Zinc in PDB 5zya: SF3B Spliceosomal Complex Bound to E7107

The structure of SF3B Spliceosomal Complex Bound to E7107 also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Zinc atom in the SF3B Spliceosomal Complex Bound to E7107 (pdb code 5zya). 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 Spliceosomal Complex Bound to E7107, PDB code: 5zya:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the SF3B Spliceosomal Complex Bound to E7107


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SF3B Spliceosomal Complex Bound to E7107 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:0.2 occ:1.00 SG D:CYS61 2.5 65.5 1.0 SG D:CYS23 2.5 68.4 1.0 SG D:CYS58 2.5 63.4 1.0 CB D:CYS26 3.1 63.4 1.0 SG D:CYS26 3.1 63.4 1.0 CB D:CYS61 3.6 65.5 1.0 CB D:CYS58 3.9 63.4 1.0 CB D:CYS23 3.9 68.4 1.0 N D:CYS61 4.0 65.5 1.0 N D:CYS23 4.3 68.4 1.0 CA D:CYS26 4.3 63.4 1.0 N D:CYS26 4.4 63.4 1.0 CA D:CYS61 4.4 65.5 1.0 O D:CYS23 4.4 68.4 1.0 CA D:CYS23 4.6 68.4 1.0 CB D:ILE60 4.6 59.1 1.0 C D:CYS23 4.8 68.4 1.0

Zinc binding site 2 out of 3 in the SF3B Spliceosomal Complex Bound to E7107


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SF3B Spliceosomal Complex Bound to E7107 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:0.2 occ:1.00 SG D:CYS46 2.5 62.0 1.0 SG D:CYS85 2.5 67.3 1.0 SG D:CYS11 2.6 71.9 1.0 SG D:CYS49 3.1 74.1 1.0 CB D:CYS11 3.4 71.9 1.0 CB D:CYS46 3.6 62.0 1.0 CB D:CYS49 3.9 74.1 1.0 CB D:CYS85 4.0 67.3 1.0 CD D:LYS13 4.3 66.8 1.0 CB D:LYS13 4.3 66.8 1.0 CG D:LYS13 4.5 66.8 1.0 N D:CYS49 4.6 74.1 1.0 NZ D:LYS13 4.7 66.8 1.0 CA D:CYS11 4.8 71.9 1.0 N D:LYS13 4.8 66.8 1.0 CA D:CYS49 4.9 74.1 1.0 CA D:CYS46 4.9 62.0 1.0 C D:CYS11 4.9 71.9 1.0 CB D:LYS87 4.9 63.7 1.0

Zinc binding site 3 out of 3 in the SF3B Spliceosomal Complex Bound to E7107


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SF3B Spliceosomal Complex Bound to E7107 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn203 b:0.2 occ:1.00 SG D:CYS33 2.4 47.7 1.0 SG D:CYS72 2.5 44.2 1.0 SG D:CYS30 2.5 52.1 1.0 SG D:CYS75 2.6 44.0 1.0 CB D:CYS30 3.6 52.1 1.0 CB D:CYS72 3.7 44.2 1.0 CB D:CYS75 3.7 44.0 1.0 CB D:CYS33 3.8 47.7 1.0 N D:CYS72 3.9 44.2 1.0 N D:CYS33 4.0 47.7 1.0 CA D:CYS72 4.3 44.2 1.0 CA D:CYS33 4.4 47.7 1.0 N D:CYS75 4.5 44.0 1.0 N D:ILE32 4.6 56.7 1.0 CA D:CYS75 4.7 44.0 1.0 N D:VAL31 4.8 53.3 1.0 CB D:SER35 4.9 56.3 1.0 O D:CYS72 4.9 44.2 1.0 C D:TYR71 4.9 42.9 1.0 CA D:CYS30 5.0 52.1 1.0 N D:ASP34 5.0 54.4 1.0 C D:CYS72 5.0 44.2 1.0 CB D:ILE32 5.0 56.7 1.0

L.I.Finci, X.Zhang, X.Huang, Q.Zhou, J.Tsai, T.Teng, A.Agrawal, B.Chan, S.Irwin, C.Karr, A.Cook, P.Zhu, D.Reynolds, P.G.Smith, P.Fekkes, S.Buonamici, N.A.Larsen. The Cryo-Em Structure of the SF3B Spliceosome Complex Bound to A Splicing Modulator Reveals A Pre-Mrna Substrate Competitive Mechanism of Action Genes Dev. V. 32 309 2018.
ISSN: ISSN 1549-5477
PubMed: 29491137
DOI: 10.1101/GAD.311043.117