t, 10, 12,
18, 79, 81, 103, 162–163
Copper, see also copper proteins:
antiferromagnetic coupling and, 17,
442
azurin and, 57–58
biological signifi cance, 2t, 4, 5t, 6t,
361
cytochrome c oxidase and, 17, 129–
131, 411–461
electron transfer and, 5t, 24, 26, 129,
132, 143–146
EXAFS studies, 81–82
model complexes, 439, 447, 450 –453,
441f, 442f
X-ray source and, 94
Copper proteins, see also azurin,
cytochrome c oxidase, methane
monooxygenase:
copper-zinc superoxide dismutase, 143
electron transfer and, 5t, 24, 26, 57–
58, 117, 129
ENDOR studies, 131–132
EPR studies and properties, 17, 129–
131, 130f, 443, 445–447, 451–452,
456, 458, 460–461
EXAFS studies, 82–83, 82–83, 461
ligands and geometries, 5t, 6t, 7t, 10 –
11, 11t, 18
model complexes, 439, 441f–442f, 447,
450–453
monooxygenase activity, 459– 460
NMR studies, 442, 453
Type I, II, III, 5t, 6t, 17, 166, 449– 450
UV-visible spectroscopy, 144, 439,
442–444, 448t
Correlation spectroscopy, see also
nuclear magnetic resonance
(NMR)/(COSY), 112–115
Cross reactions, electron-transfer, 25,
25f
Crown ethers, 6 –7, 7f, 7t, 9t
Crystallization techniques, 84–88, 96,
215, 228, 231, 241, 252, 258, 285,
292, 294, 297, 313, 399, 463, 465
Crystallography, see X-ray
crystallography
Cysteine (Cys, C), 20, 22, 31f, 33f, 34f,
43
as a ligand, 24, 131–132, 137f, 138,
362–363, 373, 384, 450–451