Hi Hasan, The pdb file you sent (zinc_finger.pdb) has heavily distorted geometry around the zinc finger, with the SG forming disulfide bonds and the ZN pushed far away from the center of the four SG. I suggest you discard that pdb file and go back to an earlier version where the geometry is still intact. Then phenix.refine should work automatically with the zn_link and apply_cif_link files as is. You can remove the disulfide_distance_cutoff re-assignment at the top of your apply_cif_link file. (I just tried 3a9j from the pdb and it works without a problem.) Ralf ----- Original Message ----

From: Hasan Demirci To: [email protected] Sent: Mon, December 6, 2010 5:47:28 PM Subject: [phenixbb] distorted (collapsed) zinc-finger motifs

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

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-- 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

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