[phenixbb] distorted (collapsed) zinc-finger motifs

[Hasan Demirci]

Hi,

I am in the middle of refining a 3.5 A (low resolution)
ribonucleo-protein complex structure.
Two of the proteins in this complex contain "zinc-finger" motif.
These zinc-finger motifs instead of forming a cysteine-zinc
interactions, cysteines are forming di or in these case tetra-sulfide
bridges.
Initially, zinc is centered but after refinement 4 cysteines come out
collapsed and forming covalent bonds to each other and also distorted
and zinc is not at the center anymore.


Below is the phenix.refine zn_link.param file I am using.

Many thanks for advice,
Hasan Demirci
----------------------------------------------------------------------------


refinement.pdb_interpretation {
  disulfide_distance_cutoff = 0.1
}
refinement.pdb_interpretation.apply_cif_link {
  data_link = ZN-CYS
  residue_selection_1 = chain D and resname ZN and resid 306
  residue_selection_2 = chain D and resname CYS and resid 9
}
refinement.pdb_interpretation.apply_cif_link {
  data_link = ZN-CYS
  residue_selection_1 = chain D and resname ZN and resid 306
  residue_selection_2 = chain D and resname CYS and resid 12
}
refinement.pdb_interpretation.apply_cif_link {
  data_link = ZN-CYS
  residue_selection_1 = chain D and resname ZN and resid 306
  residue_selection_2 = chain D and resname CYS and resid 26
}
refinement.pdb_interpretation.apply_cif_link {
  data_link = ZN-CYS
  residue_selection_1 = chain D and resname ZN and resid 306
  residue_selection_2 = chain D and resname CYS and resid 31
}
refinement.pdb_interpretation.apply_cif_link {
  data_link = ZN-CYS
  residue_selection_1 = chain N and resname ZN and resid 307
  residue_selection_2 = chain N and resname CYS and resid 24
}
refinement.pdb_interpretation.apply_cif_link {
  data_link = ZN-CYS
  residue_selection_1 = chain N and resname ZN and resid 307
  residue_selection_2 = chain N and resname CYS and resid 27
}
refinement.pdb_interpretation.apply_cif_link {
  data_link = ZN-CYS
  residue_selection_1 = chain N and resname ZN and resid 307
  residue_selection_2 = chain N and resname CYS and resid 40
}
refinement.pdb_interpretation.apply_cif_link {
  data_link = ZN-CYS
  residue_selection_1 = chain N and resname ZN and resid 307
  residue_selection_2 = chain N and resname CYS and resid 43
}
#
data_link_ZN-CYS
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
 ZN-CYS   1 ZN      2 SG        single       2.340    0.020
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
 ZN-CYS   1 ZN      2 SG      2 CB      109.000    3.000

----------------------------------------------------------------------------------------------------



-- 
Hasan DeMirci, Ph.D.
Postdoctoral Fellow
Department of Molecular Biology, Cellular Biology & Biochemistry
Brown University
185 Meeting Street
Providence, RI    02912

(401) 863-3652 lab (SFH)
(401) 863-6124 lab (ship st)
(401) 226-7852 cell

Hasan_DeMirci at Brown.edu
demircha99 at gmail.com