Atomistry » Zinc » PDB 3sud-3t5z » 3t1h
Atomistry »
  Zinc »
    PDB 3sud-3t5z »
      3t1h »

Zinc in PDB 3t1h: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aaa-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 Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aaa-Codon in the A-Site and Paromomycin, PDB code: 3t1h was solved by F.V.Murphy, F.A.P.Vendeix, W.Cantara, G.Leszczynska, E.M.Gustilo, B.Sproat, A.A.P.Malkiewicz, P.F.Agris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.72 / 3.11
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.300, 402.300, 175.250, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 27.6

Other elements in 3t1h:

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aaa-Codon in the A-Site and Paromomycin also contains other interesting chemical elements:

Magnesium (Mg) 185 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aaa-Codon in the A-Site and Paromomycin (pdb code 3t1h). 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 Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aaa-Codon in the A-Site and Paromomycin, PDB code: 3t1h:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3t1h

Go back to Zinc Binding Sites List in 3t1h
Zinc binding site 1 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aaa-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 Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aaa-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:97.0
occ:1.00
SG D:CYS26 2.5 96.3 1.0
SG D:CYS9 2.5 77.7 1.0
SG D:CYS31 2.7 0.9 1.0
O D:CYS31 3.3 0.8 1.0
SG D:CYS12 3.4 72.3 1.0
O D:LEU19 3.7 98.0 1.0
CB D:CYS9 4.0 77.7 1.0
CB D:CYS26 4.1 96.3 1.0
CB D:CYS31 4.2 0.9 1.0
C D:CYS31 4.2 0.8 1.0
CA D:CYS9 4.3 81.3 1.0
CA D:CYS31 4.5 0.8 1.0
CB D:CYS12 4.5 72.3 1.0
CB D:LYS22 4.5 0.8 1.0
CA D:CYS26 4.6 99.8 1.0
C D:LEU19 4.9 98.0 1.0

Zinc binding site 2 out of 2 in 3t1h

Go back to Zinc Binding Sites List in 3t1h
Zinc binding site 2 out of 2 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Complexed with A Human Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aaa-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 Anti-Codon Stem Loop (Hasl) of Transfer Rna Lysine 3 (TRNALYS3) Bound to An Mrna with An Aaa-Codon in the A-Site and Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:69.8
occ:1.00
SG N:CYS43 2.0 57.6 1.0
SG N:CYS27 2.2 71.5 1.0
SG N:CYS40 2.5 63.3 1.0
CB N:CYS40 2.9 63.3 1.0
SG N:CYS24 3.1 69.5 1.0
CB N:CYS27 3.1 71.5 1.0
CB N:CYS24 3.4 69.5 1.0
N N:CYS27 3.4 72.9 1.0
CB N:ARG29 3.7 78.7 1.0
CB N:CYS43 3.8 57.6 1.0
CA N:CYS27 3.8 72.9 1.0
N N:CYS40 4.0 63.1 1.0
N N:ARG29 4.1 77.7 1.0
CA N:CYS40 4.1 63.1 1.0
N N:GLY28 4.2 76.1 1.0
CB N:ARG26 4.3 65.2 1.0
C N:ARG26 4.3 69.6 1.0
C N:CYS27 4.4 72.9 1.0
CA N:ARG29 4.6 77.7 1.0
CA N:ARG26 4.7 69.6 1.0
N3 A:G1183 4.8 67.2 1.0
N2 A:G1183 4.8 67.2 1.0
N N:CYS43 4.8 58.9 1.0
CG N:ARG29 4.8 78.7 1.0
CA N:CYS43 4.8 58.9 1.0
CA N:CYS24 4.9 71.5 1.0
N N:ARG26 4.9 69.6 1.0

Reference:

F.A.Vendeix, F.V.Murphy, W.A.Cantara, G.Leszczynska, E.M.Gustilo, B.Sproat, A.Malkiewicz, P.F.Agris. Human Trna(LYS3)(Uuu) Is Pre-Structured By Natural Modifications For Cognate and Wobble Codon Binding Through Keto-Enol Tautomerism. J.Mol.Biol. V. 416 467 2012.
ISSN: ISSN 0022-2836
PubMed: 22227389
DOI: 10.1016/J.JMB.2011.12.048
Page generated: Wed Dec 16 04:51:18 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy