Zinc in PDB 6en4: SF3B Core in Complex with A Splicing Modulator

The structure of SF3B Core in Complex with A Splicing Modulator, PDB code: 6en4 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)	48.79 / 3.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.067, 154.568, 210.207, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 26.6

The binding sites of Zinc atom in the SF3B Core in Complex with A Splicing Modulator (pdb code 6en4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the SF3B Core in Complex with A Splicing Modulator, PDB code: 6en4:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the SF3B Core in Complex with A Splicing Modulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SF3B Core in Complex with A Splicing Modulator within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:82.2 occ:1.00 SG D:CYS75 2.3 75.7 1.0 SG D:CYS33 2.3 90.5 1.0 SG D:CYS30 2.4 76.5 1.0 SG D:CYS72 2.4 87.3 1.0 CB D:CYS30 3.2 77.9 1.0 CB D:CYS72 3.2 74.5 1.0 CB D:CYS75 3.6 75.1 1.0 CB D:CYS33 3.6 85.3 1.0 N D:CYS72 3.8 81.2 1.0 N D:CYS33 3.9 88.5 1.0 CA D:CYS72 4.0 73.6 1.0 N D:CYS75 4.2 80.1 1.0 CA D:CYS33 4.3 84.7 1.0 CA D:CYS75 4.5 79.6 1.0 CA D:CYS30 4.6 81.1 1.0 CB D:ILE32 4.7 80.1 1.0 C D:CYS72 4.7 79.2 1.0 O D:CYS72 4.7 79.4 1.0 CB D:SER35 4.8 88.1 1.0 C D:CYS33 4.9 86.9 1.0 C D:ILE32 4.9 91.3 1.0 C D:TYR71 4.9 75.6 1.0 N D:ILE32 4.9 81.1 1.0

Zinc binding site 2 out of 3 in the SF3B Core in Complex with A Splicing Modulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SF3B Core in Complex with A Splicing Modulator within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:88.8 occ:1.00 SG D:CYS58 2.4 94.4 1.0 SG D:CYS61 2.4 89.4 1.0 SG D:CYS23 2.5 96.2 1.0 SG D:CYS26 3.1 0.5 1.0 CB D:CYS26 3.3 98.1 1.0 CB D:CYS23 3.5 88.9 1.0 CB D:CYS58 3.6 99.6 1.0 CB D:CYS61 3.7 88.4 1.0 N D:CYS61 3.8 92.1 1.0 N D:CYS23 3.9 78.9 1.0 N D:CYS26 4.0 88.7 1.0 CB D:ILE60 4.2 99.6 1.0 CA D:CYS23 4.2 88.5 1.0 CA D:CYS26 4.3 89.0 1.0 CA D:CYS61 4.3 85.7 1.0 CG2 D:ILE60 4.7 99.5 1.0 C D:CYS23 4.8 92.4 1.0 C D:ILE60 4.8 95.2 1.0 O D:CYS23 4.9 99.3 1.0 CA D:ILE60 4.9 92.5 1.0 N D:ILE60 4.9 87.1 1.0 N D:GLY62 4.9 86.9 1.0 CA D:CYS58 5.0 96.7 1.0

Zinc binding site 3 out of 3 in the SF3B Core in Complex with A Splicing Modulator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SF3B Core in Complex with A Splicing Modulator within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn103 b:73.5 occ:1.00 SG D:CYS11 2.3 83.0 1.0 SG D:CYS46 2.4 70.6 1.0 SG D:CYS49 2.4 80.1 1.0 SG D:CYS85 2.6 96.6 1.0 CB D:CYS11 3.0 72.7 1.0 CB D:CYS85 3.1 84.6 1.0 CB D:CYS49 3.2 73.2 1.0 CB D:CYS46 3.3 76.8 1.0 N D:CYS46 3.9 73.4 1.0 CA D:CYS46 4.2 78.0 1.0 N D:CYS49 4.3 84.8 1.0 CA D:CYS49 4.3 80.8 1.0 CA D:CYS11 4.5 74.5 1.0 CA D:CYS85 4.5 82.8 1.0 CB D:LYS13 4.6 86.2 1.0 CB D:LYS87 4.7 86.2 1.0 C D:CYS46 4.8 75.4 1.0 O D:CYS46 4.8 79.9 1.0 CD D:LYS13 4.9 93.8 1.0 C D:CYS85 4.9 83.2 1.0 N D:LYS13 4.9 81.9 1.0 C D:CYS11 4.9 80.5 1.0 O D:CYS85 5.0 89.0 1.0 CG D:LYS13 5.0 90.6 1.0

C.Cretu, A.A.Agrawal, A.Cook, C.L.Will, P.Fekkes, P.G.Smith, R.Luhrmann, N.Larsen, S.Buonamici, V.Pena. Structural Basis of Splicing Modulation By Antitumor Macrolide Compounds. Mol. Cell V. 70 265 2018.
ISSN: ISSN 1097-4164
PubMed: 29656923
DOI: 10.1016/J.MOLCEL.2018.03.011