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1 BUILDING A STRUCTURAL MODEL OF KCSA 15

Selection Drawing Method Coloring Method

protein and chain C NewCartoon ColorID 6

chain C and resname CYS VDW Name

resname HIS and segname A and

chain C

VDW Name

chain C and segname A and

protein and within 5 of resname

HIS

Licorice Name

Since these residues are far away from each other, we can conclude that

there are no disulﬁde bonds present in the KcsA structure (Fig. 4 A). This

may not be the case for other proteins.

Figure 4: Inspecting the KcsA structure. (A) Cysteine and histidine residues.

No evident disulﬁde bonds or histidine protonation states can be observed. (B)

Charged residue. Notice how charged residues are distributed in solvent ac-

cessible areas. (C) Interaction b e tween residues Glutamate 71 (Glu71) and

Aspartate 80 (Glu80). One of these residues must share a proton with the

other.

Usually, visual inspection permits one to identify whether the side chain of a

histidine residue is involved in hydrogen bonding with surrounding molecules.

If that’s the case, one can then decide whether the δ nitrogen of histidine is

protonated (residue name “HSD”), the  nitrogen is protonated (“HSE”), or

both nitrogens are protonated (“HSP”).

8 Identify the histidines present in segment A.

The KcsA structure provided in 1K4C.pdb features two histidines (His25 and

His124). His124 lacks the side chain, and no obvious protonation state can be

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