Zinc in PDB 6car: Serial Femtosecond X-Ray Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin

The structure of Serial Femtosecond X-Ray Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin, PDB code: 6car was solved by H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.26 / 3.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.600, 402.600, 175.900, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 26.6

The structure of Serial Femtosecond X-Ray Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin also contains other interesting chemical elements:

Magnesium

(Mg)

283 atoms

The binding sites of Zinc atom in the Serial Femtosecond X-Ray Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin (pdb code 6car). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Serial Femtosecond X-Ray Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin, PDB code: 6car:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Serial Femtosecond X-Ray Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Serial Femtosecond X-Ray Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:84.0 occ:1.00 SG D:CYS31 2.3 89.4 1.0 SG D:CYS26 2.3 88.2 1.0 SG D:CYS12 2.3 0.8 1.0 SG D:CYS9 2.3 87.6 1.0 O D:LEU19 3.5 0.7 1.0 O D:CYS31 3.5 0.3 1.0 CB D:CYS31 3.7 94.9 1.0 CB D:CYS12 3.8 0.7 1.0 CB D:CYS9 3.8 98.2 1.0 CB D:CYS26 3.8 91.8 1.0 CA D:CYS9 4.2 0.2 1.0 CA D:CYS31 4.2 0.3 1.0 CA D:CYS26 4.2 0.4 1.0 C D:CYS31 4.3 0.1 1.0 CB D:LYS22 4.4 0.5 1.0 C D:LEU19 4.6 0.7 1.0 N D:LEU19 4.8 0.2 1.0 CG D:LYS22 4.8 0.2 1.0 N D:CYS26 4.9 0.7 1.0

Zinc binding site 2 out of 2 in the Serial Femtosecond X-Ray Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Serial Femtosecond X-Ray Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn101 b:0.8 occ:1.00 SG N:CYS27 2.3 85.4 1.0 SG N:CYS40 2.3 90.0 1.0 SG N:CYS43 2.3 89.5 1.0 SG N:CYS24 2.3 0.4 1.0 CB N:CYS27 3.1 84.3 1.0 CB N:CYS43 3.2 89.2 1.0 CB N:CYS40 3.3 91.1 1.0 CB N:CYS24 3.6 0.8 1.0 N N:CYS27 3.7 87.7 1.0 N N:CYS40 3.7 91.1 1.0 CA N:CYS27 4.0 85.8 1.0 CB N:ARG29 4.0 0.3 1.0 N N:CYS43 4.0 88.6 1.0 CA N:CYS40 4.0 91.1 1.0 CA N:CYS43 4.2 88.8 1.0 N2 A:G1202 4.5 0.3 1.0 N N:ARG29 4.6 0.9 1.0 C N:CYS27 4.6 84.9 1.0 C N:CYS40 4.7 97.7 1.0 CB N:ARG26 4.8 88.1 1.0 C N:ARG26 4.8 91.1 1.0 N N:GLY28 4.8 87.4 1.0 O N:CYS40 4.9 98.1 1.0 N3 A:G1202 4.9 97.6 1.0 C N:LEU39 4.9 94.9 1.0 CA N:CYS24 4.9 0.4 1.0 CA N:ARG29 4.9 0.1 1.0 CG N:ARG29 5.0 0.2 1.0

M.E.O'sullivan, F.Poitevin, R.G.Sierra, C.Gati, E.H.Dao, Y.Rao, F.Aksit, H.Ciftci, N.Corsepius, R.Greenhouse, B.Hayes, M.S.Hunter, M.Liang, A.Mcgurk, P.Mbgam, T.Obrinsky, F.Pardo-Avila, M.H.Seaberg, A.G.Cheng, A.J.Ricci, H.Demirci. Aminoglycoside Ribosome Interactions Reveal Novel Conformational States at Ambient Temperature. Nucleic Acids Res. V. 46 9793 2018.
ISSN: ESSN 1362-4962
PubMed: 30113694
DOI: 10.1093/NAR/GKY693