Zinc in PDB 7omf: Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I)

The structure of Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I), PDB code: 7omf was solved by C.Cretu, V.Pena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.03 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.355, 109.846, 253.3, 90, 90, 90
R / Rfree (%)	23.2 / 26.6

The binding sites of Zinc atom in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I) (pdb code 7omf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I), PDB code: 7omf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:105.4 occ:1.00 SG D:CYS23 2.3 100.4 1.0 SG D:CYS58 2.3 99.8 1.0 SG D:CYS61 2.3 126.7 1.0 S D:SCN105 2.4 119.9 1.0 CB D:CYS58 3.3 101.8 1.0 CB D:CYS61 3.5 105.2 1.0 CB D:CYS23 3.8 110.2 1.0 N D:CYS61 3.9 105.2 1.0 C D:SCN105 4.1 115.6 1.0 CA D:CYS61 4.3 111.0 1.0 CB D:ILE60 4.4 112.4 1.0 N D:CYS23 4.6 93.5 1.0 C D:ILE60 4.7 109.8 1.0 SG D:CYS26 4.7 107.5 1.0 CA D:CYS58 4.8 99.6 1.0 CA D:CYS23 4.8 101.7 1.0 N D:ILE60 4.8 100.3 1.0 CB D:CYS26 4.8 100.9 1.0 CA D:ILE60 4.8 111.5 1.0 CG1 D:ILE60 5.0 107.3 1.0

Zinc binding site 2 out of 3 in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:99.6 occ:1.00 SG D:CYS46 2.3 86.3 1.0 SG D:CYS11 2.3 85.2 1.0 SG D:CYS49 2.3 91.4 1.0 SG D:CYS85 2.4 96.3 1.0 CB D:CYS11 3.0 84.8 1.0 CB D:CYS85 3.3 88.2 1.0 CB D:CYS49 3.5 93.2 1.0 CB D:CYS46 3.6 93.1 1.0 N D:CYS46 4.0 90.7 1.0 CA D:CYS46 4.4 94.4 1.0 CB D:LYS87 4.4 97.9 1.0 CA D:CYS11 4.5 85.1 1.0 N D:CYS49 4.5 104.2 1.0 CA D:CYS49 4.6 92.8 1.0 CB D:LYS13 4.7 92.3 1.0 CA D:CYS85 4.7 79.5 1.0 C D:CYS11 5.0 88.6 1.0 C D:CYS46 5.0 95.6 1.0

Zinc binding site 3 out of 3 in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn103 b:80.9 occ:1.00 SG D:CYS33 2.3 88.6 1.0 SG D:CYS75 2.3 83.2 1.0 SG D:CYS72 2.3 90.2 1.0 SG D:CYS30 2.3 84.8 1.0 CB D:CYS33 3.3 90.1 1.0 CB D:CYS75 3.3 74.7 1.0 CB D:CYS72 3.4 74.5 1.0 CB D:CYS30 3.5 91.0 1.0 N D:CYS33 3.7 90.3 1.0 N D:CYS72 3.8 80.2 1.0 CA D:CYS33 4.1 85.1 1.0 N D:CYS75 4.1 87.3 1.0 CA D:CYS72 4.2 80.8 1.0 CA D:CYS75 4.3 81.1 1.0 CB D:ILE32 4.5 77.1 1.0 C D:ILE32 4.7 87.1 1.0 C D:CYS33 4.8 86.9 1.0 N D:ILE32 4.9 87.2 1.0 CA D:CYS30 4.9 91.0 1.0 C D:CYS72 4.9 82.2 1.0 CA D:ILE32 4.9 88.1 1.0

C.Cretu, P.Gee, X.Liu, A.Agrawal, T.V.Nguyen, A.K.Ghosh, A.Cook, M.Jurica, N.A.Larsen, V.Pena. Structural Basis of Intron Selection By U2 Snrnp in the Presence of Covalent Inhibitors. Nat Commun V. 12 4491 2021.
ISSN: ESSN 2041-1723
PubMed: 34301950
DOI: 10.1038/S41467-021-24741-1