412 IRON-CONTAINING PROTEINS AND ENZYMES
within or within hydrogen - bonding distance of three structurally important
atoms or groups: (1) the heme O2D propionate oxygen (O2D – wat166 =
4.09 Å ); (2) the OH group of tyr67 (tyr67 OH – wat166 = 2.61 Å ); and (3) the
Oγ 1 atom of thr78 (thr78 O γ 1 – wat166 = 2.72 Å ). The two other water molecules
are part of a wider hydrogen - bonding network that includes the OH group of
tyr48 and the heme O1A propionate oxygen (O1A – OH tyr48 = 2.83 Å , O1A –
wat121 = 2.81 Å , O1A – wat168 = 2.85 Å ), the heme O2A propionate oxygen
and the backbone N of gly41 (O2A – N = 3.21 Å ), the N δ 2 atom of asn52
(O2A – N δ 2 = 3.34 Å ), the N ε 1 atom of trp59 (O2A – N ε 1 = 3.09 Å ) and wat121
(O2A – wat121 = 4.01 Å ), the heme O1D propionate oxygen and the O γ 1 atom
of thr49 (O1D – O γ 1 = 2.64 Å ), the O γ 1 atom of thr78 (O1D – O γ 1 = 2.90 Å ) and
the backbone N of lys79 (O1D – N = 3.17 Å ), and the heme O2D propionate
oxygen and the backbone N of thr49 (O2D – N = 2.94 Å ). The distance data are
taken from the Pymol visualization of the PDB: 1YCC molecule (see Figure
7.33 ). All of the aa residues involved in the hydrogen - bonding scheme are
conserved (at least for yeast and horse heart cytochrome c — see the discussion
of the NMR structure of PDB: 1GIW below).
Criteria for hydrogen - bonding geometry in X - ray crystallographic struc-
tures have been established as follows: (1) The distance between the acceptor
and the hydrogen (d HA ) must be less than 2.5 Å ; (2) the distance between the
Figure 7.33 Two yeast cytochrome c molecules (PDB: 1YCC, Fe(II), green, and PDB:
2YCC, Fe(III), cyan). Visualized using The PyMOL Molecular Graphics System and
ChemDraw Ultra, version 10.0. (Printed with permission of Delano Scientifi c, LLC and
CambridgeSoft Corporation.) (See color plate)
Cytochrome c
PDB: 1YCC: green
PDB: 2YCC: cyan
water 166cys17water 121water 168thr69, redhis18met 80heme propionate
O1D, O2Dheme propionate
O1A, O2Athr78tyr67asn52cys14