Zinc in PDB 5br8: Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin

The structure of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin, PDB code: 5br8 was solved by R.G.Sierra, C.Gati, H.Laksmono, E.H.Dao, S.Gul, F.Fuller, J.Kern, R.Chatterjee, M.Ibrahim, A.Brewster, I.D.Young, T.Michels-Clark, A.Aquila, L.Mengning, M.S.Hunter, J.E.Koglin, S.Boutet, E.A.Junco, B.Hayes, M.J.Bogan, C.Y.Hampton, E.V.Puglisi, N.K.Sauter, C.A.Stan, A.Zouni, J.Yano, V.K.Yachandra, S.M.Soltis, J.D.Puglisi, H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.84 / 3.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.300, 401.300, 176.400, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.4

The structure of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin also contains other interesting chemical elements:

Magnesium

(Mg)

287 atoms

The binding sites of Zinc atom in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin (pdb code 5br8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin, PDB code: 5br8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:83.5 occ:1.00 SG D:CYS31 2.3 0.0 1.0 SG D:CYS9 2.3 68.0 1.0 SG D:CYS26 2.3 83.1 1.0 SG D:CYS12 2.3 75.7 1.0 O D:CYS31 3.4 0.3 1.0 CB D:CYS12 3.6 87.5 1.0 CB D:CYS26 3.7 0.1 1.0 CB D:CYS9 3.7 88.2 1.0 O D:LEU19 3.8 0.8 1.0 CB D:CYS31 3.9 0.5 1.0 CA D:CYS9 4.1 0.5 1.0 CA D:CYS26 4.1 0.7 1.0 CA D:CYS31 4.2 0.7 1.0 C D:CYS31 4.2 0.1 1.0 N D:CYS9 4.9 0.2 1.0 CG D:LYS18 5.0 0.0 1.0 CB D:LYS22 5.0 0.8 1.0 CB D:MET33 5.0 0.5 1.0

Zinc binding site 2 out of 2 in the Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn101 b:0.2 occ:1.00 SG N:CYS43 2.3 80.8 1.0 SG N:CYS27 2.3 92.0 1.0 SG N:CYS40 2.3 96.8 1.0 SG N:CYS24 2.3 0.8 1.0 CB N:CYS24 3.2 0.7 1.0 CB N:CYS43 3.3 76.6 1.0 CB N:CYS27 3.3 92.5 1.0 CB N:CYS40 3.4 96.3 1.0 N N:CYS27 3.6 0.4 1.0 N N:CYS40 3.8 94.5 1.0 CA N:CYS27 4.0 94.6 1.0 CB N:ARG29 4.1 0.0 1.0 N N:CYS43 4.1 75.0 1.0 CA N:CYS40 4.1 98.8 1.0 CA N:CYS43 4.3 78.8 1.0 CB N:ARG26 4.4 93.8 1.0 N2 A:G1202 4.6 0.3 1.0 C N:CYS27 4.6 0.2 1.0 CA N:CYS24 4.7 0.1 1.0 N N:ARG29 4.7 0.1 1.0 C N:CYS40 4.7 0.9 1.0 N N:GLY28 4.8 0.4 1.0 C N:ARG26 4.8 0.2 1.0 O N:CYS40 4.8 0.9 1.0 N3 A:G1202 4.9 93.6 1.0 C N:LEU39 4.9 92.1 1.0

R.G.Sierra, C.Gati, H.Laksmono, E.H.Dao, S.Gul, F.Fuller, J.Kern, R.Chatterjee, M.Ibrahim, A.Brewster, I.D.Young, T.Michels-Clark, A.Aquila, L.Mengning, M.S.Hunter, J.E.Koglin, S.Boutet, E.A.Junco, B.Hayes, M.J.Bogan, C.Y.Hampton, E.V.Puglisi, N.K.Sauter, C.A.Stan, A.Zouni, J.Yano, V.K.Yachandra, S.M.Soltis, J.D.Puglisi, H.Demirci. Ambient-Temperature Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Paromomycin To Be Published.