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Zinc in PDB 4ji1: 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: 4ji1 was solved by H.Demirci, L.Wang, F.Murphy Iv, E.Murphy, J.Carr, S.Blanchard, G.Jogl, A.E.Dahlberg, S.T.Gregory, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.65 / 3.14
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 403.171, 403.171, 173.325, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.7

Other elements in 4ji1:

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

Magnesium (Mg) 325 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus (pdb code 4ji1). 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: 4ji1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4ji1

Go back to Zinc Binding Sites List in 4ji1
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:88.5
occ:1.00
SG D:CYS31 2.3 91.2 1.0
SG D:CYS9 2.3 80.3 1.0
SG D:CYS26 2.3 93.2 1.0
SG D:CYS12 2.3 96.2 1.0
O D:CYS31 3.5 0.5 1.0
CB D:CYS12 3.7 1.0 1.0
CB D:CYS9 3.8 83.1 1.0
CB D:CYS31 3.9 0.6 1.0
CB D:CYS26 4.0 81.5 1.0
CA D:CYS9 4.1 0.3 1.0
CA D:CYS31 4.3 0.4 1.0
C D:CYS31 4.3 1.0 1.0
CA D:CYS26 4.6 0.5 1.0
N D:LEU21 4.9 1.0 1.0
N D:TYR20 5.0 0.1 1.0
N D:CYS9 5.0 0.3 1.0

Zinc binding site 2 out of 2 in 4ji1

Go back to Zinc Binding Sites List in 4ji1
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:Zn101

b:0.3
occ:1.00
SG N:CYS43 2.3 0.1 1.0
SG N:CYS27 2.3 0.7 1.0
SG N:CYS24 2.3 0.2 1.0
SG N:CYS40 2.3 1.0 1.0
CB N:CYS43 3.3 0.9 1.0
CB N:CYS40 3.6 0.1 1.0
CB N:CYS27 3.6 0.3 1.0
N N:CYS27 3.7 0.4 1.0
CB N:CYS24 3.7 0.2 1.0
N N:CYS40 3.9 0.0 1.0
O N:ARG29 4.2 0.3 1.0
CA N:CYS27 4.2 0.6 1.0
N N:CYS43 4.2 0.2 1.0
CA N:CYS40 4.3 0.2 1.0
CA N:CYS43 4.3 0.2 1.0
CB N:ARG26 4.5 0.7 1.0
N2 A:G1202 4.6 1.0 1.0
O N:CYS40 4.7 0.8 1.0
N N:GLY28 4.7 0.7 1.0
C N:ARG26 4.8 0.9 1.0
C N:CYS40 4.8 1.0 1.0
C N:CYS27 4.9 0.2 1.0
N N:ARG26 4.9 0.6 1.0
CA N:ARG26 4.9 0.4 1.0
O N:CYS24 5.0 0.7 1.0
C N:LEU39 5.0 0.7 1.0

Reference:

H.Demirci, L.Wang, F.V.Murphy, E.L.Murphy, J.F.Carr, S.C.Blanchard, G.Jogl, A.E.Dahlberg, S.T.Gregory. The Central Role of Protein S12 in Organizing the Structure of the Decoding Site of the Ribosome. Rna V. 19 1791 2013.
ISSN: ISSN 1355-8382
PubMed: 24152548
DOI: 10.1261/RNA.040030.113
Page generated: Sun Oct 27 01:16:01 2024

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