Zinc in PDB 2o4m: Structure of Phosphotriesterase Mutant I106G/F132G/H257Y

All present enzymatic activity of Structure of Phosphotriesterase Mutant I106G/F132G/H257Y:
3.1.8.1;

The structure of Structure of Phosphotriesterase Mutant I106G/F132G/H257Y, PDB code: 2o4m was solved by J.Kim, U.A.Ramagopal, P.Tsai, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.33 / 1.64
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.759, 68.906, 89.670, 90.03, 100.29, 94.12
R / Rfree (%)	18.9 / 24.4

The structure of Structure of Phosphotriesterase Mutant I106G/F132G/H257Y also contains other interesting chemical elements:

Arsenic

(As)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Zinc atom in the Structure of Phosphotriesterase Mutant I106G/F132G/H257Y (pdb code 2o4m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 23 binding sites of Zinc where determined in the Structure of Phosphotriesterase Mutant I106G/F132G/H257Y, PDB code: 2o4m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 23 in the Structure of Phosphotriesterase Mutant I106G/F132G/H257Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Phosphotriesterase Mutant I106G/F132G/H257Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3001 b:9.8 occ:0.85 O2 A:CAC4001 2.0 7.1 0.8 NE2 A:HIS55 2.1 12.2 1.0 NE2 A:HIS57 2.1 11.0 1.0 OQ1 A:KCX169 2.2 11.7 1.0 OD1 A:ASP301 2.5 10.4 1.0 CE1 A:HIS57 3.0 11.3 1.0 CX A:KCX169 3.0 15.7 1.0 CD2 A:HIS55 3.0 12.0 1.0 CE1 A:HIS55 3.1 12.7 1.0 CD2 A:HIS57 3.1 10.4 1.0 AS A:CAC4001 3.2 12.5 0.8 CG A:ASP301 3.3 13.4 1.0 OD2 A:ASP301 3.4 12.4 1.0 OQ2 A:KCX169 3.4 14.0 1.0 C1 A:CAC4001 3.6 10.7 0.8 CG2 A:VAL101 4.0 14.5 1.0 ZN A:ZN3003 4.0 10.6 0.8 O1 A:CAC4001 4.1 14.0 0.8 NZ A:KCX169 4.1 14.2 1.0 ND1 A:HIS57 4.1 11.0 1.0 ND1 A:HIS55 4.1 11.9 1.0 CG A:HIS55 4.1 8.2 1.0 CE1 A:HIS230 4.2 13.1 1.0 CG A:HIS57 4.2 10.6 1.0 NE2 A:HIS230 4.5 13.8 1.0 CB A:ASP301 4.7 10.5 1.0 C2 A:CAC4001 4.7 15.3 0.8

Zinc binding site 2 out of 23 in the Structure of Phosphotriesterase Mutant I106G/F132G/H257Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Phosphotriesterase Mutant I106G/F132G/H257Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3003 b:10.6 occ:0.85 O1 A:CAC4001 1.9 14.0 0.8 ND1 A:HIS201 2.0 7.3 1.0 NE2 A:HIS230 2.1 13.8 1.0 OQ2 A:KCX169 2.1 14.0 1.0 O2 A:CAC4001 2.9 7.1 0.8 CE1 A:HIS201 3.0 20.0 1.0 CD2 A:HIS230 3.0 12.2 1.0 CG A:HIS201 3.1 9.7 1.0 CE1 A:HIS230 3.1 13.1 1.0 CX A:KCX169 3.1 15.7 1.0 AS A:CAC4001 3.1 12.5 0.8 OQ1 A:KCX169 3.4 11.7 1.0 CB A:HIS201 3.4 11.2 1.0 NE1 A:TRP131 3.9 18.1 1.0 ZN A:ZN3001 4.0 9.8 0.8 NE2 A:HIS201 4.1 16.6 1.0 CG A:HIS230 4.2 11.6 1.0 CD2 A:HIS201 4.2 11.5 1.0 ND1 A:HIS230 4.2 12.6 1.0 NZ A:KCX169 4.2 14.2 1.0 CA A:HIS201 4.3 11.5 1.0 CE1 A:HIS55 4.4 12.7 1.0 C2 A:CAC4001 4.4 15.3 0.8 NE2 A:HIS55 4.5 12.2 1.0 CD1 A:TRP131 4.5 19.5 1.0 C1 A:CAC4001 4.6 10.7 0.8 CE A:KCX169 4.6 8.5 1.0 OD2 A:ASP301 4.8 12.4 1.0

Zinc binding site 3 out of 23 in the Structure of Phosphotriesterase Mutant I106G/F132G/H257Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Phosphotriesterase Mutant I106G/F132G/H257Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3009 b:16.3 occ:0.90 OD2 A:ASP233 1.9 16.2 1.0 NE2 A:HIS254 2.1 13.1 1.0 OXT A:ACY6003 2.3 24.2 0.8 O A:HOH6223 2.3 24.2 1.0 O A:HOH6210 2.4 26.6 1.0 O A:ACY6003 2.4 18.2 0.8 C A:ACY6003 2.6 26.1 0.8 CG A:ASP233 2.8 15.6 1.0 OD1 A:ASP233 3.0 19.2 1.0 CD2 A:HIS254 3.1 18.3 1.0 CE1 A:HIS254 3.1 16.0 1.0 CH3 A:ACY6003 3.9 25.2 0.8 O A:HOH6353 4.0 34.6 1.0 NH2 A:ARG280 4.1 17.4 1.0 ND1 A:HIS254 4.2 12.0 1.0 CB A:ASP233 4.2 15.8 1.0 O A:LEU271 4.2 14.5 1.0 CG A:HIS254 4.2 12.5 1.0 O A:HOH6129 4.3 20.6 1.0 O A:HOH6015 4.3 19.9 1.0 O A:HOH6227 4.4 27.4 1.0 O A:HOH6299 4.6 36.3 1.0 NH1 A:ARG280 4.6 13.4 1.0 CZ A:ARG280 4.8 20.5 1.0 CB A:HIS230 4.9 12.2 1.0

Zinc binding site 4 out of 23 in the Structure of Phosphotriesterase Mutant I106G/F132G/H257Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Phosphotriesterase Mutant I106G/F132G/H257Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3013 b:21.4 occ:0.60 OE2 A:GLU48 1.9 30.9 1.0 NE2 A:HIS123 2.0 14.7 1.0 CE1 A:HIS123 2.6 12.7 1.0 CD A:GLU48 2.9 33.5 1.0 CD2 A:HIS123 3.2 18.7 1.0 CG A:GLU48 3.3 19.1 1.0 ND1 A:HIS123 3.9 19.2 1.0 O A:HOH6201 3.9 23.8 1.0 OE1 A:GLU48 4.0 37.9 1.0 CG A:HIS123 4.2 13.5 1.0 NH2 A:ARG41 4.7 26.8 0.5 O A:HOH6091 4.7 24.6 1.0 CB A:GLU48 4.8 19.0 1.0 O A:GLU48 4.8 18.0 1.0 CG2 A:ILE44 4.9 16.2 1.0

Zinc binding site 5 out of 23 in the Structure of Phosphotriesterase Mutant I106G/F132G/H257Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Phosphotriesterase Mutant I106G/F132G/H257Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3018 b:23.9 occ:0.50 OE1 A:GLU344 2.1 30.1 1.0 CD A:GLU344 2.8 31.9 1.0 OE2 A:GLU344 2.9 30.9 1.0 O A:HOH6153 3.5 51.9 1.0 N A:GLN343 3.7 24.4 1.0 CB A:PRO342 4.1 22.1 1.0 CA A:PRO342 4.3 21.7 1.0 CG A:GLU344 4.3 26.3 1.0 N A:GLU344 4.3 23.8 1.0 C A:PRO342 4.4 22.4 1.0 CB A:GLN343 4.6 26.1 1.0 CA A:GLN343 4.6 25.3 1.0 CB A:GLU344 4.9 25.3 1.0

Zinc binding site 6 out of 23 in the Structure of Phosphotriesterase Mutant I106G/F132G/H257Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Phosphotriesterase Mutant I106G/F132G/H257Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3024 b:20.6 occ:0.20 OD2 A:ASP236 2.0 37.0 1.0 O A:HOH6305 2.1 42.2 1.0 NH1 A:ARG207 2.5 43.1 1.0 CG A:ASP236 2.8 31.8 1.0 NH2 A:ARG207 2.9 43.5 1.0 OG A:SER238 2.9 20.6 0.5 OD1 A:ASP236 2.9 32.9 1.0 CZ A:ARG207 3.1 40.3 1.0 O A:HOH6379 4.0 36.1 1.0 CB A:ASP236 4.2 26.1 1.0 CB A:SER238 4.3 20.1 0.5 N A:TYR239 4.3 18.0 1.0 NE A:ARG207 4.3 28.4 1.0 CB A:SER238 4.6 19.2 0.5 CB A:TYR239 4.6 18.6 1.0 O A:HOH6023 4.7 27.9 1.0 CA A:TYR239 4.8 17.2 1.0 C A:SER238 4.9 17.6 0.5 O A:HOH6310 4.9 32.7 1.0 C A:SER238 4.9 18.0 0.5

Zinc binding site 7 out of 23 in the Structure of Phosphotriesterase Mutant I106G/F132G/H257Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Phosphotriesterase Mutant I106G/F132G/H257Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3005 b:12.0 occ:0.90 O1 B:CAC4002 1.9 8.9 0.8 NE2 B:HIS57 2.0 8.5 1.0 NE2 B:HIS55 2.1 11.4 1.0 OQ2 B:KCX169 2.1 12.6 1.0 OD1 B:ASP301 2.5 12.8 1.0 CE1 B:HIS57 2.9 14.1 1.0 CX B:KCX169 3.0 14.5 1.0 CD2 B:HIS55 3.0 10.4 1.0 CD2 B:HIS57 3.1 12.1 1.0 CE1 B:HIS55 3.1 13.3 1.0 AS B:CAC4002 3.2 15.2 0.8 CG B:ASP301 3.3 20.1 1.0 OD2 B:ASP301 3.4 13.8 1.0 OQ1 B:KCX169 3.5 15.7 1.0 C2 B:CAC4002 3.6 18.1 0.8 CG2 B:VAL101 3.9 15.8 1.0 NZ B:KCX169 4.0 18.7 1.0 ZN B:ZN3006 4.0 14.1 0.9 ND1 B:HIS57 4.0 13.7 1.0 CG B:HIS57 4.2 11.9 1.0 ND1 B:HIS55 4.2 14.5 1.0 CG B:HIS55 4.2 10.2 1.0 O2 B:CAC4002 4.2 16.1 0.8 CE1 B:HIS230 4.3 14.4 1.0 NE2 B:HIS230 4.5 12.6 1.0 CB B:ASP301 4.7 14.4 1.0 C1 B:CAC4002 4.8 18.6 0.8

Zinc binding site 8 out of 23 in the Structure of Phosphotriesterase Mutant I106G/F132G/H257Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Phosphotriesterase Mutant I106G/F132G/H257Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3006 b:14.1 occ:0.90 O2 B:CAC4002 1.9 16.1 0.8 OQ1 B:KCX169 2.0 15.7 1.0 NE2 B:HIS230 2.1 12.6 1.0 ND1 B:HIS201 2.1 16.2 1.0 CD2 B:HIS230 2.9 19.1 1.0 CE1 B:HIS201 3.0 19.5 1.0 O1 B:CAC4002 3.0 8.9 0.8 CX B:KCX169 3.0 14.5 1.0 CG B:HIS201 3.1 17.0 1.0 AS B:CAC4002 3.1 15.2 0.8 CE1 B:HIS230 3.2 14.4 1.0 OQ2 B:KCX169 3.3 12.6 1.0 CB B:HIS201 3.4 14.5 1.0 NE1 B:TRP131 4.0 23.9 1.0 ZN B:ZN3005 4.0 12.0 0.9 CH3 B:ACY6002 4.1 39.0 1.0 CG B:HIS230 4.1 15.0 1.0 NE2 B:HIS201 4.1 18.1 1.0 ND1 B:HIS230 4.2 15.2 1.0 CD2 B:HIS201 4.2 17.2 1.0 NZ B:KCX169 4.2 18.7 1.0 CA B:HIS201 4.3 15.4 1.0 CE1 B:HIS55 4.4 13.3 1.0 C1 B:CAC4002 4.4 18.6 0.8 CD1 B:TRP131 4.5 21.4 1.0 C2 B:CAC4002 4.6 18.1 0.8 NE2 B:HIS55 4.6 11.4 1.0 CE B:KCX169 4.6 14.5 1.0 OD2 B:ASP301 4.8 13.8 1.0

Zinc binding site 9 out of 23 in the Structure of Phosphotriesterase Mutant I106G/F132G/H257Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Phosphotriesterase Mutant I106G/F132G/H257Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3010 b:18.4 occ:0.80 OD2 B:ASP233 1.8 23.4 1.0 O B:ACY6002 1.9 32.9 1.0 O B:HOH6139 2.0 30.1 1.0 NE2 B:HIS254 2.1 17.6 1.0 OXT B:ACY6002 2.3 31.9 1.0 C B:ACY6002 2.4 36.0 1.0 CG B:ASP233 2.8 19.5 1.0 CD2 B:HIS254 3.0 21.5 1.0 OD1 B:ASP233 3.1 21.1 1.0 CE1 B:HIS254 3.1 17.5 1.0 CH3 B:ACY6002 3.8 39.0 1.0 O B:HOH6220 4.0 32.2 1.0 NH2 B:ARG280 4.1 24.2 1.0 CB B:ASP233 4.2 22.4 1.0 CG B:HIS254 4.2 12.2 1.0 ND1 B:HIS254 4.2 15.4 1.0 O B:HOH6071 4.3 20.9 1.0 O B:LEU271 4.3 17.4 1.0 NH1 B:ARG280 4.5 21.2 1.0 O B:HOH6363 4.6 39.5 1.0 CZ B:ARG280 4.8 19.9 1.0 CB B:HIS230 4.8 17.5 1.0 CG B:HIS230 4.9 15.0 1.0

Zinc binding site 10 out of 23 in the Structure of Phosphotriesterase Mutant I106G/F132G/H257Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Phosphotriesterase Mutant I106G/F132G/H257Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3014 b:23.9 occ:0.65 NE2 B:HIS123 2.0 18.3 1.0 OE2 B:GLU48 2.1 32.3 1.0 O B:HOH6265 2.1 37.2 1.0 O2 B:GOL5002 2.5 40.0 1.0 CE1 B:HIS123 2.6 17.6 1.0 CD B:GLU48 2.9 37.2 1.0 C3 B:GOL5002 3.1 33.2 1.0 C2 B:GOL5002 3.2 31.2 1.0 CD2 B:HIS123 3.2 19.9 1.0 O3 B:GOL5002 3.3 30.8 1.0 CG B:GLU48 3.3 28.0 1.0 ND1 B:HIS123 3.8 21.2 1.0 O B:HOH6138 3.9 29.6 1.0 OE1 B:GLU48 4.0 37.6 1.0 O B:HOH6290 4.1 31.3 1.0 CG B:HIS123 4.2 14.6 1.0 O B:HOH6151 4.5 23.9 1.0 C1 B:GOL5002 4.6 35.4 1.0 CB B:GLU48 4.8 23.6 1.0 O B:GLU48 5.0 21.8 1.0 CG2 B:ILE44 5.0 18.6 1.0

J.Kim, U.A.Ramagopal, P.Tsai, F.M.Raushel, S.C.Almo. Structure of Phosphotriesterase Mutant I106G/F132G/H257Y To Be Published.