Zinc in PDB 7evn: The Cryo-Em Structure of the DDX42-SF3B Complex

All present enzymatic activity of The Cryo-Em Structure of the DDX42-SF3B Complex:
3.6.4.13;

The binding sites of Zinc atom in the The Cryo-Em Structure of the DDX42-SF3B Complex (pdb code 7evn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the The Cryo-Em Structure of the DDX42-SF3B Complex, PDB code: 7evn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the The Cryo-Em Structure of the DDX42-SF3B Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Cryo-Em Structure of the DDX42-SF3B Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:42.4 occ:1.00 SG D:CYS72 2.3 18.2 1.0 SG D:CYS75 2.3 17.5 1.0 SG D:CYS33 2.4 21.9 1.0 SG D:CYS30 2.4 19.5 1.0 CB D:CYS33 3.3 21.9 1.0 CB D:CYS30 3.4 19.5 1.0 CB D:CYS75 3.4 17.5 1.0 CB D:CYS72 3.6 18.2 1.0 N D:CYS33 3.8 21.9 1.0 N D:CYS72 4.1 18.2 1.0 N D:CYS75 4.1 17.5 1.0 CA D:CYS33 4.2 21.9 1.0 CA D:CYS75 4.3 17.5 1.0 CA D:CYS72 4.4 18.2 1.0 CB D:ILE32 4.5 19.9 1.0 CG2 D:ILE32 4.7 19.9 1.0 C D:ILE32 4.8 19.9 1.0 CA D:CYS30 4.8 19.5 1.0 C D:CYS33 4.9 21.9 1.0 C D:CYS72 5.0 18.2 1.0

Zinc binding site 2 out of 3 in the The Cryo-Em Structure of the DDX42-SF3B Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Cryo-Em Structure of the DDX42-SF3B Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:48.6 occ:1.00 SG D:CYS61 2.3 29.6 1.0 SG D:CYS23 2.4 29.2 1.0 SG D:CYS58 2.4 27.7 1.0 SG D:CYS26 2.5 33.4 1.0 CB D:CYS61 3.2 29.6 1.0 CB D:CYS58 3.4 27.7 1.0 CB D:CYS23 3.6 29.2 1.0 N D:CYS61 3.6 29.6 1.0 CA D:CYS61 3.9 29.6 1.0 N D:CYS23 4.1 29.2 1.0 CB D:CYS26 4.2 33.4 1.0 CA D:CYS23 4.4 29.2 1.0 N D:GLY62 4.4 29.1 1.0 N D:CYS26 4.5 33.4 1.0 CB D:ILE60 4.6 25.7 1.0 C D:CYS61 4.6 29.6 1.0 N D:GLY63 4.6 29.6 1.0 O D:CYS26 4.7 33.4 1.0 C D:ILE60 4.7 25.7 1.0 CA D:CYS58 4.8 27.7 1.0 CA D:CYS26 4.9 33.4 1.0 C D:CYS23 5.0 29.2 1.0 CA D:ILE60 5.0 25.7 1.0

Zinc binding site 3 out of 3 in the The Cryo-Em Structure of the DDX42-SF3B Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Cryo-Em Structure of the DDX42-SF3B Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn203 b:44.2 occ:1.00 SG D:CYS11 2.3 21.1 1.0 SG D:CYS46 2.4 21.5 1.0 SG D:CYS85 2.5 20.0 1.0 SG D:CYS49 2.6 27.6 1.0 CB D:CYS85 3.1 20.0 1.0 CB D:CYS11 3.2 21.1 1.0 CB D:CYS49 3.4 27.6 1.0 CB D:CYS46 3.5 21.5 1.0 N D:CYS46 4.1 21.5 1.0 CA D:CYS46 4.3 21.5 1.0 N D:CYS49 4.4 27.6 1.0 CA D:CYS49 4.5 27.6 1.0 CB D:LYS13 4.5 19.1 1.0 CA D:CYS85 4.6 20.0 1.0 CB D:LYS87 4.6 24.1 1.0 CA D:CYS11 4.7 21.1 1.0 CD D:LYS13 4.8 19.1 1.0 C D:CYS46 4.9 21.5 1.0 O D:CYS46 4.9 21.5 1.0 N D:LYS13 5.0 19.1 1.0

X.Zhang, X.Zhan, F.Yang, T.Bian, Y.Lu, Y.Shi. Structural Mechanisms of the Rna Helicases DDX42 and PRP5 in Pre-Spliceosome Assembly To Be Published.