Zinc in PDB 4dwz: Crystal Structure of TON_0340

The structure of Crystal Structure of TON_0340, PDB code: 4dwz was solved by S.G.Lee, K.H.Lee, S.S.Cha, B.H.Oh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.92 / 2.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.442, 107.442, 355.031, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 27

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 38;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of TON_0340 (pdb code 4dwz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 38 binding sites of Zinc where determined in the Crystal Structure of TON_0340, PDB code: 4dwz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 38 in the Crystal Structure of TON_0340


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 TON_0340 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:34.0 occ:1.00 OE2 A:GLU161 2.2 35.6 1.0 OE2 A:GLU115 2.3 35.9 1.0 OD1 A:ASP157 2.3 30.0 1.0 O A:HOH404 2.5 38.4 1.0 OE1 A:GLU115 2.8 35.5 1.0 CD A:GLU115 2.9 34.4 1.0 CD A:GLU161 3.2 35.8 1.0 CG A:ASP157 3.6 30.3 1.0 CG A:GLU161 3.6 34.9 1.0 O A:HOH403 3.6 13.3 1.0 ZN A:ZN303 3.8 28.4 1.0 N A:GLY158 3.9 31.1 1.0 O A:HOH407 4.1 38.4 1.0 N A:ASP157 4.1 31.8 1.0 OE1 A:GLU161 4.2 37.5 1.0 OD1 A:ASN160 4.2 36.0 1.0 OD2 A:ASP157 4.2 32.2 1.0 C A:ASP157 4.3 31.2 1.0 CA A:GLY158 4.4 29.7 1.0 CG A:GLU115 4.4 31.8 1.0 CA A:ASP157 4.6 30.2 1.0 OG A:SER196 4.6 24.1 1.0 CB A:ASP157 4.7 29.8 1.0 O A:ASP157 5.0 33.0 1.0

Zinc binding site 2 out of 38 in the Crystal Structure of TON_0340


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 TON_0340 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:41.0 occ:1.00 O A:HOH403 1.9 13.3 1.0 OE2 A:GLU59 2.0 38.1 1.0 OD1 A:ASP246 2.2 31.3 1.0 O A:HOH401 2.4 34.7 1.0 CD A:GLU59 2.4 39.2 1.0 OE1 A:GLU59 2.6 39.5 1.0 CG A:ASP246 3.3 32.5 1.0 ZN A:ZN303 3.4 28.4 1.0 O A:HOH407 3.7 38.4 1.0 CG A:GLU59 3.7 38.6 1.0 OD2 A:ASP246 4.0 35.1 1.0 CA A:GLY236 4.0 43.8 1.0 OE2 A:GLU115 4.2 35.9 1.0 CB A:ASP246 4.3 33.0 1.0 CB A:ASP61 4.4 31.1 1.0 CA A:ASP246 4.4 34.8 1.0 N A:GLY236 4.6 43.2 1.0 C A:GLY236 4.7 45.8 1.0 OD1 A:ASP61 4.7 29.0 1.0 CB A:GLU59 4.8 36.8 1.0 N A:ASP246 4.8 35.5 1.0

Zinc binding site 3 out of 38 in the Crystal Structure of TON_0340


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 TON_0340 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:28.4 occ:1.00 OD1 A:ASP61 2.2 29.0 1.0 OD2 A:ASP246 2.2 35.1 1.0 O A:HOH403 2.2 13.3 1.0 OD2 A:ASP157 2.5 32.2 1.0 CG A:ASP246 2.9 32.5 1.0 OD1 A:ASP246 2.9 31.3 1.0 OD1 A:ASP157 3.2 30.0 1.0 CG A:ASP157 3.2 30.3 1.0 CG A:ASP61 3.3 30.8 1.0 OE2 A:GLU115 3.4 35.9 1.0 ZN A:ZN302 3.4 41.0 1.0 CB A:ASP61 3.7 31.1 1.0 ZN A:ZN301 3.8 34.0 1.0 OE2 A:GLU59 3.8 38.1 1.0 CD A:GLU115 3.9 34.4 1.0 OE1 A:GLU115 4.2 35.5 1.0 CB A:ASP246 4.3 33.0 1.0 N A:SER196 4.3 26.2 1.0 OD2 A:ASP61 4.4 30.8 1.0 OG A:SER196 4.5 24.1 1.0 CB A:ASP157 4.6 29.8 1.0 CA A:VAL195 4.7 26.9 1.0 CG1 A:VAL195 4.7 24.8 1.0 CG A:GLU115 4.7 31.8 1.0 CD A:GLU59 4.7 39.2 1.0 CB A:SER196 4.9 25.9 1.0 OE1 A:GLU59 4.9 39.5 1.0

Zinc binding site 4 out of 38 in the Crystal Structure of TON_0340


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 TON_0340 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:89.8 occ:1.00 NE2 A:HIS31 2.4 40.1 1.0 OE2 A:GLU210 2.7 57.0 1.0 OE1 A:GLU210 2.8 54.0 1.0 CD A:GLU210 2.9 54.2 1.0 O A:HOH406 3.0 35.7 1.0 CE1 A:HIS31 3.0 37.6 1.0 CD2 A:HIS31 3.7 37.3 1.0 CG A:GLU210 4.1 51.0 1.0 ND1 A:HIS31 4.3 34.7 1.0 CG A:HIS31 4.6 33.4 1.0 O A:HOH408 4.7 47.6 1.0 CE A:LYS35 5.0 51.9 1.0

Zinc binding site 5 out of 38 in the Crystal Structure of TON_0340


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of TON_0340 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:61.8 occ:1.00 NE2 A:HIS177 2.4 40.2 1.0 CD2 A:HIS177 3.1 40.0 1.0 CE1 A:HIS177 3.5 39.5 1.0 CG A:HIS177 4.3 39.6 1.0 ND1 A:HIS177 4.5 40.6 1.0 CB A:PRO176 4.9 33.6 1.0

Zinc binding site 6 out of 38 in the Crystal Structure of TON_0340


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of TON_0340 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:47.1 occ:1.00 OD2 A:ASP21 2.1 41.6 1.0 NE2 A:HIS174 2.1 40.4 1.0 O A:HOH413 2.4 38.0 1.0 CE1 A:HIS174 2.8 40.9 1.0 CG A:ASP21 2.9 41.8 1.0 OD1 A:ASP21 3.0 43.5 1.0 CD2 A:HIS174 3.3 40.4 1.0 ND1 A:HIS174 4.0 41.3 1.0 CG A:HIS174 4.3 41.5 1.0 CB A:ASP21 4.3 38.9 1.0 NE F:ARG24 4.7 56.8 1.0 NH2 F:ARG24 4.8 60.3 1.0

Zinc binding site 7 out of 38 in the Crystal Structure of TON_0340


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of TON_0340 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:0.3 occ:1.00 OD2 A:ASP107 3.1 57.8 1.0 OD1 A:ASP107 3.7 58.2 1.0 CG A:ASP107 3.8 55.3 1.0 CG A:GLU104 4.6 58.0 1.0 CB A:GLU104 4.7 54.7 1.0 O A:HOH410 4.7 59.4 1.0

Zinc binding site 8 out of 38 in the Crystal Structure of TON_0340


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of TON_0340 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:37.9 occ:1.00 OD1 B:ASP61 2.0 42.3 1.0 OD2 B:ASP246 2.2 44.4 1.0 OD2 B:ASP157 2.3 47.3 1.0 O B:HOH408 2.7 31.6 1.0 OD1 B:ASP246 2.8 47.2 1.0 OE2 B:GLU115 2.8 41.8 1.0 CG B:ASP246 2.8 45.9 1.0 CG B:ASP157 3.0 45.7 1.0 ZN B:ZN302 3.1 54.7 1.0 OD1 B:ASP157 3.1 44.6 1.0 CG B:ASP61 3.1 41.0 1.0 CB B:ASP61 3.6 39.2 1.0 CD B:GLU115 3.9 42.2 1.0 ZN B:ZN303 4.0 43.1 1.0 N B:SER196 4.2 31.1 1.0 OG B:SER196 4.2 32.4 1.0 OD2 B:ASP61 4.2 41.5 1.0 O B:HOH411 4.2 36.4 1.0 CB B:ASP246 4.3 44.2 1.0 CB B:ASP157 4.5 43.5 1.0 CA B:VAL195 4.6 32.4 1.0 OE1 B:GLU115 4.7 40.6 1.0 CB B:SER196 4.7 31.7 1.0 CG1 B:VAL195 4.8 32.1 1.0 OE2 B:GLU59 4.8 39.2 1.0 CG B:GLU115 4.9 42.0 1.0 OE1 B:GLU59 4.9 40.9 1.0 C B:VAL195 4.9 32.0 1.0 O B:ALA194 4.9 34.3 1.0 O B:HOH409 5.0 42.0 1.0

Zinc binding site 9 out of 38 in the Crystal Structure of TON_0340


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of TON_0340 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:54.7 occ:1.00 O B:HOH408 2.0 31.6 1.0 OD1 B:ASP246 2.1 47.2 1.0 OE2 B:GLU59 2.3 39.2 1.0 O B:HOH409 2.4 42.0 1.0 OE1 B:GLU59 2.5 40.9 1.0 CD B:GLU59 2.7 39.0 1.0 ZN B:ZN301 3.1 37.9 1.0 CG B:ASP246 3.2 45.9 1.0 CB B:ASP61 3.7 39.2 1.0 OD2 B:ASP246 3.8 44.4 1.0 OE2 B:GLU115 3.8 41.8 1.0 OD1 B:ASP61 4.1 42.3 1.0 CG B:GLU59 4.2 38.8 1.0 CA B:GLY236 4.3 46.4 1.0 O B:HOH406 4.4 39.1 1.0 CB B:ASP246 4.4 44.2 1.0 CG B:ASP61 4.4 41.0 1.0 CA B:ASP246 4.4 43.0 1.0 O B:HOH411 4.5 36.4 1.0 N B:ASP246 4.7 41.7 1.0 N B:GLY236 4.8 46.0 1.0 CD B:GLU115 4.9 42.2 1.0 CA B:ASP61 5.0 37.9 1.0

Zinc binding site 10 out of 38 in the Crystal Structure of TON_0340


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of TON_0340 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:43.1 occ:1.00 O B:HOH411 2.2 36.4 1.0 OD1 B:ASP157 2.3 44.6 1.0 O B:HOH410 2.3 42.7 1.0 OE2 B:GLU161 2.3 40.5 1.0 OE2 B:GLU115 2.4 41.8 1.0 OE1 B:GLU115 2.6 40.6 1.0 CD B:GLU115 2.8 42.2 1.0 CD B:GLU161 3.1 41.2 1.0 O B:HOH408 3.1 31.6 1.0 CG B:ASP157 3.5 45.7 1.0 CG B:GLU161 3.6 39.7 1.0 N B:GLY158 3.8 43.0 1.0 N B:ASP157 3.9 38.9 1.0 ZN B:ZN301 4.0 37.9 1.0 OE1 B:GLU161 4.0 43.5 1.0 C B:ASP157 4.1 42.0 1.0 OD1 B:ASN160 4.2 50.2 1.0 CG B:GLU115 4.2 42.0 1.0 OD2 B:ASP157 4.2 47.3 1.0 CA B:GLY158 4.3 44.5 1.0 O B:HOH406 4.3 39.1 1.0 CA B:ASP157 4.4 41.8 1.0 OG B:SER196 4.5 32.4 1.0 CB B:ASP157 4.5 43.5 1.0 O B:ASP157 4.8 43.2 1.0 CE1 B:PHE50 5.0 45.2 1.0 CE B:MET128 5.0 79.3 1.0

S.S.Cha, Y.J.An, C.S.Jeong, M.K.Kim, S.G.Lee, K.H.Lee, B.H.Oh. Experimental Phasing Using Zinc Anomalous Scattering Acta Crystallogr.,Sect.D V. 68 1253 2012.
ISSN: ISSN 0907-4449
PubMed: 22948927
DOI: 10.1107/S0907444912024420