Serine

Atom Label Key

Naming Convention for α-amino acids

The Organic acid carbon is labled the acid.
Each carbon afterwards is labeled in order by the greek alphabet
α, β, γ, δ, ε, etc.
Every atom is labeled by element type and then its position ie. the alpha carbon is CA; the beta carbon is CB

Atom Label	Description

C	Main chain Carbon of amide/acid
CA	Main chain α carbon
N	Main chain nitrogen of amide/amine
O	Main chain Oxygen of amide/acid
H	Main chain hydrogen of amide
HA	Main chain hydrogen of on the α carbon
CB	β Carbon, first carbon of the sidechain
HB?	Hydrogen on the β Carbon. '?' is a number 1,2 or 3
OG	Oxygen on the β Carbon.
CG?	γ Carbon. - the '?' if present is a number 1 or 2

The results are shown. The H from the -OH group on C6 is now on the amino acid side chain. The phosphate group has been transferred to the alcohol carbon of glucose and ADP is the other product.

Serine

Name

3 Letter

1 Letter

Serine

SER

protonated (acid form and neutral)
This is the dominant form
Serine

unprotonated (base form and negative)
There is very little of this under normal conditions

Drawn as if part of protein to emphasize the sidechain properties

The "Sidechain Polarity" button draws an an envelope around the sidechain that is colored by charge according to the scale above.

pK_R in H₂O= ~15

Free amino acid mass = 105 g/M

Probability of being found in a:

α-Helix

β-Sheet

β-Turn

50%

80%

Special Attributes

Polar amino acid can act as a hydrogen bond donor or acceptor. This is its most frequent role in structure. The pK of about 15 for the sidechain -OH is way above the physiological range. Normally deprotonation of this group can be ignored.

However, there are some exceptions that we will run into in this course. In the serine proteases (blood clotting enzymes) a serine is very close to a HIS in the active site. This special case has the effect of greatly lowering the pK and allowing it to deprotonate under physiological conditions. More on this in later modules

In the demonstration below, the SER is in a β-sheet and is exposed to water. It is safe to assume in this NORMAL case that the serine has a normal pK and is protonated and neutral.

In the demonstration below you may "left click and drag" to rotate the molecule "SHIFT left click and drag (up or down)" to make smaller or bigger
Click on the white squares in succession to turn or/off identifying features. Some text describing the issues is in the lower right text box

	Atom Label Description
	Click an atom to diplay it's identity here
	Messages about the currently highlighted features

Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/