Analyse the structures of Copper containing proteins and look
for errors Keep making protein structures more and more accurate
Relying on improved software and better knowledge of protein
structure
Slide 3
Difficulty in distinguish certain atoms Errors are kept because
its not a curated database.
Slide 4
Iron, Zinc, Calcium, Magnesium, Chlorine or Iodine, etc. Copper
Two stable oxidation states [Ar] s 1 d 10 Copper proteins
classification
Slide 5
Blue Proteins 2 Histidines, 1 Cysteine and 1 Methionine There
are about 50.000 proteins in this family CuN - Histidine S -
Methionine Cysteine - S
Slide 6
Slide 7
3 Histidines + Histidine or H 2 O or Methionine or Cysteine
Colorless CuN - Histidine X
Slide 8
Peptidylglycine - Hydroxylating Monooxygenase
Slide 9
Cu A Cu B
Slide 10
Binuclear centers: 3 Histidines and O 2 CuN - Histidine Cu O N
- Histidine O
Slide 11
*Deoxygenated state 4,6 *Oxygenated state 3,6 * Not validated
by us
Slide 12
REDUCED FORM - CUPROUS OXIDIZED FORM - CUPRIC [Ar] 4s 0 3d 10
Soft ion Soft ligands (S/P) C.N: 2, 3 and 4 [Ar] 4s 0 3d 9 Hard ion
Hard ligands (N/O) C.N: 4, 5 and 6
Slide 13
PDB Files: X-ray Crystallography Resolution better than 2.0 Cu
+ Cu 2+ Total Files 114562 Cu + Cu 2+ Used Files 35321
Slide 14
WHAT IF: Calculations SKPNOO GRSION Distances plot YASARA:
Pictures
Slide 15
Cu + Total Files 114 Files Used 35 Num of ligands Num of Copper
Ions 311 437 529 Geometry Num of Copper Ions Tetrahedral24 Other13
Ligands Num of Copper Ions 2 His, 1 Met, 1 Cys14 4 His7 Others3 Cu
2+ Total Files 562 Files Used 321 Num of ligands Num of Copper Ions
345 4384 5231 Geometry Num of Copper Ions Tetrahedral331 Square
Planar8 Other45 Ligands Num of Copper Ions 2 His, 1 Met, 1 Cys210 3
His, 1 H 2 O69 Others52
Slide 16
Geometry Num of Copper Ions Tetrahedral24 Regular tetrahedral14
Ligands Num of Copper Ions 2 His, 1 Met, 1 Cys13 3 Met, 1 SCN1
Geometry Num of Copper Ions Tetrahedral331 Regular tetrahedral215
Ligands Num of Copper Ions 2 His, 1 Met, 1 Cys149 3 His, 1 H 2 O43
Others23 13 Cu + ions (spread over 8 PDB files) and 149 Cu 2+ ions
(spread over 94 PDB files) distances plot
Slide 17
Average positions for all the intervenient residues in the
regular tetrahedrals difference between the average positions is of
0.6 , being this value close to the error expected in the X-ray
structure determination
Slide 18
When superposed, 5PCY* and 6PCY* show no differences in its
structures besides: a small change in a Proline residue, and a
rotation of an Imidazole ring by 180 about C - C . * Guss, J.M.,
Harrowell, P.R., Murata, M., Norris, V.A., Freeman, H.C. (1986).
Crystal Structure Analysis Of Reduced (Cu I) Poplar Plastocyanin At
Six pH Values. J.Mol. Biol 192 (1986): 361-387
Slide 19
No reason for the flipping of the Histidine At a resolution of
both 5PCY (1.80 ) and 6PCY (1.90 ) the Pro puckering tends to be
unobservable 5PCY6PCY
Slide 20
Too few data Coordination Numbers: For Cu + and Cu 2+ : most
often seen C.N. is 4, 5 and 3. Contradicting some older studies* No
differences between the structures of Cu + and Cu 2+ Contradicting
some older studies** *Belle, C., Rammal, W., Pierre, J.L., (2005).
Sulfur Ligation in Copper Enzymes and Models. Journal of Inorganic
Biochemistry 99: 1929-1936 **Taylor, M.K., Stevenson, D.E.,
Berlouis, L.E.A., Kennedy, A.R., Reglinski J. (2006). Modeling the
Impact of Geometric Parameters On The Redox Potential Of Blue
Copper Proteins. Journal of Inorganic Biochemistry 100:
250-259
Slide 21
For coppers with C.N. 4, the most common geometry is
tetrahedral Copper proteins classifications should be revised, for
example, Type II classification is ambiguous. Some older
publications should be reviewed
Slide 22
What distinguishes between both oxidation states for copper?
Are the differences too small to be detected? Are there any
differences at all? One of the possibilities to be studied would be
the protonation states for Histidine and Cysteine or other factors
like protein bond