Zinc in PDB 4yhh: Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline

Protein crystallography data

The structure of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline, PDB code: 4yhh was solved by A.Schedlbauer, T.Kaminishi, B.Ochoa-Lizarralde, N.Dhimole, S.Zhou, J.P.Lopez-Alonso, S.R.Connell, P.Fucini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.72 / 3.42
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 409.590, 409.590, 171.730, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 28.7

Other elements in 4yhh:

The structure of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline also contains other interesting chemical elements:

Magnesium (Mg) 103 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline (pdb code 4yhh). 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 Thermus Thermophilus in Complex with Tigecycline, PDB code: 4yhh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4yhh

Go back to Zinc Binding Sites List in 4yhh
Zinc binding site 1 out of 2 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline


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 Thermus Thermophilus in Complex with Tigecycline within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:0.2
occ:1.00
SG D:CYS26 2.5 0.0 1.0
SG D:CYS31 2.7 0.9 1.0
CB D:LYS22 2.7 0.1 1.0
N D:LYS22 2.7 0.1 1.0
SG D:CYS9 2.9 0.1 1.0
SG D:CYS12 3.0 0.6 1.0
CA D:LYS22 3.2 0.6 1.0
CG D:LYS22 3.5 0.9 1.0
O D:LEU19 3.5 0.9 1.0
CB D:CYS9 3.6 84.6 1.0
CB D:CYS26 3.6 0.1 1.0
C D:LEU21 3.9 0.6 1.0
N D:LEU21 3.9 0.6 1.0
CA D:CYS9 4.1 0.6 1.0
CB D:CYS31 4.1 0.8 1.0
CB D:CYS12 4.2 0.3 1.0
N D:CYS9 4.4 0.9 1.0
C D:LYS22 4.4 0.6 1.0
CA D:LEU21 4.4 0.9 1.0
N D:GLY23 4.6 0.8 1.0
C D:LEU19 4.7 0.9 1.0
CA D:CYS26 4.8 0.9 1.0
CD D:LYS22 4.8 0.4 1.0
CB D:LEU21 4.9 0.1 1.0
C D:TYR20 4.9 0.8 1.0
O D:LEU21 4.9 0.6 1.0
CA D:TYR20 4.9 0.1 1.0
C D:VAL8 5.0 0.6 1.0

Zinc binding site 2 out of 2 in 4yhh

Go back to Zinc Binding Sites List in 4yhh
Zinc binding site 2 out of 2 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline


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 Thermus Thermophilus in Complex with Tigecycline within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:0.8
occ:1.00
SG N:CYS27 2.7 0.7 1.0
SG N:CYS40 2.8 0.9 1.0
SG N:CYS24 2.8 0.3 1.0
CB N:CYS40 2.9 0.7 1.0
CB N:CYS24 3.0 0.2 1.0
SG N:CYS43 3.2 0.7 1.0
N N:CYS40 3.5 0.6 1.0
CA N:CYS40 3.8 0.5 1.0
CB N:CYS43 4.0 0.9 1.0
O N:ARG29 4.0 0.1 1.0
CB N:ARG29 4.3 0.3 1.0
CB N:CYS27 4.4 0.6 1.0
CA N:CYS24 4.5 0.6 1.0
N N:ARG29 4.5 0.8 1.0
C N:CYS40 4.6 0.2 1.0
C N:LEU39 4.6 0.7 1.0
N N:CYS43 4.7 0.6 1.0
N N:CYS27 4.8 1.0 1.0
CA N:ARG29 4.8 0.4 1.0
C N:ARG29 4.9 0.9 1.0
N N:GLY28 4.9 0.2 1.0
CA N:CYS43 5.0 0.7 1.0
CA N:CYS27 5.0 0.8 1.0

Reference:

A.Schedlbauer, T.Kaminishi, B.Ochoa-Lizarralde, N.Dhimole, S.Zhou, J.P.Lopez-Alonso, S.R.Connell, P.Fucini. Structural Characterization of An Alternative-Binding Mode For Tigecycline to the Bacterial Ribosome. Antimicrob.Agents Chemother. 2015.
ISSN: ESSN 1098-6596
PubMed: 25753625
DOI: 10.1128/AAC.04895-14
Page generated: Wed Dec 16 05:57:29 2020

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