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

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

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

Protein crystallography data

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

Resolution Low / High (Å) 30.00 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.700, 111.100, 135.200, 90.00, 93.50, 90.00
R / Rfree (%) 21.5 / 22.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with A Threonyl Adenylate Analog (pdb code 1evl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with A Threonyl Adenylate Analog, PDB code: 1evl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1evl

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Zinc binding site 1 out of 4 in the Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with A Threonyl 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 with A Threonyl Adenylate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:12.3
occ:1.00
 NE2 A:HIS385 2.2 12.3 1.0
ND1 A:HIS511 2.2 12.4 1.0
N A:TSB2002 2.3 11.9 1.0
OG1 A:TSB2002 2.4 11.9 1.0
SG A:CYS334 2.4 12.4 1.0
CE1 A:HIS511 3.1 12.3 1.0
CE1 A:HIS385 3.1 11.9 1.0
CA A:TSB2002 3.1 11.9 1.0
CD2 A:HIS385 3.2 12.0 1.0
CG A:HIS511 3.2 12.6 1.0
CB A:TSB2002 3.2 11.6 1.0
CB A:CYS334 3.4 11.8 1.0
CB A:HIS511 3.6 12.5 1.0
O A:HOH2004 3.8 11.8 1.0
NE2 A:HIS511 4.2 12.8 1.0
ND1 A:HIS385 4.2 12.1 1.0
N A:CYS334 4.2 11.4 1.0
CA A:CYS334 4.3 11.5 1.0
CG A:HIS385 4.3 12.2 1.0
CD2 A:HIS511 4.3 12.7 1.0
OD2 A:ASP383 4.3 12.4 1.0
OH A:TYR462 4.3 14.7 1.0
OD1 A:ASP383 4.3 12.5 1.0
C A:TSB2002 4.5 12.3 1.0
CG2 A:TSB2002 4.5 11.5 1.0
CA A:HIS511 4.6 12.8 1.0
CG A:ASP383 4.8 12.7 1.0
OE1 A:GLN484 4.8 15.2 1.0
O A:TSB2002 4.9 12.8 1.0
CZ A:TYR462 4.9 14.5 1.0
SD A:MET332 5.0 11.7 1.0
O A:HOH2186 5.0 28.8 1.0

Zinc binding site 2 out of 4 in 1evl

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Zinc binding site 2 out of 4 in the Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with A Threonyl 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 with A Threonyl Adenylate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:10.7
occ:1.00
 ND1 B:HIS511 2.2 13.2 1.0
NE2 B:HIS385 2.2 12.4 1.0
N B:TSB3002 2.3 11.8 1.0
OG1 B:TSB3002 2.3 10.7 1.0
SG B:CYS334 2.4 13.1 1.0
CA B:TSB3002 3.1 11.4 1.0
CE1 B:HIS511 3.1 13.4 1.0
CE1 B:HIS385 3.2 12.1 1.0
CD2 B:HIS385 3.2 12.1 1.0
CB B:TSB3002 3.2 10.9 1.0
CG B:HIS511 3.2 13.0 1.0
CB B:CYS334 3.4 12.5 1.0
CB B:HIS511 3.6 12.9 1.0
O B:HOH3003 3.8 11.7 1.0
NE2 B:HIS511 4.2 13.4 1.0
N B:CYS334 4.3 12.0 1.0
ND1 B:HIS385 4.3 12.3 1.0
CA B:CYS334 4.3 12.4 1.0
OH B:TYR462 4.3 15.2 1.0
CD2 B:HIS511 4.3 13.5 1.0
CG B:HIS385 4.3 12.1 1.0
OD2 B:ASP383 4.3 12.6 1.0
OD1 B:ASP383 4.3 11.9 1.0
C B:TSB3002 4.4 11.8 1.0
CG2 B:TSB3002 4.4 10.8 1.0
CA B:HIS511 4.6 12.9 1.0
CG B:ASP383 4.8 12.2 1.0
OE1 B:GLN484 4.8 14.4 1.0
CZ B:TYR462 4.8 15.2 1.0
O B:TSB3002 4.9 12.1 1.0
O B:HOH3236 5.0 30.2 1.0
SD B:MET332 5.0 13.1 1.0

Zinc binding site 3 out of 4 in 1evl

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Zinc binding site 3 out of 4 in the Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with A Threonyl Adenylate Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with A Threonyl Adenylate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:13.5
occ:1.00
 NE2 C:HIS385 2.2 11.8 1.0
ND1 C:HIS511 2.2 12.7 1.0
N C:TSB4002 2.3 11.8 1.0
OG1 C:TSB4002 2.3 11.7 1.0
SG C:CYS334 2.4 12.9 1.0
CA C:TSB4002 3.1 11.9 1.0
CE1 C:HIS511 3.1 12.8 1.0
CE1 C:HIS385 3.1 11.1 1.0
CD2 C:HIS385 3.2 11.3 1.0
CB C:TSB4002 3.2 11.3 1.0
CG C:HIS511 3.2 12.8 1.0
CB C:CYS334 3.4 12.3 1.0
CB C:HIS511 3.6 12.6 1.0
O C:HOH4005 3.8 12.4 1.0
NE2 C:HIS511 4.2 13.2 1.0
ND1 C:HIS385 4.3 11.3 1.0
CA C:CYS334 4.3 12.1 1.0
N C:CYS334 4.3 11.9 1.0
CG C:HIS385 4.3 11.6 1.0
CD2 C:HIS511 4.3 12.9 1.0
OD2 C:ASP383 4.3 12.6 1.0
OD1 C:ASP383 4.3 12.7 1.0
OH C:TYR462 4.4 15.8 1.0
CG2 C:TSB4002 4.4 11.3 1.0
C C:TSB4002 4.4 12.4 1.0
CA C:HIS511 4.6 13.1 1.0
OE1 C:GLN484 4.8 15.3 1.0
CG C:ASP383 4.8 12.4 1.0
O C:TSB4002 4.9 12.8 1.0
CZ C:TYR462 4.9 15.9 1.0
SD C:MET332 5.0 13.1 1.0

Zinc binding site 4 out of 4 in 1evl

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Zinc binding site 4 out of 4 in the Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with A Threonyl Adenylate Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Truncated Form of Threonyl-Trna Synthetase with A Threonyl Adenylate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:13.5
occ:1.00
 NE2 D:HIS385 2.2 14.0 1.0
ND1 D:HIS511 2.2 14.7 1.0
N D:TSB5002 2.3 13.2 1.0
OG1 D:TSB5002 2.4 13.1 1.0
SG D:CYS334 2.4 14.4 1.0
CA D:TSB5002 3.1 13.0 1.0
CE1 D:HIS511 3.1 14.9 1.0
CE1 D:HIS385 3.1 13.5 1.0
CD2 D:HIS385 3.2 13.6 1.0
CG D:HIS511 3.2 15.0 1.0
CB D:TSB5002 3.2 12.9 1.0
CB D:CYS334 3.4 13.5 1.0
CB D:HIS511 3.6 14.8 1.0
O D:HOH5315 3.7 14.1 1.0
NE2 D:HIS511 4.2 15.0 1.0
ND1 D:HIS385 4.2 13.5 1.0
N D:CYS334 4.3 12.7 1.0
CA D:CYS334 4.3 13.3 1.0
CG D:HIS385 4.3 13.8 1.0
OD2 D:ASP383 4.3 12.9 1.0
CD2 D:HIS511 4.3 15.0 1.0
OD1 D:ASP383 4.3 13.0 1.0
OH D:TYR462 4.4 16.2 1.0
C D:TSB5002 4.5 13.5 1.0
CG2 D:TSB5002 4.5 12.7 1.0
CA D:HIS511 4.6 15.0 1.0
OE1 D:GLN484 4.8 16.1 1.0
CG D:ASP383 4.8 13.2 1.0
O D:TSB5002 4.9 13.3 1.0
SD D:MET332 4.9 13.2 1.0
CZ D:TYR462 4.9 16.4 1.0

Reference:

R.Sankaranarayanan, A.C.Dock-Bregeon, B.Rees, M.Bovee, J.Caillet, P.Romby, C.S.Francklyn, D.Moras. Zinc Ion Mediated Amino Acid Discrimination By Threonyl-Trna Synthetase. Nat.Struct.Biol. V. 7 461 2000.
ISSN: ISSN 1072-8368
PubMed: 10881191
DOI: 10.1038/75856
Page generated: Sun Oct 13 00:26:38 2024

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