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Zinc in PDB 5wnp: Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus

Protein crystallography data

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 5wnp was solved by H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 3.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400.000, 400.000, 173.000, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.4

Other elements in 5wnp:

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus also contains other interesting chemical elements:

Magnesium (Mg) 253 atoms
Potassium (K) 22 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus (pdb code 5wnp). 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 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 5wnp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5wnp

Go back to Zinc Binding Sites List in 5wnp
Zinc binding site 1 out of 2 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:0.8
occ:1.00
SG D:CYS31 2.3 0.8 1.0
SG D:CYS9 2.3 0.2 1.0
SG D:CYS26 2.3 0.2 1.0
SG D:CYS12 2.3 0.1 1.0
CB D:CYS12 3.5 0.3 1.0
O D:LEU19 3.5 0.6 1.0
CB D:CYS9 3.6 0.9 1.0
CB D:CYS31 3.7 0.5 1.0
CB D:CYS26 3.7 1.0 1.0
O D:CYS31 3.7 0.2 1.0
CA D:CYS9 4.0 0.4 1.0
CA D:CYS31 4.2 1.0 1.0
CA D:CYS26 4.3 0.4 1.0
C D:CYS31 4.4 0.8 1.0
C D:LEU19 4.5 0.8 1.0
N D:CYS9 4.9 0.5 1.0
CA D:CYS12 4.9 0.4 1.0
N D:CYS26 5.0 0.2 1.0

Zinc binding site 2 out of 2 in 5wnp

Go back to Zinc Binding Sites List in 5wnp
Zinc binding site 2 out of 2 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn102

b:0.9
occ:1.00
SG N:CYS43 2.3 0.4 1.0
SG N:CYS27 2.3 0.2 1.0
SG N:CYS40 2.3 0.1 1.0
SG N:CYS24 2.3 0.8 1.0
CB N:CYS40 3.2 0.1 1.0
CB N:CYS27 3.2 0.3 1.0
CB N:CYS43 3.2 0.3 1.0
CB N:CYS24 3.4 0.0 1.0
N N:CYS27 3.7 0.3 1.0
N N:CYS40 3.7 0.4 1.0
N N:CYS43 3.9 0.9 1.0
CA N:CYS27 4.0 0.2 1.0
CA N:CYS40 4.0 0.4 1.0
CA N:CYS43 4.2 0.7 1.0
CB N:ARG29 4.3 0.3 1.0
C N:CYS27 4.6 0.0 1.0
CB N:ARG26 4.7 0.5 1.0
N2 A:G1202 4.7 0.4 1.0
C N:CYS40 4.7 0.3 1.0
N N:ARG29 4.7 0.2 1.0
N N:GLY28 4.8 0.2 1.0
C N:ARG26 4.8 0.1 1.0
CA N:CYS24 4.8 0.0 1.0
C N:LEU39 4.9 0.4 1.0
N3 A:G1202 5.0 0.9 1.0

Reference:

J.Choi, G.Indrisiunaite, H.Demirci, K.W.Ieong, J.Wang, A.Petrov, A.Prabhakar, G.Rechavi, D.Dominissini, C.He, M.Ehrenberg, J.D.Puglisi. 2'-O-Methylation in Mrna Disrupts Trna Decoding During Translation Elongation. Nat. Struct. Mol. Biol. V. 25 208 2018.
ISSN: ESSN 1545-9985
PubMed: 29459784
DOI: 10.1038/S41594-018-0030-Z
Page generated: Wed Dec 16 11:17:21 2020

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