Zinc in PDB 3oto: Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)

The structure of Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8), PDB code: 3oto was solved by H.Demirci, F.Murphy Iv, R.Belardinelli, A.C.Kelley, V.Ramakrishnan, S.T.Gregory, A.E.Dahlberg, G.Jogl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.84 / 3.69
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.089, 402.089, 173.254, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 23.1

The structure of Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) also contains other interesting chemical elements:

Magnesium	(Mg)	94 atoms
Potassium	(K)	42 atoms

The binding sites of Zinc atom in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) (pdb code 3oto). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8), PDB code: 3oto:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn210 b:85.2 occ:1.00 SG D:CYS31 2.3 57.0 1.0 SG D:CYS26 2.3 67.1 1.0 SG D:CYS9 2.4 53.4 1.0 SG D:CYS12 2.7 92.0 1.0 O D:LEU19 3.2 1.0 1.0 CB D:CYS9 3.6 0.6 1.0 CB D:CYS31 3.8 1.0 1.0 O D:CYS31 3.8 0.2 1.0 CA D:CYS9 3.8 0.7 1.0 CB D:CYS26 4.1 0.6 1.0 CA D:CYS31 4.2 0.0 1.0 CB D:CYS12 4.2 0.3 1.0 C D:LEU19 4.4 0.1 1.0 C D:CYS31 4.4 0.1 1.0 N D:LEU21 4.7 0.3 1.0 N D:CYS9 4.8 0.5 1.0 O D:CYS9 4.8 0.5 1.0 C D:CYS9 4.8 0.6 1.0 CA D:CYS26 4.9 0.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn141 b:0.3 occ:1.00 O N:CYS27 2.3 0.6 1.0 CB N:CYS27 2.5 0.7 1.0 C N:CYS27 2.6 0.5 1.0 SG N:CYS43 2.8 0.9 1.0 SG N:CYS40 2.9 0.8 1.0 CB N:ARG29 3.0 0.1 1.0 CA N:CYS27 3.1 0.5 1.0 N N:ARG29 3.1 0.8 1.0 N N:GLY28 3.4 0.9 1.0 CA N:ARG29 3.5 0.4 1.0 C N:GLY28 3.5 0.5 1.0 O2' A:G1202 3.7 0.2 1.0 CB N:CYS24 3.7 0.4 1.0 SG N:CYS24 3.8 0.1 1.0 CA N:GLY28 4.0 0.3 1.0 CG N:ARG29 4.0 0.1 1.0 CD N:ARG29 4.0 0.4 1.0 O N:GLY28 4.1 0.9 1.0 CB N:CYS40 4.1 1.0 1.0 SG N:CYS27 4.2 0.0 1.0 N N:CYS27 4.2 0.1 1.0 N3 A:G1202 4.5 0.5 1.0 CB N:CYS43 4.6 0.5 1.0 C2' A:G1202 4.7 0.7 1.0 C1' A:G1202 4.7 0.5 1.0 C N:ARG29 4.9 0.3 1.0 N2 A:G1202 5.0 0.8 1.0

H.Demirci, F.Murphy, R.Belardinelli, A.C.Kelley, V.Ramakrishnan, S.T.Gregory, A.E.Dahlberg, G.Jogl. Modification of 16S Ribosomal Rna By the Ksga Methyltransferase Restructures the 30S Subunit to Optimize Ribosome Function. Rna V. 16 2319 2010.
ISSN: ISSN 1355-8382
PubMed: 20962038
DOI: 10.1261/RNA.2357210