[smilebabe]

Hi,

my chemical knowledge is very limited so I have really big problems to understand the following (from a paper):

Asp 34 can make up to three hydrogen bonds to peptide nitrogen atoms from residues 36 –38.
 This requires an appropriately positioned hydrogen-bond acceptor atom like OD1 of Asp or OD1 from Asn or OG1 from
Ser/Thr.

So my questions are:
1. What is OD1 in Asp
2. What is OG1 in Ser/Thr
3. I remember that O can make ONE hydrogen bonding with H, so how is it possible here that there are 3 hydrogen bonds to N (or is it NH3+)

Thanks for any *delete me*

[Arkcon]

This is a tough passage to figure out for me as well, I may not be as well caught up on the jargon, as I used to be.

OK, asparganine, can form 3 hydrogen bonds, with nitrogen's on other amino acids.  Can you find the 3 -H's on ASP available for hydrogen bonding?  Can you find the nitrogen hydrogen bond acceptors on asparganine, serine and threonine?  Can you use that info to discover what OD1 and OG1 mean?  (And can you tell us, I wanna know, too.)  Can you forget about oxygen hydrogen bonds, for now, because the passage mentions only nitrogen hydrogen bond acceptors?  Or is that impossible, and I'm misunderstanding the passage?

[aHerraez]

1. Caution: Asp = aspartic, different from asparagine = Asn

2. OD1 is a standard abbreviation in the PDB database for "Oxygen Delta 1", and OG1 for "Oxygen Gamma 1". That means they are, respectively, one of the Os in the carboxy group in the sidechain and the O in the hydroxyl group in the sidechain.

3. O has 2 electron pairs, so if can make two hydrogen bonds as acceptor. A hydroxyl group can additionalyy act as a donor, making 3 H bonds total. In fact, water HOH makes 4 H bonds in water and ice (2 donor, 2 acceptor).
An aspartic residue has in its sidechain carboxyl one carbonyl oxygen (C=O) that can make 2 bonds and one hydroxyl oxygen (C-OH) that can make up to 3 H bonds.
The peptide amino group, in turn, can make only one H bonds as it has a single electron pair, but the text you quote does not imply that there is a single N group involved: "to peptide nitrogen atoms from residues 36 to 38."