Stick representation

Left side of Fig. 4 shows a ribbon model of the catalytic (C-) subunit of the mammalian cAMP-dependent protein kinase. This was the first protein kinase whose structure was determined [35]. Figure 4 includes also a ribbon model of the peptide substrate, and ATP (stick representation) with two manganese ions (CPK representation). All kinetic evidence is consistent with a preferred ordered mechanism of catalysis with ATP binding proceeding substrate binding. 

Fig. 4.1.13 A ribbon representation of the crystal structure of recombinant acquorin molecule showing the secondary structure elements in the protein. Alpha-helices are denoted in cyan, beta-sheet in yellow, loops in magenta coelenterazine (yellow) and the side chain of tyrosine 184 are shown as stick representations. From Head et al., 2000, with permission from Macmillan Publishers.

When they were challenged by another gronp to really explain the occnrrence of the transformation, they constracted more than one ball and stick representations for each species in order to snpport the production of their model. Moreover, the students discussed their colleagues models, making it evident that they had nnderstood other models of representation. 

Fig. 18.2 Ball and stick representations of the crystal packing of (a) CsCujClj, (b) (HjNMejjCujClj and (c) (NMe4)Cu2Cl3.

Ball-and-stick representations of two forms of metasilicates, the six-Si ring of beryl left) and a portion of the linear chain of jade right). 

Ball-and-stick representation and stmctural formula common to all of the naturally occurring amino acids. 

Figure 17.5 The protein environment around the Cu centers (gold spheres) of laccase from Melanocarpus albomyces (PDB file IGWO) showing a substrate O2 molecule bound in the trinuciear Cu site [Hakulinen et al., 2002], The protein is depicted in stick representation with atoms in their conventional coloring. (Courtesy of Armand W. J. W. Tepper.) (See color insert.)...

Fig. 3.2 Superposition of E. coli and S. aureus PDF. Comparison of the overall structure of E. coli PDF (Blue, PDB code 2A18 ) and S. aureus PDF (mangenta, PDB code 2A19). The bound nickel is shown in red and His-132, His-136 and Cys-90 from E. coli PDF are shown as ball and stick representation.

Fig. 5. Ball and stick representations of [Fei2(SePh)24] in the side-on view, the carbon atoms of the phenyl rings have been omitted for clarity.

Fig. 6. Ball and stick representation of (>-[Na2FeIKS .(lls Na atoms, crosshatched spheres the Na-S bonds are drawn as dotted lines.

Fig. 7. Ball and stick representations of (a) Na C Fee[N(CH2CH20)3]6 i and (b) Cs C Fe8[N(CH2CH20)3lg +, showing the template effect of the alkaline cation.

Fig. 9. Ball and stick representations of [Ni24(OH)8(mpo)16(02CMe)24(Hmpo)i6] and trinuclear oligomer.

Fig. 15. Ball and stick representations of (a) [P4Mo6028(OH)3]9 (P4MoGOe), (b) [P4Mo6S3025(OH)3]9 (P4MogS303), (c) [P4Mo6S6022(0H)3]9- (P4Mo6S6) (d) their common polyhedral representation (e) a view of the dimeric species formed by an M2+ ion (M = Cr, Mn, Fe, Co, Ni, Zn, Cd) or a sodium cation sandwiched by two P4Mo6EG units.

Fig. 12 (A) The d(CGCGAATTCGCG)2 duplex with a narrow groove and a sodium ion coordinated at the ApT step. (I) The DNA is shown in stick representation and the ion in space-filling size. Left view is directly into the central minor groove. Right view left view rotated 90° counterclockwise and tilted 30° to show the ion in the minor groove. (II) The base pair views are of the central ApT step. Top view is down the helix axis, bottom view is directly into the minor groove. (B) The DNA duplex with a phosphate-oxygen pair-sodium ion interaction and a water molecule coordinated at the ApT step. (II) Views as in Fig. 12A for the phosphate-ion-water-base complex at the AT site. Reproduced with permission from Ref. (42). Copyright 2000, American Chemical Society.

Figure 14-11. Snapshots from the conformational switch path explored in the vicinity of the active conformation (unfolded docked conformation) and starting from the inactive (undocked) conformation found in crystal. Stems A and B were aligned (best fitted) and are shown in yellow, different instances of stem C are shown in stick representation with different colors. A schematic of the non-canonical binding scheme of the ligation site is shown in the right panel and the general mechanism of ligation in the left panel...

Fig. 5.1. Ribbon diagram of a fluorescent protein (citrine, PDB entry 1HUI) crystal structure. The chromophore is buried in the protein s interior and shown in balls and sticks representation.

Fig. 10.6 (A) Stick representation of the packing of 3 in the crystal, showing the formation of directional tubular conduction pathways (B) schematic representation ofthe hierarchically organized system 3 (top) self-organization in solution and (bottom) sol-gel transcription of encoded molecular features into a hybrid heteropolysiloxane matrix [18].

Fig. 10.7 Crystal structure of com pounds 4 stick representation of H-bond (dotted lines) superstructures of (A) phenyl, (B) indole, (C) phenol ureido-silsesquioxanes H atoms were omitted for clarity.

Fig. 14 Ball and stick representation of trinuclear complexes with M = Co or Mn (hydrogen atoms have been removed for simplicity). Coordination details are given separately (in the circle) where, for simplicity, we have removed aromatic rings of benzoates as well as TTF—CH=CH—py...

Fig. 8. Lck SH2 domain-peptide complex (Ac-cmF-Glu-Glu-Ile-OH, 12) revealing the twopronged plug engaging a two-holed socket 1 binding mode, reminiscent of the majority of SH2 domains (Protein Databank entry code 1BHF.PDB [118]). The protein is depicted in a Connolly surface mode, the ligand is given in a ball-and-stick representation. The cmF residue is deeply buried in its binding pocket (left)...

Fig. 2. Ball-and-stick representations of two differently oriented asparagine ladders of (A) W-arcade taken from the crystal structures of pectate lyase C (Lietzke et al., 1996) and (b) ppl-arcade taken from l DP-.V-aretylglucosamine acyltransferase (Raetz and Roderick, 1995). b, l, and so on refer to a one-letter conformational code (Fig. IOC). The ladders are viewed from within the respective /(-solenoids. The arrow shows the orientation (N- to C-terminal) of the solenoid. Oxygen atoms are in red, nitrogen in blue, and carbon in green. Dotted lines designate H-bonds of side chains (red) and inter-coil H-bonds of the polypeptide backbone (black). Except for the ladder-forming asparagines, only the backbones of the coils are shown. Panels are reprinted from Hennetin et al. (2006) with the permission of the publisher.

Fig. 3. A gallery of structures representative of the distinct /8-solenoid groups shown in Tables I and II. The /8-solenoid domains are in blue and other domains are in yellow. In the oligomeric structures, only one subunit is colored while the other ones are gray. Small ligand molecules are shown in the ball-and-stick representation and colored magenta.

Fig. 4. Representative structures of the distinct types of coil shapes, viewed along the //-solenoid axis. The structures shown are limited to two coils. The /1-strands are shown as red arrows connected by loops. The side chains are shown in the ball-and-stick representation and colored gray.

Fig. 4. The molecular structure, determined by solution NMR (James et al., 1997), of Syrian hamster 90-231 (SHa90-231) prion with ball-and-stick representation of the HI domain (SHal09-122 MKHMAGAAAAGAW). Note that two short /(-chains (SI, S2) nearly stack in the hydrogen-bonding direction. If the palindromic polyalanine region was also in a /(-conformation, there would be a three-stranded /(-sheet. The structural difference between PrPc and PrPSc is in the 90-145 domain. [Model drawn using MOLSCRIPT (Kraulis, 1991)].

B) Surface and stick representation of the model, viewed down the fibril axis. (The top coil is shown as sticks, with the remainder showing van derWaals radii.) The glutamine side chains are proposed to form hydrogen-bonded stacks parallel to the fibril axis. The large diameter of the cylinder results in a pore down the center. Both panels were generated with Pymol (DeLano, 2002). 

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.)...

Ro 05-8733. The ligand is shown in a ball-and-stick representation the protein backbone is displayed by tubes connecting the C atoms. White balls along the protein backbone indicate residues for which a difference in chemical shift greater than 0.2 ppm was observed. 

Fig. 3.5. MoeB-catalyzed reaction. (A) Structure of the MoeB-MoaD heterodimer with MoaD in yellow and MoeB in red. Atoms in MoeB are shown as gray spheres representing their van der Waals radii and are rendered transparent. Residues 75 to 81 of MoaD, the AMP and sulfate molecule are shown in ball-and-stick representation. (B) Close-up stereo...

Fig. 7. Structure of the singly-bridged Au-oxo complex, 3. Top left, combination polyhedral/ball-and-stick representation right, thermal ellipsoid plot. The PO4 and WOe polyhedra (or W atom) are shown in lighter and darker gray. Bottom left. X-ray structure of the coordination polyhedron...

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