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Zinc in PDB 2bte: Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue

Enzymatic activity of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue

All present enzymatic activity of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue:
6.1.1.4;

Protein crystallography data

The structure of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue, PDB code: 2bte was solved by S.Cusack, M.Tukalo, A.Yaremchuk, R.Fukunaga, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.89 / 2.9
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 204.121, 125.705, 175.432, 90.00, 120.86, 90.00
R / Rfree (%) 21.7 / 25.3

Other elements in 2bte:

The structure of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue also contains other interesting chemical elements:

Mercury (Hg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue (pdb code 2bte). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue, PDB code: 2bte:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2bte

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Zinc binding site 1 out of 4 in the Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1877

b:0.8
occ:1.00
SG A:CYS439 2.3 0.1 1.0
SG A:CYS484 2.3 0.1 1.0
SG A:CYS442 2.3 0.1 1.0
SG A:CYS487 2.4 0.7 1.0
CB A:CYS484 3.2 0.3 1.0
CB A:CYS442 3.2 0.7 1.0
CB A:CYS439 3.2 0.8 1.0
CB A:CYS487 3.3 0.3 1.0
N A:CYS487 3.5 1.0 1.0
N A:CYS442 3.7 0.6 1.0
CA A:CYS487 4.0 0.2 1.0
CA A:CYS442 4.1 0.5 1.0
CB A:LYS486 4.2 0.6 1.0
N A:GLY488 4.5 98.8 1.0
CB A:ALA441 4.5 0.0 1.0
C A:LYS486 4.6 0.9 1.0
CA A:CYS484 4.6 100.0 1.0
CA A:CYS439 4.7 99.5 1.0
C A:ALA441 4.8 0.6 1.0
C A:CYS487 4.8 0.7 1.0
CG2 A:VAL445 4.8 85.0 1.0
CA A:LYS486 4.8 0.6 1.0
CG A:LYS486 4.9 0.1 1.0
N A:ALA441 4.9 0.9 1.0
N A:LYS486 5.0 0.3 1.0
CD A:LYS486 5.0 0.1 1.0
CA A:ALA441 5.0 0.8 1.0

Zinc binding site 2 out of 4 in 2bte

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Zinc binding site 2 out of 4 in the Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1878

b:68.5
occ:1.00
ND1 A:HIS179 2.1 88.3 1.0
CE1 A:HIS179 2.2 93.0 1.0
SG A:CYS162 2.3 81.2 1.0
SG A:CYS176 2.3 89.7 1.0
SG A:CYS159 2.3 72.4 1.0
CB A:CYS162 3.1 77.2 1.0
CB A:CYS176 3.3 83.5 1.0
CB A:CYS159 3.3 71.8 1.0
CG A:HIS179 3.5 92.4 1.0
NE2 A:HIS179 3.5 94.0 1.0
N A:CYS162 3.8 74.1 1.0
CA A:CYS162 3.9 74.9 1.0
CD2 A:HIS179 4.1 91.5 1.0
CD1 A:LEU166 4.4 68.1 1.0
CB A:HIS179 4.5 90.5 1.0
N A:HIS179 4.7 87.2 1.0
CB A:ARG178 4.7 84.1 1.0
CA A:CYS176 4.8 82.5 1.0
CA A:CYS159 4.8 72.0 1.0
CD2 A:LEU166 4.8 71.2 1.0
CB A:LYS161 4.9 76.4 1.0
C A:LYS161 4.9 74.3 1.0

Zinc binding site 3 out of 4 in 2bte

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Zinc binding site 3 out of 4 in the Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1877

b:0.7
occ:1.00
SG D:CYS484 2.3 0.4 1.0
SG D:CYS439 2.4 0.5 1.0
SG D:CYS442 2.4 0.6 1.0
SG D:CYS487 2.4 0.1 1.0
CB D:CYS484 3.1 0.2 1.0
CB D:CYS439 3.2 0.7 1.0
CB D:CYS442 3.2 0.3 1.0
CB D:CYS487 3.3 0.5 1.0
N D:CYS487 3.8 0.6 1.0
N D:CYS442 3.9 0.1 1.0
CA D:CYS487 4.1 0.1 1.0
CA D:CYS442 4.2 0.9 1.0
CB D:LYS486 4.5 0.8 1.0
N D:GLY488 4.6 0.9 1.0
CA D:CYS484 4.6 0.4 1.0
CA D:CYS439 4.7 0.5 1.0
C D:LYS486 4.9 0.6 1.0
CB D:ALA441 4.9 0.3 1.0
C D:CYS487 4.9 0.5 1.0
CD D:LYS486 5.0 0.7 1.0
CG2 D:VAL445 5.0 0.4 1.0
N D:GLY489 5.0 0.1 1.0

Zinc binding site 4 out of 4 in 2bte

Go back to Zinc Binding Sites List in 2bte
Zinc binding site 4 out of 4 in the Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thermus Thermophilus Leucyl-Trna Synthetase Complexed with with A Trnaleu Transcript in the Post-Editing Conformation and A Post-Transfer Editing Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1878

b:97.3
occ:1.00
ND1 D:HIS179 2.1 0.3 1.0
SG D:CYS162 2.3 0.5 1.0
SG D:CYS159 2.3 0.5 1.0
SG D:CYS176 2.3 0.8 1.0
CE1 D:HIS179 2.7 0.1 1.0
CB D:CYS162 3.3 0.6 1.0
CG D:HIS179 3.4 0.3 1.0
CB D:CYS159 3.5 0.9 1.0
CB D:CYS176 3.6 0.2 1.0
N D:CYS162 4.0 0.2 1.0
CB D:HIS179 4.0 0.6 1.0
NE2 D:HIS179 4.0 0.4 1.0
CA D:CYS162 4.2 0.2 1.0
CD1 D:LEU166 4.2 94.2 1.0
CD2 D:HIS179 4.3 0.2 1.0
CB D:LYS161 4.7 0.9 1.0
N D:HIS179 4.8 0.7 1.0
C D:LYS161 4.9 0.1 1.0
CA D:CYS176 4.9 0.8 1.0
CA D:CYS159 4.9 0.9 1.0

Reference:

M.Tukalo, A.Yaremchuk, R.Fukunaga, S.Yokoyama, S.Cusack. The Crystal Structure of Leucyl-Trna Synthetase Complexed with Trna(Leu) in the Post-Transfer- Editing Conformation. Nat.Struct.Mol.Biol. V. 12 923 2005.
ISSN: ISSN 1545-9993
PubMed: 16155583
DOI: 10.1038/NSMB986
Page generated: Wed Dec 16 03:18:50 2020

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