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Zinc in PDB 1fyf: Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase Complexed with A Seryl Adenylate Analog

Enzymatic activity of Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase Complexed with A Seryl Adenylate Analog

All present enzymatic activity of Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase Complexed with A Seryl Adenylate Analog:
6.1.1.3;

Protein crystallography data

The structure of Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase Complexed with A Seryl Adenylate Analog, PDB code: 1fyf was solved by R.Sankaranarayanan, A.C.Dock-Bregeon, D.Moras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.93 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.950, 109.520, 115.370, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase Complexed with A Seryl Adenylate Analog (pdb code 1fyf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase Complexed with A Seryl Adenylate Analog, PDB code: 1fyf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1fyf

Go back to Zinc Binding Sites List in 1fyf
Zinc binding site 1 out of 2 in the Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase Complexed with A Seryl Adenylate Analog


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 A Truncated Form of Threonyl-Trna Synthetase Complexed with A Seryl Adenylate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn650

b:15.3
occ:1.00
NE2 A:HIS385 2.2 15.1 1.0
ND1 A:HIS511 2.2 16.1 1.0
N10 A:SSA1001 2.3 17.0 1.0
OG A:SSA1001 2.4 17.2 1.0
SG A:CYS334 2.4 16.0 1.0
CD2 A:HIS385 3.1 15.3 1.0
CA A:SSA1001 3.1 17.1 1.0
CE1 A:HIS511 3.1 16.5 1.0
CE1 A:HIS385 3.2 15.2 1.0
CG A:HIS511 3.2 16.3 1.0
CB A:SSA1001 3.3 16.9 1.0
CB A:CYS334 3.4 15.6 1.0
CB A:HIS511 3.6 16.2 1.0
O A:HOH1012 3.8 16.6 1.0
N A:CYS334 4.2 15.1 1.0
CA A:CYS334 4.2 15.3 1.0
OH A:TYR462 4.2 17.6 1.0
NE2 A:HIS511 4.2 16.2 1.0
OD2 A:ASP383 4.3 16.1 1.0
CG A:HIS385 4.3 15.4 1.0
ND1 A:HIS385 4.3 15.2 1.0
CD2 A:HIS511 4.3 16.3 1.0
OD1 A:ASP383 4.4 16.2 1.0
C9 A:SSA1001 4.5 17.2 1.0
CA A:HIS511 4.6 16.2 1.0
OE1 A:GLN484 4.7 17.1 1.0
CG A:ASP383 4.8 16.1 1.0
O9 A:SSA1001 4.8 17.2 1.0
CZ A:TYR462 4.9 17.4 1.0
SD A:MET332 4.9 16.8 1.0

Zinc binding site 2 out of 2 in 1fyf

Go back to Zinc Binding Sites List in 1fyf
Zinc binding site 2 out of 2 in the Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase Complexed with A Seryl Adenylate Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase Complexed with A Seryl Adenylate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn650

b:12.6
occ:1.00
NE2 B:HIS385 2.1 11.7 1.0
ND1 B:HIS511 2.2 13.3 1.0
N10 B:SSA2001 2.3 14.0 1.0
OG B:SSA2001 2.5 14.0 1.0
SG B:CYS334 2.5 14.1 1.0
CA B:SSA2001 3.0 14.3 1.0
CE1 B:HIS511 3.1 13.6 1.0
CE1 B:HIS385 3.1 12.2 1.0
CD2 B:HIS385 3.1 12.2 1.0
CG B:HIS511 3.2 13.5 1.0
CB B:SSA2001 3.3 14.2 1.0
CB B:CYS334 3.4 13.0 1.0
CB B:HIS511 3.5 13.4 1.0
O B:HOH2006 3.8 17.2 1.0
NE2 B:HIS511 4.2 13.6 1.0
ND1 B:HIS385 4.2 12.1 1.0
N B:CYS334 4.3 12.9 1.0
CA B:CYS334 4.3 13.0 1.0
CG B:HIS385 4.3 12.0 1.0
CD2 B:HIS511 4.3 13.5 1.0
OH B:TYR462 4.3 16.3 1.0
OD2 B:ASP383 4.3 14.7 1.0
C9 B:SSA2001 4.4 14.6 1.0
OD1 B:ASP383 4.4 14.4 1.0
CA B:HIS511 4.6 13.6 1.0
OE1 B:GLN484 4.7 16.1 1.0
O9 B:SSA2001 4.8 14.3 1.0
CZ B:TYR462 4.8 16.0 1.0
CG B:ASP383 4.8 14.0 1.0
SD B:MET332 4.9 15.1 1.0

Reference:

A.Dock-Bregeon, R.Sankaranarayanan, P.Romby, J.Caillet, M.Springer, B.Rees, C.S.Francklyn, C.Ehresmann, D.Moras. Transfer Rna-Mediated Editing in Threonyl-Trna Synthetase. the Class II Solution to the Double Discrimination Problem. Cell(Cambridge,Mass.) V. 103 877 2000.
ISSN: ISSN 0092-8674
PubMed: 11136973
DOI: 10.1016/S0092-8674(00)00191-4
Page generated: Wed Dec 16 02:49:44 2020

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