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Zinc in PDB 2uuc: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gua-Codon in the A-Site and Paromomycin.

Protein crystallography data

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gua-Codon in the A-Site and Paromomycin., PDB code: 2uuc was solved by A.Weixlbaumer, F.V.Murphy, A.Dziergowska, A.Malkiewicz, F.A.P.Vendeix, P.F.Agris, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.89 / 3.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400.965, 400.965, 174.368, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24.5

Other elements in 2uuc:

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gua-Codon in the A-Site and Paromomycin. also contains other interesting chemical elements:

Magnesium (Mg) 184 atoms
Potassium (K) 56 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gua-Codon in the A-Site and Paromomycin. (pdb code 2uuc). 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 Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gua-Codon in the A-Site and Paromomycin., PDB code: 2uuc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2uuc

Go back to Zinc Binding Sites List in 2uuc
Zinc binding site 1 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gua-Codon in the A-Site and 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 Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gua-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:69.6
occ:1.00
SG D:CYS31 2.0 71.8 1.0
SG D:CYS9 2.3 55.4 1.0
SG D:CYS26 2.4 72.2 1.0
SG D:CYS12 3.0 65.1 1.0
CB D:CYS31 3.6 78.6 1.0
O D:CYS31 3.6 86.9 1.0
O D:LEU19 3.7 82.7 1.0
CB D:CYS9 3.9 62.5 1.0
CB D:CYS26 3.9 76.2 1.0
CA D:CYS31 4.2 82.7 1.0
CA D:CYS9 4.3 64.8 1.0
C D:CYS31 4.3 84.4 1.0
CB D:CYS12 4.4 64.4 1.0
CA D:CYS26 4.4 78.6 1.0
CD D:LYS22 4.8 82.7 1.0
C D:LEU19 4.9 80.5 1.0

Zinc binding site 2 out of 2 in 2uuc

Go back to Zinc Binding Sites List in 2uuc
Zinc binding site 2 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gua-Codon in the A-Site and 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 Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gua-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:64.0
occ:1.00
SG N:CYS43 1.9 48.8 1.0
SG N:CYS27 2.1 51.7 1.0
SG N:CYS24 2.4 61.9 1.0
SG N:CYS40 2.5 53.9 1.0
CB N:CYS27 2.9 52.3 1.0
CB N:CYS40 3.2 53.3 1.0
CB N:CYS43 3.3 49.8 1.0
CB N:CYS24 3.5 60.4 1.0
N N:CYS27 3.7 55.3 1.0
CA N:CYS27 3.8 54.7 1.0
N N:CYS40 3.9 55.8 1.0
N N:CYS43 4.1 52.4 1.0
CB N:ARG29 4.1 63.0 1.0
CA N:CYS40 4.1 54.2 1.0
CA N:CYS43 4.3 51.1 1.0
C N:ARG26 4.4 55.2 1.0
N2 A:G1202 4.5 69.3 1.0
CB N:ARG26 4.6 55.0 1.0
C N:CYS27 4.6 55.6 1.0
O N:CYS40 4.7 53.2 1.0
CG N:ARG26 4.7 53.4 1.0
C N:CYS40 4.7 53.9 1.0
N N:ARG29 4.8 61.7 1.0
N N:GLY28 4.9 57.0 1.0
CA N:ARG26 4.9 55.7 1.0
N3 A:G1202 4.9 66.5 1.0
CA N:CYS24 4.9 59.8 1.0

Reference:

A.Weixlbaumer, F.V.Murphy, A.Dziergowska, A.Malkiewicz, F.A.Vendeix, P.F.Agris, V.Ramakrishnan. Mechanism For Expanding the Decoding Capacity of Transfer Rnas By Modification of Uridines. Nat. Struct. Mol. Biol. V. 14 498 2007.
ISSN: ISSN 1545-9993
PubMed: 17496902
DOI: 10.1038/NSMB1242
Page generated: Wed Dec 16 03:53:45 2020

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