Zinc in PDB 7bl6: 50S-Obge-Gmppnp Particle

The structure of 50S-Obge-Gmppnp Particle also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the 50S-Obge-Gmppnp Particle (pdb code 7bl6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the 50S-Obge-Gmppnp Particle, PDB code: 7bl6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the 50S-Obge-Gmppnp Particle


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 50S-Obge-Gmppnp Particle within 5.0Å range: probe atom residue distance (Å) B Occ g:Zn101 b:323.1 occ:1.00 ND1 g:HIS33 2.1 290.9 1.0 SG g:CYS11 2.3 278.0 1.0 SG g:CYS27 2.3 293.1 1.0 SG g:CYS14 2.3 281.1 1.0 CE1 g:HIS33 2.6 290.9 1.0 CG g:HIS33 2.6 290.9 1.0 NE2 g:HIS33 3.2 290.9 1.0 CD2 g:HIS33 3.3 290.9 1.0 CB g:HIS33 3.3 290.9 1.0 CB g:CYS11 3.6 278.0 1.0 CB g:CYS27 3.6 293.1 1.0 CB g:CYS14 3.8 281.1 1.0 N g:CYS11 4.0 278.0 1.0 O g:ASN13 4.0 285.1 1.0 C g:ASN13 4.0 285.1 1.0 N g:CYS14 4.0 281.1 1.0 CA g:CYS14 4.2 281.1 1.0 CA g:CYS11 4.2 278.0 1.0 C g:CYS11 4.5 278.0 1.0 O g:CYS11 4.6 278.0 1.0 N g:ASN13 4.6 285.1 1.0 CA g:ASN13 4.7 285.1 1.0 CA g:CYS27 4.7 293.1 1.0 CA g:HIS33 4.8 290.9 1.0 CB g:ASN13 4.9 285.1 1.0

Zinc binding site 2 out of 2 in the 50S-Obge-Gmppnp Particle


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 50S-Obge-Gmppnp Particle within 5.0Å range: probe atom residue distance (Å) B Occ d:Zn100 b:461.1 occ:1.00 SG d:CYS37 2.3 411.4 1.0 SG d:CYS16 2.3 436.9 1.0 N d:CYS37 2.3 411.4 1.0 CB d:CYS37 2.5 411.4 1.0 CA d:CYS37 2.9 411.4 1.0 C d:VAL36 3.1 418.2 1.0 CB d:CYS18 3.2 446.5 1.0 SG d:CYS18 3.4 446.5 1.0 CB d:CYS16 3.4 436.9 1.0 CA d:VAL36 3.5 418.2 1.0 C d:CYS37 3.9 411.4 1.0 CG2 d:VAL36 4.1 418.2 1.0 O d:VAL36 4.1 418.2 1.0 O d:LYS39 4.1 389.1 1.0 N d:CYS18 4.2 446.5 1.0 CA d:CYS18 4.2 446.5 1.0 CB d:ASN20 4.3 424.3 1.0 O d:CYS37 4.3 411.4 1.0 CB d:VAL36 4.4 418.2 1.0 N d:VAL36 4.5 418.2 1.0 SG d:CYS40 4.7 385.7 1.0 O d:ASP35 4.8 440.2 1.0 CA d:CYS16 4.8 436.9 1.0 N d:SER38 4.9 384.1 1.0 C d:CYS18 4.9 446.5 1.0 N d:ASN20 5.0 424.3 1.0

R.Nikolay, T.Hilal, S.Schmidt, B.Qin, D.Schwefel, C.H.Vieira-Vieira, T.Mielke, J.Burger, J.Loerke, K.Amikura, T.Flugel, T.Ueda, M.Selbach, E.Deuerling, C.M.T.Spahn. Snapshots of Native Pre-50S Ribosomes Reveal A Biogenesis Factor Network and Evolutionary Specialization. Mol.Cell V. 81 1200 2021.
ISSN: ISSN 1097-2765
PubMed: 33639093
DOI: 10.1016/J.MOLCEL.2021.02.006