Space-filling representations

Molecules are most commonly represented on a computer graphics screen using stick or space-filling representations, which are analogous to the Dreiding and Corey-PauUng-Koltun (CPK) mechanical models. Sophisticated variations on these two basic types have... 

Figure 1 Chemical structure and space-filling representation of a phosphatidylcholine, DPPC. Different parts of the molecule are referred to by the labels at the left together the choline and phosphate are referred to as the headgroup, which is zwitteriomc. In the space-filling model, H atoms are white, O and P gray, and C black. (From Ref. 55.)...

Figure 15.15 Space-filling representation of a complex between lysozyme (green) and the Fab fragment of a monoclonal antilysozyme (blue and yellow). The Fab fragment and the antigen (lysozyme) have been separated in this diagram, and their combining surfaces are viewed end-on. Atoms that ate in contact in the complex are colored red both in Fab and lysozyme, except Gin 121 in lysozyme, which is violet. The diagram illustrates the large size of the interaction surfaces. (After A.G. Amit et al.. Science 233 747-753, 1986 courtesy of R. Poljak.)...

Figure 15.16 Detailed views of the environment of Gin 121 in the lysozyme-antilysozyme complex. Gin 121 in lysozyme is colored green both in the space-filling representation to the left and in the ball and stick model to the right. This side chain of the antigen fits into a hole between CDR3 regions of both the heavy (Tyr 101) and the light (Trp 92) chains as well as CDRl from the light chain (Tyr 32). (After A.G. Amit et al.. Science 233 747-753, 1986.)...

FIGURE 17.23 The mechanism of skeletal muscle contraction. The free energy of ATP hydrolysis drives a conformational change in the myosin head, resulting in net movement of the myosin heads along the actin filament. Inset) A ribbon and space-filling representation of the actin—myosin interaction. (SI myosin image courtesy of Ivan Rayment and Hazel M. Holden, University of Wiseonsin, Madison.)... 

Both space-filling and electron density models yield similar molecular volumes, and both show the obvious differences in overall size. Because the electron density surfaces provide no discernible boundaries between atoms (and employ no colors to highlight these boundaries), the surfaces may appear to be less informative than space-filling models in helping to decide to what extent a particular atom is exposed . This weakness raises an important point, however. Electrons are associated with a molecule as a whole and not with individual atoms. The space-filling representation of a molecule in terms of discernible atoms does not reflect reality, but rather is an artifact of the model. The electron density surface is more accurate in that it shows a single electron cloud for the entire molecule. 

Fig. 2. Ribbon diagram of the structures of (a) the water-soluble Rieske fragment from bovine heart bci complex (ISF, left, PDB file IRIE), (b) the water-soluble Rieske fragment from spinach b f complex (RFS, middle, PDB file IRFS), and (c) the Rieske domain of naphthalene dioxygenase (NDO, right, PDB file INDO). The [2Fe-2S] cluster is shown in a space-filling representation, the ligands as ball-and-stick models, and residues Pro 175 (ISF)/Pro 142 (RFS)/Pro 118 (NDO) as well as the disulfide bridge in the ISF and RFS as wireframes.

Fig. 8. (a) Structure of the full-length Rieske protein from bovine heart mitochondrial bci complex. The catalytic domain is connected to the transmembrane helix by a flexible linker, (b) Superposition of the three positional states of the catalytic domain of the Rieske protein observed in different crystal forms. The ci state is shown in white, the intermediate state in gray, and the b state in black. Cytochrome b consists of eight transmembrane helices and contains two heme centers, heme and Sh-Cytochrome c i has a water-soluble catalytic domain containing heme c i and is anchored by a C-terminal transmembrane helix. The heme groups are shown as wireframes, the iron atoms as well as the Rieske cluster in the three states as space-filling representations. 

Figure 4 Mononuclear quinquepyridine (4, 4" -bis(4-chlorophenyl analogue) Co11 complex (left, reproduced with permission of the Royal Society of Chemistry from J. Chem. Soc., Chem. Commun., 1992, 768-771) and dinuclear septipyridine (4,4"" -bis(4-mercaptomethylphenyl)-4"",4"" -bis(4-mercaptopropylphenyl) derivative) dicobalt(II) complex (right, reproduced with permission of the American Chemical Society from Inorg. Chem., 1993, 32, 5477-5484). Space filling representations also shown.

Fig. 27. Packing relations in the crystal structure of 47 benzene (1 1) 64>. Stereo drawing of complementary stick style and space filling representations of host and guest molecules, respectively (atomic radii of the corresponding guest atoms in the space filling style are set to about half of their common van der Waals values the H atoms of the host molecules are omitted)...

Fig. 32. Packing relations and steric fit of the 26 acetic acid (1 1) clathrate (isomorphous with the corresponding propionic acid clathrate of 26)1U- (a) Stereoscopic packing illustration acetic acid (shown in stick style) forms dimers in the tunnel running along the c crystal axis of the 26 host matrix (space filling representation, O atoms shaded), (b) Electron density contours in the plane of the acetic acid dimer sa First contour (solid line) is at 0.4 eA" while subsequent ones are with arbitrary spacings of either 0.5 and 1 eA 3. Density of the enclosing walls comes from C and H atoms of host molecules.

Figure 26 Space-filling representation of a portion of a stack observed in the structure of [137-C10H8[.

Figure 1.1. A space-filling representation of cyclam coordinated in a planar arrangement. In a number of complexes, monodentate ligands also occupy the axial sites.

Scheme 9.5 Synthesis of Rh(0) nanoclusters from (1,5-COD)RhP2W15Nb3Oj polyoxoanion-supported nano-cluster-forming precatalyst (space-filling representation). (Adapted from [63].)...

Figure 4.14 The B-form of the DNA double-helix viewed along the helix axis, in a ball-and-stick representation (left) and a space-filling representation (right). (From Voet and Voet, 2004. Reproduced with permission from John Wiley Sons., Inc.)...

Fig. 2.3-15. Ball-and-stick models and space-filling representations of the Al clusters 61a, 63a, and 64.

FlC. 64. The tightly associated domains (one shown light and the other dark) of elastase. Figures 64 through 66 use a space-filling representation with a sphere around each a-carbon position they were photographed from Richard Feldmann s molecular graphics display at the National Institutes of Health. 

Space-filling representation of the Fe(CN)2(CO) model compound studied by Darensbourg et al. (1997)... 

Fig. 1. The core particle, the DNA superhelix and H2B and H3 N-terminal tails, (a) Space-filling representation of the 2.8 A crystal structure of the 146 bp human a-satellite nucleosome core particle [22]. The dyad is in the plane of the paper and the superhelix axis slightly off that plane. Positive and negative numbers mark the superhelix locations (SHL) in the upper and lower gyres, respectively, and the dotted curve follows the path of the double helix axis, (b) Ribbon representation of the DNA superhelix slit along a line parallel to its axis, opened out and laid flat on the paper surface. SHL are also indicated, together with H2B and H3 tails passage points between the gyres. (From Fig. 5 in Ref [29].)...

Fig. 2. Computer-generated space-filling representation of vinblastine.

P, and A, described later in the text the tRNA anticodons are in orange. Proteins appear as blue wormlike structures the rRNA as a blended space-filling representation designed to highlight surface features, with the bases in white and the backbone in green. The structure on the right is the 30S subunit... 

B) Space-filling representation of the open (left) and closed (right) forms of the same enzyme.200 Courtesy of Stephen J. Remington. 

ORTEP drawing (a) and space-filling representations of the side view (b) and top view (c). 

Fig. 7. Coiled-coil tubes. The structures are shown in side view and cross section, and molecules found in the channels are shown in space-filling representation.

Fig. 3. The ribbon structure of coil-Ser [pdb identifier, lcos (Lovejoy et al, 1993)]. The structure reveals a mixed parallel/antiparallel three-helix bundle, which is influenced by the three core tryptophan side chains, shown in space-filling representation.

Figure 7-13. A space-filling representation of the cobalt(m) sepulchrate cation showing that the cobalt centre is buried deep within the ligand. The cobalt and nitrogen atoms are shaded. The ligand is oriented such that the two capping nitrogen atoms lie along the x axis.

Figure 8.69 Space-filling representation of the three polymorphic forms of ferrocene (a) triclinic, (b) monoclinic, and (c) orthorhombic. (Reprinted with permission from [3] 1998 American Chemical Society) (d) Phase behaviour of ferrocene.

Figure 15.1 Structure of the BmPBP-bombykol complex highlighting the three disulfide bridges that play a pivotal role in the rigidity of the three-dimensional structure of PBPs. Helices are shown as ribbons and loop regions as thin tubes. Bombykol is displayed in space-filling representation with all atoms. This figure was prepared by Fred Damberger by using the program molmol (Koradi et al., 1996).

Figure 2.4 Space-filling representations of segments of the linear chain of linked [Ag Movl8026Agl]2 showing the growth of the structure into linear chains encapsulated by the organic n-Bu4N+ cations and the arrangement of the packed array of these chains, along with a stick representation of...

Fig. 6. The space-filling representation of the solid-state structure of the 1 1 complex formed between (7) and the potassium cation.

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