Atomistry » Zinc » PDB 1my2-1ndy » 1n32
Atomistry »
  Zinc »
    PDB 1my2-1ndy »
      1n32 »

Zinc in PDB 1n32: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin

Protein crystallography data

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin, PDB code: 1n32 was solved by J.M.Ogle, F.V.Murphy Iv, M.J.Tarry, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 141.42 / 3.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400.296, 400.296, 175.483, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 27

Other elements in 1n32:

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin also contains other interesting chemical elements:

Magnesium (Mg) 158 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin (pdb code 1n32). 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin, PDB code: 1n32:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1n32

Go back to Zinc Binding Sites List in 1n32
Zinc binding site 1 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn306

b:24.8
occ:0.68
SG D:CYS31 2.0 44.5 1.0
SG D:CYS9 2.1 45.9 1.0
SG D:CYS26 2.3 59.4 1.0
SG D:CYS12 2.9 60.8 1.0
O D:LEU19 3.6 0.2 1.0
CB D:CYS31 3.6 44.5 1.0
CB D:CYS9 3.8 45.9 1.0
O D:CYS31 3.8 0.3 1.0
CB D:CYS26 3.9 59.4 1.0
CA D:CYS31 4.2 0.3 1.0
CA D:CYS9 4.2 0.8 1.0
CB D:CYS12 4.4 60.8 1.0
CA D:CYS26 4.5 82.0 1.0
C D:CYS31 4.5 0.3 1.0
C D:LEU19 4.8 0.2 1.0

Zinc binding site 2 out of 2 in 1n32

Go back to Zinc Binding Sites List in 1n32
Zinc binding site 2 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with 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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn307

b:24.8
occ:0.55
SG N:CYS43 1.9 41.6 1.0
SG N:CYS27 2.1 55.0 1.0
SG N:CYS24 2.4 66.3 1.0
SG N:CYS40 2.5 56.1 1.0
CB N:CYS27 2.7 55.0 1.0
N N:CYS27 3.4 68.1 1.0
CB N:CYS24 3.6 66.3 1.0
CA N:CYS27 3.6 68.1 1.0
CB N:CYS43 3.6 41.6 1.0
CB N:CYS40 3.7 56.1 1.0
N2 A:G1202 4.0 66.2 1.0
CB N:ARG26 4.2 63.2 1.0
N N:CYS43 4.3 52.1 1.0
N N:CYS40 4.4 0.7 1.0
C N:ARG26 4.4 86.5 1.0
CB N:ARG29 4.5 98.2 1.0
C N:CYS27 4.6 68.1 1.0
N N:GLY28 4.6 85.3 1.0
CA N:CYS40 4.6 0.7 1.0
CA N:CYS43 4.6 52.1 1.0
N3 A:G1202 4.7 66.2 1.0
CG N:ARG26 4.7 63.2 1.0
CD N:ARG26 4.7 63.2 1.0
CA N:ARG26 4.8 86.5 1.0
C2 A:G1202 4.9 66.2 1.0
N N:ARG29 4.9 88.1 1.0
O N:CYS40 4.9 0.7 1.0
N N:ARG26 5.0 86.5 1.0
CA N:CYS24 5.0 76.6 1.0

Reference:

J.M.Ogle, F.V.Murphy Iv, M.J.Tarry, V.Ramakrishnan. Selection of Trna By the Ribosome Requires A Transition From An Open to A Closed Form Cell(Cambridge,Mass.) V. 111 721 2002.
ISSN: ISSN 0092-8674
PubMed: 12464183
DOI: 10.1016/S0092-8674(02)01086-3
Page generated: Wed Oct 16 17:10:05 2024

Last articles

As in 2J6E
As in 2IWR
As in 2J13
As in 2IYO
As in 2IUC
As in 2IM2
As in 2IA5
As in 2IM1
As in 2IM0
As in 2ILZ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy