Zinc in PDB 1jke: D-Tyr Trnatyr Deacylase From Escherichia Coli

The structure of D-Tyr Trnatyr Deacylase From Escherichia Coli, PDB code: 1jke was solved by M.L.Ferri-Fioni, E.Schmitt, J.Soutourina, P.Plateau, Y.Mechulam, S.Blanquet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	500.00 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	118.300, 82.930, 83.510, 90.00, 128.29, 90.00
R / Rfree (%)	20.9 / 22.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the D-Tyr Trnatyr Deacylase From Escherichia Coli (pdb code 1jke). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the D-Tyr Trnatyr Deacylase From Escherichia Coli, PDB code: 1jke:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the D-Tyr Trnatyr Deacylase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of D-Tyr Trnatyr Deacylase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn906 b:40.4 occ:1.00 O A:HOH1325 2.0 29.4 1.0 OE2 A:GLU16 2.2 33.2 1.0 CD A:GLU16 2.9 34.8 1.0 OE1 A:GLU16 3.0 37.7 1.0 CG A:GLU16 4.4 33.0 1.0 CA A:GLU16 4.7 31.0 1.0 CB A:GLU16 4.8 31.6 1.0 O A:HOH1309 5.0 37.6 1.0

Zinc binding site 2 out of 12 in the D-Tyr Trnatyr Deacylase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of D-Tyr Trnatyr Deacylase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn908 b:39.7 occ:1.00 OE2 C:GLU22 2.1 21.0 1.0 O C:HOH1353 2.2 32.1 1.0 O C:HOH1230 2.2 32.6 1.0 O C:HOH1350 2.3 30.6 1.0 OE2 A:GLU111 2.4 33.5 1.0 O A:HOH1234 2.4 46.0 1.0 OE1 A:GLU111 2.8 34.1 1.0 CD A:GLU111 2.9 31.0 1.0 CD C:GLU22 3.0 19.4 1.0 OE1 C:GLU22 3.2 22.4 1.0 CB A:ARG114 4.2 17.9 1.0 O C:HOH1343 4.3 34.4 1.0 CG A:GLU111 4.4 27.8 1.0 CG C:GLU22 4.4 15.6 1.0 O C:HOH1224 4.7 32.5 1.0 CD A:ARG114 4.7 21.1 1.0 O A:HOH1348 4.8 25.3 1.0 O C:HOH1068 4.8 21.6 1.0 O A:GLU111 4.9 19.7 1.0

Zinc binding site 3 out of 12 in the D-Tyr Trnatyr Deacylase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of D-Tyr Trnatyr Deacylase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn909 b:33.2 occ:1.00 O C:HOH1416 2.1 39.1 1.0 O C:HOH1404 2.1 35.2 1.0 OD2 A:ASP107 2.1 26.9 1.0 OE2 C:GLU18 2.2 35.5 1.0 OE2 A:GLU103 2.3 37.9 1.0 OE1 C:GLU18 2.5 33.0 1.0 CD C:GLU18 2.7 33.5 1.0 CG A:ASP107 3.0 24.2 1.0 CD A:GLU103 3.1 37.4 1.0 OD1 A:ASP107 3.2 26.2 1.0 CG A:GLU103 3.3 36.0 1.0 CG C:GLU18 4.1 32.0 1.0 OE1 A:GLU103 4.2 37.9 1.0 CB A:ASP107 4.4 22.6 1.0 CB A:GLU103 4.8 34.9 1.0 O A:GLU103 4.9 30.2 1.0 O C:HOH1229 4.9 30.3 1.0

Zinc binding site 4 out of 12 in the D-Tyr Trnatyr Deacylase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of D-Tyr Trnatyr Deacylase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn912 b:48.7 occ:1.00 O B:HOH1370 2.0 27.7 1.0 O B:HOH1413 2.2 44.1 1.0 O B:HOH1254 2.2 27.7 1.0 O B:HOH1418 2.4 39.5 1.0 O B:HOH1417 2.4 36.2 1.0 O B:HOH1419 2.5 37.5 1.0 O B:GLN67 3.8 20.9 1.0 OE1 B:GLU117 4.1 27.6 1.0 CA B:GLY70 4.1 21.2 1.0 OE2 B:GLU117 4.1 27.9 1.0 O B:GLY71 4.5 19.6 1.0 C B:GLY70 4.5 21.9 1.0 CA B:GLN67 4.5 19.9 1.0 CD B:GLU117 4.6 28.4 1.0 C B:GLN67 4.6 20.9 1.0 N B:GLY70 4.9 21.0 1.0 N B:GLY71 4.9 19.9 1.0 CB B:GLN67 4.9 21.2 1.0 O B:GLY70 4.9 22.9 1.0

Zinc binding site 5 out of 12 in the D-Tyr Trnatyr Deacylase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of D-Tyr Trnatyr Deacylase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn905 b:22.4 occ:1.00 OD2 C:ASP107 2.0 19.5 1.0 OE2 C:GLU103 2.1 21.3 1.0 O A:HOH1134 2.1 24.7 1.0 OE1 A:GLU18 2.2 26.8 1.0 OE2 A:GLU18 2.6 27.1 1.0 CD A:GLU18 2.7 28.5 1.0 CD C:GLU103 2.9 21.1 1.0 OE1 C:GLU103 3.0 20.7 1.0 CG C:ASP107 3.1 20.4 1.0 OD1 C:ASP107 3.5 20.1 1.0 O C:HOH1152 3.7 22.9 1.0 O A:HOH1140 3.9 33.7 1.0 O C:HOH1387 4.2 33.4 1.0 CG A:GLU18 4.2 28.1 1.0 CG C:GLU103 4.3 18.7 1.0 CB C:ASP107 4.4 17.8 1.0 O C:GLU103 4.9 16.6 1.0 CB A:GLU18 5.0 29.0 1.0

Zinc binding site 6 out of 12 in the D-Tyr Trnatyr Deacylase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of D-Tyr Trnatyr Deacylase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn910 b:39.9 occ:1.00 O C:HOH1316 2.0 26.1 1.0 O C:HOH1415 2.1 36.1 1.0 O C:HOH1308 2.2 37.8 1.0 O C:HOH1414 2.2 34.5 1.0 OE1 C:GLU117 2.3 27.3 1.0 OE2 C:GLU117 2.6 28.0 1.0 CD C:GLU117 2.7 28.0 1.0 OD1 C:ASN119 4.1 26.7 1.0 O C:HOH1303 4.1 33.6 1.0 CG C:GLU117 4.2 27.7 1.0 O C:GLY71 4.3 17.2 1.0 NE2 C:GLN67 4.3 26.4 1.0 CA C:GLN67 4.5 18.0 1.0 O C:GLN67 4.5 18.3 1.0 CB C:GLN67 4.6 20.0 1.0 CG C:GLN67 4.7 22.8 1.0 CB C:GLU117 4.9 25.4 1.0 CA C:GLU117 5.0 25.4 1.0 CG C:ASN119 5.0 21.6 1.0 C C:GLN67 5.0 17.3 1.0 CD C:GLN67 5.0 25.4 1.0

Zinc binding site 7 out of 12 in the D-Tyr Trnatyr Deacylase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of D-Tyr Trnatyr Deacylase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn911 b:34.1 occ:1.00 O C:HOH1118 2.0 23.9 1.0 O C:HOH1044 2.2 19.1 1.0 O C:HOH1105 2.2 23.7 1.0 O C:HOH1288 2.2 32.0 1.0 O C:HOH1380 2.4 40.4 1.0 O C:HOH1378 2.4 33.1 1.0 O C:HOH1045 3.5 21.7 1.0 NZ C:LYS41 3.6 25.9 1.0 O C:HOH1294 4.0 33.2 1.0 O C:HOH1106 4.0 31.6 1.0 O C:VAL145 4.1 20.4 1.0 O C:HOH1382 4.3 43.4 1.0 OE1 C:GLU34 4.3 17.7 1.0 CE C:LYS41 4.5 26.2 1.0 OXT C:VAL145 4.5 22.5 1.0 OD1 C:ASP37 4.5 17.3 1.0 C C:VAL145 4.7 21.4 1.0 CD C:LYS41 4.8 24.9 1.0 CD C:GLU34 4.9 16.7 1.0 N C:MET1 4.9 14.7 1.0 O C:HOH1383 4.9 44.9 1.0

Zinc binding site 8 out of 12 in the D-Tyr Trnatyr Deacylase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of D-Tyr Trnatyr Deacylase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn901 b:18.0 occ:1.00 OE2 D:GLU18 2.0 18.6 1.0 CD D:GLU18 2.9 20.0 1.0 OE1 D:GLU18 3.1 18.2 1.0 O D:HOH1080 3.7 26.1 1.0 CG D:GLU18 4.3 16.5 1.0 O D:HOH1081 4.7 37.0 1.0 N D:VAL19 4.7 13.6 1.0

Zinc binding site 9 out of 12 in the D-Tyr Trnatyr Deacylase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of D-Tyr Trnatyr Deacylase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn902 b:19.6 occ:1.00 O D:HOH1088 2.0 18.3 1.0 O D:HOH1087 2.1 29.8 1.0 OD2 D:ASP107 2.1 16.2 1.0 OE2 D:GLU103 2.3 24.5 1.0 CG D:ASP107 3.0 15.1 1.0 CD D:GLU103 3.2 21.5 1.0 OD1 D:ASP107 3.2 15.1 1.0 CG D:GLU103 3.3 16.4 1.0 O D:HOH1277 4.1 32.7 1.0 O D:HOH1268 4.2 37.6 1.0 O D:HOH1089 4.3 28.0 1.0 OE1 D:GLU103 4.3 24.5 1.0 CB D:ASP107 4.4 12.8 1.0 O D:GLU103 4.8 14.1 1.0 CB D:GLU103 4.8 15.4 1.0

Zinc binding site 10 out of 12 in the D-Tyr Trnatyr Deacylase From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of D-Tyr Trnatyr Deacylase From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn903 b:29.2 occ:1.00 OE2 D:GLU111 2.0 25.8 1.0 O D:HOH1270 2.3 30.4 1.0 OE1 D:GLU111 2.5 23.4 1.0 CD D:GLU111 2.5 23.7 1.0 CG D:GLU111 4.0 19.9 1.0 CG D:GLN115 4.8 28.8 1.0 NE2 D:GLN115 4.9 34.8 1.0 CB D:ARG114 4.9 16.9 1.0 O D:GLU111 4.9 15.5 1.0

M.L.Ferri-Fioni, E.Schmitt, J.Soutourina, P.Plateau, Y.Mechulam, S.Blanquet. Structure of Crystalline D-Tyr-Trna(Tyr) Deacylase. A Representative of A New Class of Trna-Dependent Hydrolases. J.Biol.Chem. V. 276 47285 2001.
ISSN: ISSN 0021-9258
PubMed: 11568181
DOI: 10.1074/JBC.M106550200