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Zinc in PDB 2uu9: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Valine-Asl with CMO5U in Position 34 Bound to An Mrna with A Gug-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 Gug-Codon in the A-Site and Paromomycin., PDB code: 2uu9 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 (°) 400.943, 400.943, 174.219, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.8

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 Gug-Codon in the A-Site and Paromomycin. (pdb code 2uu9). 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 Gug-Codon in the A-Site and Paromomycin., PDB code: 2uu9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2uu9

Go back to Zinc Binding Sites List in 2uu9
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 Gug-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 Gug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:42.5
occ:1.00
SG D:CYS31 2.1 53.0 1.0
SG D:CYS26 2.3 55.2 1.0
SG D:CYS9 2.3 46.7 1.0
SG D:CYS12 2.7 50.7 1.0
O D:CYS31 3.1 70.7 1.0
CB D:CYS31 3.4 63.0 1.0
CA D:CYS31 3.7 67.8 1.0
C D:CYS31 3.8 70.0 1.0
CB D:CYS26 3.8 62.6 1.0
O D:LEU19 3.9 66.8 1.0
CB D:CYS9 4.0 53.2 1.0
CB D:CYS12 4.2 52.8 1.0
CA D:CYS26 4.3 64.8 1.0
CA D:CYS9 4.5 55.0 1.0
CD D:LYS22 4.6 66.5 1.0

Zinc binding site 2 out of 2 in 2uu9

Go back to Zinc Binding Sites List in 2uu9
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 Gug-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 Gug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn102

b:55.2
occ:1.00
SG N:CYS27 1.9 49.5 1.0
SG N:CYS43 2.0 44.2 1.0
SG N:CYS40 2.4 51.2 1.0
SG N:CYS24 2.6 60.5 1.0
CB N:CYS27 3.0 51.1 1.0
CB N:CYS40 3.1 53.2 1.0
CB N:CYS43 3.2 44.9 1.0
N N:CYS27 3.6 53.3 1.0
CB N:CYS24 3.7 57.9 1.0
N N:CYS40 3.8 54.6 1.0
CB N:ARG29 3.8 60.2 1.0
CA N:CYS27 3.8 52.9 1.0
CA N:CYS40 4.0 54.2 1.0
N N:CYS43 4.1 48.9 1.0
CA N:CYS43 4.2 46.9 1.0
O N:CYS40 4.4 54.4 1.0
C N:ARG26 4.5 52.6 1.0
N2 A:G1202 4.5 62.6 1.0
C N:CYS27 4.5 53.8 1.0
CB N:ARG26 4.6 50.6 1.0
C N:CYS40 4.6 54.3 1.0
N N:ARG29 4.6 60.4 1.0
CG N:ARG29 4.7 60.1 1.0
N N:GLY28 4.8 56.0 1.0
CG N:ARG26 4.9 49.9 1.0
CA N:ARG29 4.9 60.5 1.0
CA N:ARG26 4.9 52.2 1.0
N3 A:G1202 4.9 61.3 1.0

Reference:

A.Weixlbaumer, F.V.Murphy 4Th., 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: Sat Sep 26 03:55:59 2020
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