Zinc in PDB 8s1p: Ylmh Bound to Ptrna-50S

The structure of Ylmh Bound to Ptrna-50S also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Potassium	(K)	47 atoms
Magnesium	(Mg)	158 atoms

The binding sites of Zinc atom in the Ylmh Bound to Ptrna-50S (pdb code 8s1p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Ylmh Bound to Ptrna-50S, PDB code: 8s1p:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ 4:Zn101 b:44.0 occ:1.00 ND1 4:HIS32 2.1 40.5 1.0 SG 4:CYS11 2.3 48.3 1.0 SG 4:CYS27 2.3 47.9 1.0 SG 4:CYS14 2.3 44.3 1.0 CE1 4:HIS32 3.1 41.1 1.0 CG 4:HIS32 3.1 39.5 1.0 CB 4:CYS27 3.4 47.9 1.0 CB 4:HIS32 3.4 37.1 1.0 CB 4:CYS11 3.5 47.1 1.0 N 4:CYS14 3.5 53.1 1.0 CB 4:CYS14 3.5 48.4 1.0 CA 4:CYS14 3.7 50.2 1.0 N 4:CYS11 3.8 46.5 1.0 CA 4:CYS11 4.1 48.2 1.0 NE2 4:HIS32 4.2 40.4 1.0 CD2 4:HIS32 4.2 39.3 1.0 C 4:LYS13 4.3 56.6 1.0 C 4:CYS11 4.4 53.9 1.0 O 4:CYS11 4.5 56.3 1.0 CB 4:ASN29 4.6 51.3 1.0 CB 4:LYS13 4.7 67.2 1.0 N 4:LYS13 4.7 61.3 1.0 CA 4:CYS27 4.8 47.4 1.0 C 4:ILE10 4.8 45.0 1.0 CA 4:LYS13 4.8 62.0 1.0 CA 4:HIS32 4.9 36.2 1.0 CB 4:ILE10 4.9 44.2 1.0 O 4:LYS13 5.0 57.1 1.0 N 4:ILE10 5.0 41.7 1.0

Zinc binding site 2 out of 4 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn5001 b:468.8 occ:1.00 SG 6:CYS39 2.3 477.2 1.0 SG 6:CYS18 2.3 469.3 1.0 SG 6:CYS16 2.3 458.5 1.0 SG 6:CYS36 2.3 463.7 1.0 CB 6:CYS39 3.2 478.0 1.0 N 6:CYS36 3.2 457.4 1.0 CB 6:CYS36 3.3 460.8 1.0 CB 6:CYS16 3.3 454.4 1.0 CB 6:CYS18 3.4 467.2 1.0 CA 6:CYS36 3.7 458.6 1.0 N 6:CYS39 3.8 471.9 1.0 CA 6:CYS39 4.1 478.1 1.0 N 6:CYS18 4.1 466.3 1.0 O 6:CYS36 4.3 458.2 1.0 C 6:CYS36 4.3 457.5 1.0 C 6:ILE35 4.3 456.7 1.0 CA 6:CYS18 4.4 465.9 1.0 CA 6:ILE35 4.6 456.8 1.0 CA 6:CYS16 4.6 451.4 1.0 C 6:GLU38 4.7 464.6 1.0 ND2 6:ASN20 4.8 445.2 1.0 N 6:ALA17 4.9 460.3 1.0 O 6:GLU34 4.9 455.0 1.0 C 6:CYS16 4.9 455.9 1.0 N 6:GLU38 4.9 456.7 1.0

Zinc binding site 3 out of 4 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ 0:Zn5001 b:39.4 occ:1.00 SG 0:CYS33 2.3 46.4 1.0 SG 0:CYS43 2.3 37.1 1.0 SG 0:CYS30 2.3 42.2 1.0 SG 0:CYS46 2.3 41.2 1.0 CB 0:CYS43 3.2 35.0 1.0 CB 0:CYS30 3.2 41.6 1.0 CB 0:CYS33 3.3 48.0 1.0 CB 0:CYS46 3.4 43.2 1.0 N 0:CYS33 3.7 51.6 1.0 N 0:CYS46 3.9 45.6 1.0 CA 0:CYS33 4.1 49.2 1.0 CA 0:CYS46 4.3 43.5 1.0 CB 0:SER32 4.4 55.5 1.0 CB 0:ALA45 4.7 48.0 1.0 CA 0:CYS43 4.7 34.6 1.0 CA 0:CYS30 4.7 42.8 1.0 N 0:GLY34 4.7 50.8 1.0 C 0:CYS33 4.7 50.0 1.0 C 0:SER32 4.8 53.0 1.0 CB 0:SER48 5.0 41.3 1.0 OG 0:SER32 5.0 59.2 1.0 C 0:CYS46 5.0 42.5 1.0

Zinc binding site 4 out of 4 in the Ylmh Bound to Ptrna-50S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ylmh Bound to Ptrna-50S within 5.0Å range: probe atom residue distance (Å) B Occ 1:Zn101 b:44.0 occ:1.00 OD2 1:ASP39 2.0 48.9 1.0 SG 1:CYS36 2.3 39.2 1.0 SG 1:CYS12 2.3 51.1 1.0 SG 1:CYS9 2.3 41.5 1.0 CG 1:ASP39 2.5 48.7 1.0 OD1 1:ASP39 3.0 48.7 1.0 CB 1:CYS12 3.3 52.9 1.0 CB 1:CYS36 3.3 38.5 1.0 CB 1:CYS9 3.4 43.0 1.0 CB 1:ASP39 3.6 49.0 1.0 N 1:CYS12 3.8 56.8 1.0 CA 1:CYS12 4.1 53.8 1.0 N 1:ASP39 4.1 48.5 1.0 OG1 1:THR43 4.4 48.9 1.0 CB 1:GLU11 4.4 62.1 1.0 CA 1:ASP39 4.5 48.8 1.0 CB 1:ARG38 4.6 55.3 1.0 CG2 1:THR43 4.7 49.3 1.0 CA 1:CYS36 4.7 37.7 1.0 ND2 1:ASN16 4.7 40.4 1.0 CA 1:CYS9 4.8 43.1 1.0 C 1:GLU11 4.9 59.4 1.0 C 1:CYS12 5.0 52.6 1.0

H.Takada, H.Paternoga, K.Fujiwara, J.A.Nakamoto, E.N.Park, L.Dimitrova-Paternoga, B.Beckert, M.Saarma, T.Tenson, A.R.Buskirk, G.C.Atkinson, S.Chiba, D.N.Wilson, V.Hauryliuk. A Role For the S4-Domain Containing Protein Ylmh in Ribosome-Associated Quality Control in Bacillus Subtilis. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38811035
DOI: 10.1093/NAR/GKAE399