Atomistry » Zinc » PDB 1i96-1im5 » 1ibl
Atomistry »
  Zinc »
    PDB 1i96-1im5 »
      1ibl »

Zinc in PDB 1ibl: Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin

Protein crystallography data

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin, PDB code: 1ibl was solved by J.M.Ogle, D.E.Brodersen, W.M.Clemons Jr., M.J.Tarry, A.P.Carter, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 316.23 / 3.11
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400.800, 400.800, 175.885, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / 27.5

Other elements in 1ibl:

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin also contains other interesting chemical elements:

Magnesium (Mg) 125 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin (pdb code 1ibl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin, PDB code: 1ibl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1ibl

Go back to Zinc Binding Sites List in 1ibl
Zinc binding site 1 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn306

b:20.0
occ:0.86
SG D:CYS9 2.1 51.7 1.0
SG D:CYS31 2.2 32.2 1.0
SG D:CYS26 2.4 42.3 1.0
SG D:CYS12 2.9 59.0 1.0
O D:CYS31 3.3 0.4 1.0
CB D:CYS9 3.5 51.7 1.0
CB D:CYS31 3.6 32.2 1.0
CA D:CYS31 3.8 0.4 1.0
CB D:CYS26 3.9 42.3 1.0
CA D:CYS9 4.0 94.8 1.0
C D:CYS31 4.0 0.4 1.0
O D:LEU19 4.0 0.0 1.0
CB D:CYS12 4.2 59.0 1.0
CA D:CYS26 4.3 0.7 1.0
N D:CYS9 4.7 94.8 1.0

Zinc binding site 2 out of 2 in 1ibl

Go back to Zinc Binding Sites List in 1ibl
Zinc binding site 2 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with A Messenger Rna Fragment and Cognate Transfer Rna Anticodon Stem-Loop Bound at the A Site and with the Antibiotic Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn307

b:20.0
occ:0.68
SG N:CYS43 2.3 41.9 1.0
SG N:CYS27 2.3 39.7 1.0
CB N:CYS27 2.5 39.7 1.0
SG N:CYS40 2.6 36.0 1.0
SG N:CYS24 2.7 46.0 1.0
CB N:CYS43 2.9 41.9 1.0
N N:CYS27 3.2 48.4 1.0
CA N:CYS27 3.5 48.4 1.0
CB N:CYS40 3.8 36.0 1.0
N N:CYS43 3.9 65.1 1.0
CB N:CYS24 4.0 46.0 1.0
N2 A:G1202 4.0 67.3 1.0
CA N:CYS43 4.0 65.1 1.0
CG N:ARG26 4.1 71.5 1.0
CB N:ARG26 4.2 71.5 1.0
N N:CYS40 4.3 79.7 1.0
C N:ARG26 4.4 88.7 1.0
C N:CYS27 4.5 48.4 1.0
CA N:CYS40 4.6 79.7 1.0
CB N:ARG29 4.7 79.0 1.0
N N:GLY28 4.7 76.5 1.0
O N:CYS40 4.8 79.7 1.0
N3 A:G1202 4.8 67.3 1.0
CA N:ARG26 4.8 88.7 1.0
C2 A:G1202 4.8 67.3 1.0
NE N:ARG26 4.9 71.5 1.0
C N:CYS40 5.0 79.7 1.0

Reference:

J.M.Ogle, D.E.Brodersen, W.M.Clemons Jr., M.J.Tarry, A.P.Carter, V.Ramakrishnan. Recognition of Cognate Transfer Rna By the 30S Ribosomal Subunit. Science V. 292 897 2001.
ISSN: ISSN 0036-8075
PubMed: 11340196
DOI: 10.1126/SCIENCE.1060612
Page generated: Wed Dec 16 02:52:47 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy