Visualizing Proteins Using Chimera
Sarah Goodman
Active site of RNA Polymerase (1S0V)
DNA non-template
strand (yellow)
DNA Template strand
(blue)
RNA transcript (green)
RNA Polymerase (red)
TYR 639
Incoming
nucleotide
TYR 639
Hydroxyl
group
RNA transcript
Magnesium ion
Tyrosine 639 of RNA polymerase has a hydroxyl group, which allows it to distinguish
between DNA and RNA because the ribose sugar in RNA also has a hydroxyl group.
Complete Biological Assembly of 1HHO
Chain A 2
Chain A 1
Heme group
Chain B 1
Chain B 2
1HHO
Coordinating
Histidine
Chain A 1
Heme group
Coordinating
Histidine
This image shows Chain A of oxyhemoglobin
interacting with a heme group. The coordinating
histidine residues are shown in yellow.
Heme group and Oxygen in 1HHO
Oxygen
Iron
Heme group
The oxygen
molecule,
shown in red, is
stabilized by
the heme
group and the
iron in the
center of the
heme group
(brown).
2HHB and 1MBO structure alignment
Other chains
of
Hemoglobin
(yellow, blue,
and light
green)
Chain D of
Hemoglobin (red)
and Myoglobin
(purple)
The structure of Myoglobin (shown in purple) coincides
with the structure of Chain D of Hemoglobin (shown in
red). These two chains have a 24.66% identity.
Additional residues in the C-terminus
of 1MBO compared to 2HHB
Hemoglobin
Myoglobin
Both chains have an alpha helix towards
the C-terminus, but the alpha helix in
myoglobin is longer than the one in
hemoglobin by 6 residues. These
residues are alanine, alanine, tyrosine,
lysine, glutamic acid, and leucine. Two
additional residues , tyrosine and
glutamine, follow the alpha helix. Past
the last alpha helix, hemoglobin ends
with histidine, lysine, tyrosine, and
histidine. The additional residues at the
C-terminus of myoglobin could prevent
it from forming a tetramer with other
units of itself. The fact that the residues
toward the C-terminus are different for
both of these proteins could also
account for this difference because they
will have different chemical properties,
making them interact differently.
Hydrophilic regions in 1MBO account
for monomeric form
Myoglobin.
Hydrophobic
regions are
shown in purple.
Hemoglobin.
Hydrophobic regions
are shown in red.
Because Hemoglobin has more hydrophobic regions, it forms a tetramer to
prevent these regions from interacting with water. However, Myoglobin has
fewer hydrophobic surfaces, making it unnecessary for it to form a tetramer.