Zinc in PDB 7b92: Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form II)

The structure of Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form II), PDB code: 7b92 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)	46.52 / 3.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.429, 107.429, 361.474, 90, 90, 120
R / Rfree (%)	22.3 / 25.8

The binding sites of Zinc atom in the Structure of A Minimal SF3B Core in Complex with Sudemycin D6 (Form II) (pdb code 7b92). 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 II), PDB code: 7b92:
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 II)


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:78.4 occ:1.00 SG D:CYS49 2.2 81.4 1.0 SG D:CYS11 2.3 69.4 1.0 SG D:CYS46 2.3 72.2 1.0 SG D:CYS85 2.7 83.6 1.0 CB D:CYS11 3.1 74.1 1.0 CB D:CYS85 3.3 74.9 1.0 CB D:CYS49 3.3 83.3 1.0 CB D:CYS46 3.7 79.0 1.0 CB D:LYS87 4.1 75.7 1.0 N D:CYS46 4.1 77.4 1.0 N D:CYS49 4.4 85.6 1.0 CA D:CYS46 4.4 79.0 1.0 CA D:CYS49 4.5 81.8 1.0 CA D:CYS11 4.6 83.1 1.0 CB D:LYS13 4.6 82.7 1.0 O D:CYS46 4.7 79.1 1.0 CA D:CYS85 4.8 67.3 1.0 CG D:LYS87 4.8 82.3 1.0 C D:CYS46 4.9 80.6 1.0 CD D:LYS13 4.9 75.1 1.0

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:69.7 occ:1.00 SG D:CYS75 2.3 74.7 1.0 SG D:CYS33 2.4 75.7 1.0 SG D:CYS72 2.4 67.4 1.0 SG D:CYS30 2.5 81.3 1.0 CB D:CYS75 3.4 70.4 1.0 CB D:CYS72 3.4 55.8 1.0 CB D:CYS33 3.4 81.4 1.0 CB D:CYS30 3.6 76.9 1.0 N D:CYS33 3.7 77.4 1.0 N D:CYS72 3.7 73.3 1.0 CA D:CYS72 4.1 65.6 1.0 CA D:CYS33 4.1 78.1 1.0 N D:CYS75 4.2 75.3 1.0 CB D:ILE32 4.3 75.0 1.0 CA D:CYS75 4.4 69.3 1.0 C D:ILE32 4.7 77.0 1.0 N D:ILE32 4.7 71.5 1.0 CA D:ILE32 4.8 74.9 1.0 C D:CYS72 4.8 70.3 1.0 C D:CYS33 4.8 81.0 1.0 CG2 D:ILE32 4.8 76.0 1.0 O D:CYS72 4.8 70.3 1.0 C D:TYR71 4.8 69.3 1.0 CA D:CYS30 5.0 71.5 1.0 CB D:SER35 5.0 80.0 1.0

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


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 II) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn103 b:97.9 occ:1.00 O D:HOH201 2.1 97.2 1.0 SG D:CYS61 2.3 101.2 1.0 SG D:CYS23 2.3 89.2 1.0 SG D:CYS58 2.7 84.5 1.0 CB D:CYS61 2.7 103.1 1.0 N D:CYS61 3.5 99.3 1.0 CA D:CYS61 3.7 106.8 1.0 CB D:CYS58 3.8 89.8 1.0 CB D:CYS23 3.8 93.9 1.0 N D:GLY62 4.3 101.2 1.0 CD D:LYS25 4.3 107.7 1.0 CB D:CYS26 4.4 94.3 1.0 C D:CYS61 4.5 107.2 1.0 CG D:LYS25 4.6 108.3 1.0 N D:CYS23 4.6 80.7 1.0 N D:CYS26 4.7 100.5 1.0 C D:ILE60 4.7 97.7 1.0 CB D:ILE60 4.7 85.2 1.0 CB D:LYS25 4.7 109.2 1.0 NZ D:LYS25 4.8 110.8 1.0 CA D:CYS23 4.8 87.1 1.0 N D:GLY63 4.8 100.5 1.0 C2 D:T2W104 5.0 101.5 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