Backbone carbonyl groups

Once the pore is open, K+ ions appear to move outward in single file. Analysis of crystals shows four K+ ions interacting with the backbone carbonyl groups of the amino acid residues that form the ion selectivity filter (Fig. 6-8B). It is thought that two K+ ions occupy sites 1 and 3 (Fig. 6-8B, orange) and then switch to sites 2 and 4 (gray). The K+ ion in site 4 would dissociate into the extracellular space, the K+ ion in site 2 would move to site 3 and another... 

Fig. 6. Mechanisms for the reduction of compounds I and II of HRP C by ferulic acid, after Henriksen et al. 195). This scheme is based on new information from the 1.45 A resolution crystal structure of the ternary complex of ferulic acid and cyanide-ligated HRP C 195). The direction of proton transfer is indicated by the dotted arrows. The mechanism is discussed in Section IV,B,2, and the crystal structure data in Section IV,F,4. Note that a distal site water molecule makes an important hydrogen bond with the backbone carbonyl group of Prol39 (a residue conserved in all members of the plant peroxidase superfamily).

All sidechains in X and Y positions of the triple helix are exposed to solvent and appear to have multiple options of interacting through solvent and with available backbone carbonyl groups, in addition to sidechain-sidechain interactions. NMR studies on collagen fibrils show there are two interconverting conformations of Leu in fibrils, and considerable reorientation around the helix axis (Batchelder et al., 1982 Sarkar et al., 1983). This suggests there may be switching between alternative interaction sets in solution and even in fibrils. Thus, the sidechain orientations and interactions seen in the crystal structure may represent one of a number of possibilities, rather than a uniquely determined interaction. 

Figure 24 Stereo views of (A) computed39 179 and (B) X-ray180 structures of gramicidin S, showing (among other things) a hydrogen bond between the ornithine side chain and the phenylalanine backbone carbonyl group.

Thrombin binds sodium better than potassium. The cation is bound by backbone carbonyl groups of Arg22 la and Lys224 and by four buried water molecules. One water molecule connects the sodium ion to OD2 of Asp819 this accounts for the primary specificity of the enzyme. When sodium is released, Asp819 reorients and this perturbation extends to the catalytic site. 

A conserved aspartate residue (Asp 351) that binds a phosphoryl group ties in the P domain. The designation bb refers to backbone carbonyl groups. [Drawn from lSU4.pdb.]... 

Mn and Ca ions are large magenta and yellow spheres, respectively. All putative metal coordinating sidechains and backbone carbonyl groups are shown, with N, O, and S atoms in blue, red, and yellow, respectively. The carbonyl and sidechain oxygens of S123 are marked O and O7, respectively. 

In contrast to the case of tryptophan the photoreactions with tyrosine and histidine probably involve hydrogen atom transfer as the primary step. There are several indications for this. First, 0-methylated tyrosine (p-methoxy phenylalanine) did not show any photo-CIDNP effect and its reactivity as a photo-reductant towards flavins is strongly reduced (19). Similarly, 1-N-methyl histidine is not polarized at high pH (> 7.5), when no abstractable hydrogen is present. Secondly, in the protein ribonuclease A, which has a well known 3-dimensional structure, the residues Tyr 92 and His 105 have exposed rings, but their OH and NH protons are hydrogen bonded to backbone carbonyl groups. 

Electron-Capture Dissociation BCD is applicable to ESI-produced multiply charged peptide ions [101,102]. It is most conveniently implemented in an FT-ICR instrument. Multiply protonated peptides [M - - nH]"+, capture a low-energy (<0.2 eV) electron to produce an odd-electron ion [M - -nH] " +, which dissociates rapidly via an energetic H transfer to the backbone carbonyl group to form c and z sequence-specific ions ... 

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