Fig. 3: Zinc binding sites predicted by PMM. | Nature Communications

Fig. 3: Zinc binding sites predicted by PMM.

From: PinMyMetal: a hybrid learning system to accurately model transition metal binding sites in macromolecules

Fig. 3

a 1nik, wild-type RNA polymerase II, chain L, 4-residue zinc site, 2Fo − Fc map with 3.0 σ cutoff. b 2zp9, TRAP-Anti-TRAP complex, chain H, 4-residue zinc sites, 2Fo − Fc map with 1.0 σ cutoff. c 6xz7, E. coli 50S ribosomal subunit complex, chain e, 4-residue zinc site, EM map with 5.0 σ cutoff. d 6exv, mammalian RNA polymerase II subunit RPB7, chain I, 3-residue zinc site, EM map with 5.0 σ cutoff. e 7pw5, human SMG1-8-9 kinase complex, chain B, 4-residue zinc site, EM map with 5.0 σ cutoff. f PMM predicts a single zinc site in the cryo-EM structure 7lyt (CasPhi-2 (Cas12j) complex with crRNA and Phosphorothioate-DNA). EM map with 5.0 σ cutoff. CS: certainty score; Blue spheres represent predicted zinc sites, while gray spheres depict experimentally determined zinc sites; Electron density maps (2Fo − Fc or EM) are shown in gray mesh with optimal σ cutoff in the proximity of the metal sites. M method, Res resolution.

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