488 INDEX
metal binding to, 48t
Te t ra hym e n a pre-rRNA ribozyme
and, 239–241
Guanosine monophosphate, 48t
cyclic guanosine monophosphate
(cGMP), 194
Guanosine triphosphate (GTP), 239
Hamiltonian equation, 123, 127
Hammerhead ribozyme:
base rescue 274f, 276f
cadmium (Cd) and, 257t, 268, 280 –
283, 288, 290
constructs, 264f, 265f, 266f
exogenous base addition and, 273–277
hammerhead fold and, 263, 292, 298
hydroxyl radical footprinting and,
289–292, 291t, 300
inline fi tness and, 286–287, 294, 295t,
297
magnesium and, 267t, 268–269, 270–
271t, 272, 277–284, 287–301
manganese and, 267t, 269, 270 –271t,
272, 280, 282, 284, 288–290
orbital steering and, 286 –287
(^31) P NMR, 281–283, 288–289, 298
pH and, 267t, 269, 270–271t, 272, 279,
282, 287–288, 291, 294, 297
phosphorothioate metal rescue (PS-
rescue), 268, 281–284, 288, 301
prochiral phosphate (pro-R, pro-S),
262, 265, 267t, 268, 271t, 272,
280–282, 282f, 284, 288, 297–299
role of metal ion, 241–244
scissile phosphate, 264f, 265f, 266f,
266, 268–269, 273f, 279–281, 284,
286, 293f, 296, 300
SN2 mechanism and, 262, 262f, 264,
268, 272, 279, 284, 287, 294, 296–
297, 300
terbium (Tb) and, 267t, 277–278, 286
time-resolved crystallography, 269,
278
X-ray crystallography, 262–264, 266,
267t, 268, 270–271t, 272, 274,
277–278, 280–291, 285–286, 288,
292–294, 296, 300
Hanging drop method, 84
Hard anions, 6 –8, 7t, 40
Hard cations, 6 –8, 7t, 40, 242
Hard-soft acid-base theory (HSAB), 6 –
8, 7t
Harmonic oscillators, electron
exchange, 25
Hartree-Fock (HF) theory, 161, 168–
169, 171–173, 175, 178, 18 0
Helical rise, defi ned, 51, 53t
Heme(s), see also porphyrin, 117–118,
129, 166 –168, 343 –345, 354, 357f,
359, 384f, 387t, 406f, 409f, 441f
Hemerythrin, 459
Hemocyanin, (Hc), 4–5, 5t
Hemoglobin (Hb):
Bohr effect, 192
carbon monoxide binding, 349–350,
356 –359
cooperativity, 90–91, 346, 359
deoxy-, 90–91, 344–348, 345f, 348f,
349–351, 351t
dioxygen binding, 345–349, 357f, 359
diphosphoglycerate, DPG, 192–193,
193f
distal histidine, 346, 350–351, 350f,
356 –358, 357f
EPR, 17
ferryl-oxo iron intermediate, 354, 364,
371, 376
ligands, 344, 344f, 347, 350–352,
351t
met-346, 349, 363
model compounds, 90 –91, 349–359
Mössbauer spectroscopy, 135t
μ-oxo iron species, 346, 350, 353–355,
354f, 355f
oxy-, 90 –91, 135t, 344–346, 348f, 350 –
352, 350f, 351t, 352t, 353–355
proximal histidine, 345–351, 347f,
350f
quaternary structure, 344–348, 345f,
359
R- and T-states, 91, 146, 347–348,
347f, 351, 355–358, 356f
resonance Raman, 146, 348, 358
subunits, 346–347
tetramer, 345f, 346–348
time-resolved X-ray crystallography,
358
vibrational spectroscopy, 348, 358