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Zinc in PDB 2d5b: Crystal Structure of Thermus Thermophilus Methionyl Trna Synthetase Y225F Mutant Obtained in the Presence of PEG6000

Enzymatic activity of Crystal Structure of Thermus Thermophilus Methionyl Trna Synthetase Y225F Mutant Obtained in the Presence of PEG6000

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Methionyl Trna Synthetase Y225F Mutant Obtained in the Presence of PEG6000:
6.1.1.10;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Methionyl Trna Synthetase Y225F Mutant Obtained in the Presence of PEG6000, PDB code: 2d5b was solved by M.Konno, R.Takeda, R.Takasaka, Y.Mori, R.Ishii, S.Yokoyama, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.140, 82.250, 121.410, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 24.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thermus Thermophilus Methionyl Trna Synthetase Y225F Mutant Obtained in the Presence of PEG6000 (pdb code 2d5b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Thermus Thermophilus Methionyl Trna Synthetase Y225F Mutant Obtained in the Presence of PEG6000, PDB code: 2d5b:

Zinc binding site 1 out of 1 in 2d5b

Go back to Zinc Binding Sites List in 2d5b
Zinc binding site 1 out of 1 in the Crystal Structure of Thermus Thermophilus Methionyl Trna Synthetase Y225F Mutant Obtained in the Presence of PEG6000


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 Thermus Thermophilus Methionyl Trna Synthetase Y225F Mutant Obtained in the Presence of PEG6000 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:20.6
occ:1.00
 ND1 A:HIS147 2.1 20.5 1.0
SG A:CYS127 2.3 15.3 1.0
SG A:CYS130 2.3 22.2 1.0
SG A:CYS144 2.3 22.2 1.0
CE1 A:HIS147 2.9 22.5 1.0
CG A:HIS147 3.3 23.2 1.0
CB A:CYS130 3.3 21.4 1.0
CB A:CYS127 3.3 15.3 1.0
CB A:CYS144 3.4 25.6 1.0
N A:CYS130 3.6 19.4 1.0
CB A:HIS147 3.8 23.3 1.0
N A:HIS147 3.9 26.1 1.0
CA A:CYS130 4.0 19.1 1.0
NE2 A:HIS147 4.0 23.1 1.0
CB A:ILE146 4.1 26.0 1.0
CD2 A:HIS147 4.3 22.8 1.0
CE1 A:TYR134 4.3 22.0 1.0
CB A:SER129 4.3 19.7 1.0
OH A:TYR134 4.3 22.1 1.0
C A:SER129 4.5 18.9 1.0
CA A:HIS147 4.5 25.7 1.0
CG2 A:ILE146 4.6 24.8 1.0
CA A:CYS127 4.7 17.0 1.0
CZ A:TYR134 4.8 23.5 1.0
C A:ILE146 4.8 27.0 1.0
CA A:CYS144 4.8 27.2 1.0
CA A:ILE146 4.8 26.3 1.0
CA A:SER129 4.9 18.4 1.0
N A:ILE146 4.9 25.8 1.0
N A:SER129 5.0 17.8 1.0
OG A:SER129 5.0 20.8 1.0
CG1 A:ILE146 5.0 27.5 1.0

Reference:

M.Konno, R.Takeda, R.Takasaka, Y.Mori, R.Ishii, S.Yokoyama. Y225F/A Mutation For Met-Trna Synthetase Reveals Importance of Hydrophobic Circumstances To Be Published.
Page generated: Wed Oct 16 22:36:27 2024

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