Atomistry » Zinc » PDB 4gfj-4gsc » 4gkj
Atomistry »
  Zinc »
    PDB 4gfj-4gsc »
      4gkj »

Zinc in PDB 4gkj: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aug-Codon in the A-Site and Paromomycin.

Protein crystallography data

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aug-Codon in the A-Site and Paromomycin., PDB code: 4gkj was solved by W.A.Cantara, F.V.Murphy Iv, J.L.Spears, H.Demirci, P.F.Agris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.15 / 3.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400.550, 400.550, 176.190, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.2

Other elements in 4gkj:

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aug-Codon in the A-Site and Paromomycin. also contains other interesting chemical elements:

Magnesium (Mg) 186 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aug-Codon in the A-Site and Paromomycin. (pdb code 4gkj). 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 Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aug-Codon in the A-Site and Paromomycin., PDB code: 4gkj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4gkj

Go back to Zinc Binding Sites List in 4gkj
Zinc binding site 1 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aug-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 Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:64.9
occ:1.00
SG D:CYS31 2.1 65.8 1.0
SG D:CYS26 2.3 86.5 1.0
SG D:CYS9 2.3 64.8 1.0
SG D:CYS12 2.6 62.8 1.0
CB D:CYS31 3.6 67.4 1.0
CB D:CYS26 4.0 86.2 1.0
CB D:CYS9 4.1 64.0 1.0
CB D:CYS12 4.1 62.0 1.0
CA D:CYS31 4.5 68.1 1.0
CG D:LYS22 4.6 89.4 1.0
CD D:LYS22 4.6 90.0 1.0
CA D:CYS9 4.7 62.7 1.0
CA D:CYS26 4.7 86.4 1.0
N D:TYR20 4.8 95.4 1.0
N D:LEU21 5.0 62.9 1.0
CA D:TYR20 5.0 95.9 1.0

Zinc binding site 2 out of 2 in 4gkj

Go back to Zinc Binding Sites List in 4gkj
Zinc binding site 2 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aug-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 Human Mitochondrial Anticodon Stem Loop (Asl) of Transfer Rna Methionine (Trnamet) Bound to An Mrna with An Aug-Codon in the A-Site and Paromomycin. within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn102

b:73.0
occ:1.00
SG N:CYS27 2.2 71.4 1.0
SG N:CYS43 2.2 71.7 1.0
SG N:CYS40 2.3 71.0 1.0
SG N:CYS24 2.3 74.2 1.0
CB N:CYS27 3.1 71.7 1.0
CB N:CYS24 3.1 74.4 1.0
CB N:CYS40 3.2 72.0 1.0
CB N:CYS43 3.3 72.2 1.0
N N:CYS27 3.8 74.0 1.0
N N:CYS40 4.0 73.9 1.0
CB N:ARG29 4.0 99.2 1.0
CA N:CYS27 4.0 73.0 1.0
N N:CYS43 4.0 70.3 1.0
CA N:CYS40 4.2 72.8 1.0
CA N:CYS43 4.3 71.2 1.0
N2 A:G1183 4.6 68.8 1.0
CA N:CYS24 4.6 75.8 1.0
C N:CYS27 4.6 73.1 1.0
N N:ARG29 4.6 99.3 1.0
N N:GLY28 4.7 74.5 1.0
C N:CYS40 4.7 72.0 1.0
CB N:ARG26 4.8 75.2 1.0
C N:ARG26 4.8 74.7 1.0
N3 A:G1183 4.9 68.1 1.0
O N:CYS40 4.9 72.3 1.0
CG N:ARG29 4.9 99.3 1.0
CA N:ARG29 5.0 99.6 1.0

Reference:

W.A.Cantara, F.V.Murphy, H.Demirci, P.F.Agris. Expanded Use of Sense Codons Is Regulated By Modified Cytidines in Trna. Proc.Natl.Acad.Sci.Usa V. 110 10964 2013.
ISSN: ISSN 0027-8424
PubMed: 23781103
DOI: 10.1073/PNAS.1222641110
Page generated: Wed Dec 16 05:20:06 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy