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Potassium in PDB 3ugq: Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution

Enzymatic activity of Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution

All present enzymatic activity of Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution:
6.1.1.3;

Protein crystallography data

The structure of Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution, PDB code: 3ugq was solved by K.M.Peterson, J.Ling, I.Simonovic, C.Cho, D.Soll, M.Simonovic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.46 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.970, 67.970, 191.367, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25

Other elements in 3ugq:

The structure of Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution (pdb code 3ugq). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution, PDB code: 3ugq:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 3ugq

Go back to Potassium Binding Sites List in 3ugq
Potassium binding site 1 out of 4 in the Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K468

b:59.4
occ:1.00
 OG A:SER190 4.0 40.7 1.0
OG1 A:THR188 4.1 23.6 1.0
CB A:THR188 4.2 27.6 1.0
CB A:SER190 4.3 34.1 1.0
CD A:PRO189 4.4 30.6 1.0
N A:SER190 4.4 28.9 1.0
N A:PRO189 4.8 31.6 1.0
CG A:PRO189 4.8 32.9 1.0
CB A:PRO189 4.9 33.8 1.0

Potassium binding site 2 out of 4 in 3ugq

Go back to Potassium Binding Sites List in 3ugq
Potassium binding site 2 out of 4 in the Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K469

b:62.8
occ:1.00
 ZN A:ZN1 3.7 24.9 1.0
OE1 A:GLN180 3.8 39.3 1.0
O4 A:SO42 3.9 53.4 1.0
O2 A:SO42 3.9 47.7 1.0
NE2 A:GLN292 4.0 23.4 1.0
OE1 A:GLN292 4.3 25.9 1.0
OD1 A:ASP182 4.3 38.6 1.0
SD A:MET131 4.4 37.4 1.0
CD A:GLN292 4.4 26.2 1.0
CB A:MET131 4.5 30.1 1.0
S A:SO42 4.5 61.0 1.0
OH A:TYR270 4.5 21.6 1.0
CB A:HIS319 4.6 19.9 1.0
CE A:MET131 4.6 34.3 1.0
O A:HOH701 4.7 41.8 1.0
CG2 A:THR290 4.7 22.2 1.0
CG A:ASP182 4.7 37.1 1.0
OD2 A:ASP182 4.7 35.8 1.0
CD A:GLN180 4.8 35.4 1.0

Potassium binding site 3 out of 4 in 3ugq

Go back to Potassium Binding Sites List in 3ugq
Potassium binding site 3 out of 4 in the Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K470

b:67.2
occ:1.00
 O A:HOH578 3.8 33.0 1.0
O A:HOH612 4.0 32.3 1.0
N A:VAL403 4.1 22.7 1.0
CA A:PRO402 4.1 28.1 1.0
O A:HOH692 4.3 25.2 1.0
CB A:PRO402 4.4 26.4 1.0
CG1 A:VAL403 4.4 24.2 1.0
C A:PRO402 4.7 27.2 1.0

Potassium binding site 4 out of 4 in 3ugq

Go back to Potassium Binding Sites List in 3ugq
Potassium binding site 4 out of 4 in the Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of the Apo Form of the Yeast Mitochondrial Threonyl- Trna Synthetase Determined at 2.1 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K471

b:48.3
occ:1.00
 N A:LYS444 3.9 27.0 1.0
NZ A:LYS444 4.1 34.0 1.0
O A:HOH666 4.1 42.5 1.0
CE A:LYS444 4.3 32.6 1.0
CA A:GLU443 4.4 26.8 1.0
O A:PHE442 4.5 34.9 1.0
CB A:LYS444 4.5 28.2 1.0
C A:GLU443 4.6 30.2 1.0
CA A:LYS444 4.8 28.8 1.0
O A:LYS444 4.8 26.9 1.0
CG A:LYS444 5.0 33.2 1.0

Reference:

J.Ling, K.M.Peterson, I.Simonovic, C.Cho, D.Soll, M.Simonovic. Yeast Mitochondrial Threonyl-Trna Synthetase Recognizes Trna Isoacceptors By Distinct Mechanisms and Promotes Cun Codon Reassignment. Proc.Natl.Acad.Sci.Usa V. 109 3281 2012.
ISSN: ISSN 0027-8424
PubMed: 22343532
DOI: 10.1073/PNAS.1200109109
Page generated: Mon Aug 12 09:41:57 2024

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