Zinc in PDB 2wkn: Gamma Lactamase From Delftia Acidovorans

All present enzymatic activity of Gamma Lactamase From Delftia Acidovorans:
3.5.1.49;

The structure of Gamma Lactamase From Delftia Acidovorans, PDB code: 2wkn was solved by M.N.Isupov, K.Line, I.S.Gonsalvez, P.Gange-Harris, M.Lanzotti, V.Saneei, J.A.Littlechild, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.78 / 2.08
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.871, 94.621, 152.297, 105.71, 90.27, 108.46
R / Rfree (%)	22 / 26.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Gamma Lactamase From Delftia Acidovorans (pdb code 2wkn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Gamma Lactamase From Delftia Acidovorans, PDB code: 2wkn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Gamma Lactamase From Delftia Acidovorans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Gamma Lactamase From Delftia Acidovorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn411 b:55.9 occ:1.00 OD2 A:ASP250 2.1 32.2 1.0 OD2 A:ASP225 2.2 31.4 1.0 OD1 A:ASN223 2.3 25.7 1.0 O A:HOH2332 2.5 26.5 1.0 OD1 A:ASP225 2.6 22.5 1.0 CG A:ASP225 2.7 28.1 1.0 CG A:ASN223 3.0 25.1 1.0 ND2 A:ASN223 3.1 20.7 1.0 CG A:ASP250 3.1 21.9 1.0 ZN A:ZN412 3.5 42.1 1.0 OD1 A:ASP250 3.6 34.5 1.0 NE2 A:HIS70 3.8 38.2 1.0 OE1 A:GLU259 4.1 38.0 1.0 O A:GLY153 4.1 32.4 1.0 CE1 A:HIS252 4.2 31.1 1.0 CB A:ASP225 4.2 22.5 1.0 NE2 A:HIS252 4.3 30.4 1.0 C A:GLY153 4.3 29.9 1.0 CA A:GLY153 4.3 26.9 1.0 CB A:ASP250 4.4 27.6 1.0 CB A:ASN223 4.4 20.7 1.0 CD2 A:HIS70 4.5 41.0 1.0 OE2 A:GLU259 4.5 39.4 1.0 OD1 B:ASP367 4.5 37.0 1.0 OD2 B:ASP367 4.6 36.7 1.0 CE1 A:HIS70 4.7 41.8 1.0 CD A:GLU259 4.8 40.5 1.0 CA A:ASP225 4.9 26.6 1.0 CA A:ASN223 4.9 24.6 1.0 N A:LEU154 5.0 31.1 1.0 N A:ASP225 5.0 25.4 1.0 CG B:ASP367 5.0 38.1 1.0

Zinc binding site 2 out of 16 in the Gamma Lactamase From Delftia Acidovorans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Gamma Lactamase From Delftia Acidovorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn412 b:42.1 occ:1.00 OE2 A:GLU267 1.9 24.7 1.0 OD1 A:ASP250 2.1 34.5 1.0 NE2 A:HIS252 2.1 30.4 1.0 CD A:GLU267 2.6 29.6 1.0 OE1 A:GLU267 2.6 28.6 1.0 CG A:ASP250 2.8 21.9 1.0 OD2 A:ASP250 2.9 32.2 1.0 CD2 A:HIS252 3.0 20.9 1.0 O A:HOH2332 3.1 26.5 1.0 CE1 A:HIS252 3.1 31.1 1.0 ZN A:ZN411 3.5 55.9 1.0 OE2 A:GLU259 3.7 39.4 1.0 O A:ASP250 4.0 28.3 1.0 CG A:GLU267 4.1 24.4 1.0 CB A:ASP250 4.2 27.6 1.0 CG A:HIS252 4.2 25.3 1.0 ND1 A:HIS252 4.2 30.4 1.0 OD2 A:ASP225 4.4 31.4 1.0 C A:ASP250 4.5 25.9 1.0 CD2 A:TRP47 4.5 32.3 1.0 CA A:ASP250 4.6 26.0 1.0 CG A:TRP47 4.6 30.1 1.0 CA A:GLY264 4.7 32.0 1.0 CD A:GLU259 4.8 40.5 1.0 CE2 A:TRP47 4.8 31.0 1.0 O A:HOH2256 4.8 31.9 1.0 CB A:ALA265 4.8 27.3 1.0 CD1 A:TRP47 4.8 32.8 1.0 N A:GLY264 4.8 29.8 1.0 CE3 A:TRP47 4.9 31.5 1.0 NE1 A:TRP47 5.0 32.1 1.0 CB A:TRP47 5.0 29.6 1.0

Zinc binding site 3 out of 16 in the Gamma Lactamase From Delftia Acidovorans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Gamma Lactamase From Delftia Acidovorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn411 b:48.3 occ:1.00 OD2 B:ASP250 2.1 32.0 1.0 OD2 B:ASP225 2.1 31.9 1.0 OD1 B:ASN223 2.3 25.2 1.0 O B:HOH2219 2.4 20.2 1.0 OD1 B:ASP225 2.5 22.6 1.0 CG B:ASP225 2.7 28.1 1.0 CG B:ASN223 3.0 25.4 1.0 ND2 B:ASN223 3.1 20.6 1.0 CG B:ASP250 3.2 21.7 1.0 ZN B:ZN412 3.5 45.5 1.0 OD1 B:ASP250 3.7 35.1 1.0 NE2 B:HIS70 3.9 38.1 1.0 OE1 B:GLU259 4.1 38.3 1.0 O B:GLY153 4.1 32.5 1.0 CB B:ASP225 4.2 21.9 1.0 CE1 B:HIS252 4.2 31.5 1.0 C B:GLY153 4.2 30.3 1.0 NE2 B:HIS252 4.2 30.7 1.0 CA B:GLY153 4.2 27.0 1.0 CB B:ASP250 4.4 27.7 1.0 CB B:ASN223 4.4 20.9 1.0 OD1 A:ASP367 4.6 37.4 1.0 CD2 B:HIS70 4.6 41.0 1.0 OD2 A:ASP367 4.6 37.1 1.0 OE2 B:GLU259 4.6 39.7 1.0 CE1 B:HIS70 4.8 41.9 1.0 CD B:GLU259 4.8 40.8 1.0 CA B:ASP225 4.8 27.0 1.0 N B:ASP225 4.9 25.6 1.0 N B:LEU154 4.9 31.0 1.0 CA B:ASN223 4.9 24.6 1.0 CG A:ASP367 5.0 38.2 1.0

Zinc binding site 4 out of 16 in the Gamma Lactamase From Delftia Acidovorans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Gamma Lactamase From Delftia Acidovorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn412 b:45.5 occ:1.00 OD1 B:ASP250 1.7 35.1 1.0 OE2 B:GLU267 2.1 23.8 1.0 O B:HOH2219 2.2 20.2 1.0 NE2 B:HIS252 2.3 30.7 1.0 CG B:ASP250 2.6 21.7 1.0 OE1 B:GLU267 2.6 29.2 1.0 CD B:GLU267 2.7 29.2 1.0 OD2 B:ASP250 2.8 32.0 1.0 CD2 B:HIS252 3.1 21.1 1.0 CE1 B:HIS252 3.3 31.5 1.0 ZN B:ZN411 3.5 48.3 1.0 O B:ASP250 3.8 28.8 1.0 CB B:ASP250 4.0 27.7 1.0 OE2 B:GLU259 4.0 39.7 1.0 CG B:GLU267 4.2 25.2 1.0 C B:ASP250 4.3 26.6 1.0 CA B:ASP250 4.3 26.7 1.0 CG B:HIS252 4.3 25.4 1.0 CD2 B:TRP47 4.4 32.3 1.0 CG B:TRP47 4.4 29.8 1.0 ND1 B:HIS252 4.4 30.5 1.0 O B:HOH2138 4.5 32.8 1.0 OD2 B:ASP225 4.5 31.9 1.0 CE2 B:TRP47 4.7 31.1 1.0 CD1 B:TRP47 4.7 32.5 1.0 CE3 B:TRP47 4.7 31.4 1.0 CB B:TRP47 4.7 29.4 1.0 NE1 B:TRP47 4.9 31.9 1.0 CA B:GLY264 5.0 32.0 1.0 CD2 B:HIS70 5.0 41.0 1.0 CD B:GLU259 5.0 40.8 1.0 NE2 B:HIS70 5.0 38.1 1.0

Zinc binding site 5 out of 16 in the Gamma Lactamase From Delftia Acidovorans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Gamma Lactamase From Delftia Acidovorans within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn411 b:56.9 occ:1.00 OD1 C:ASN223 2.1 24.6 1.0 OD2 C:ASP250 2.1 32.0 1.0 OD2 C:ASP225 2.3 31.4 1.0 O C:HOH2197 2.4 33.1 1.0 OD1 C:ASP225 2.6 22.8 1.0 CG C:ASP225 2.8 27.9 1.0 CG C:ASN223 2.8 25.5 1.0 ND2 C:ASN223 2.9 20.7 1.0 CG C:ASP250 3.2 21.6 1.0 ZN C:ZN412 3.5 48.0 1.0 OD1 C:ASP250 3.7 34.8 1.0 NE2 C:HIS70 3.8 38.2 1.0 OE1 C:GLU259 4.2 38.3 1.0 O C:GLY153 4.2 32.4 1.0 CB C:ASP225 4.3 21.9 1.0 CB C:ASN223 4.3 20.9 1.0 CE1 C:HIS252 4.3 31.7 1.0 C C:GLY153 4.3 30.1 1.0 NE2 C:HIS252 4.3 30.4 1.0 CA C:GLY153 4.4 26.9 1.0 CB C:ASP250 4.4 27.8 1.0 CD2 C:HIS70 4.4 40.9 1.0 OD1 D:ASP367 4.5 36.9 1.0 CE1 C:HIS70 4.6 41.9 1.0 OD2 D:ASP367 4.6 36.7 1.0 OE2 C:GLU259 4.7 40.0 1.0 CD C:GLU259 4.8 40.6 1.0 CA C:ASN223 4.9 24.5 1.0 CG D:ASP367 4.9 38.3 1.0 CA C:ASP225 5.0 26.8 1.0

Zinc binding site 6 out of 16 in the Gamma Lactamase From Delftia Acidovorans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Gamma Lactamase From Delftia Acidovorans within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn412 b:48.0 occ:1.00 OD1 C:ASP250 1.8 34.8 1.0 OE2 C:GLU267 2.1 24.3 1.0 O C:HOH2197 2.2 33.1 1.0 NE2 C:HIS252 2.2 30.4 1.0 CG C:ASP250 2.6 21.6 1.0 CD C:GLU267 2.7 29.2 1.0 OE1 C:GLU267 2.7 29.1 1.0 OD2 C:ASP250 2.8 32.0 1.0 CD2 C:HIS252 3.1 21.1 1.0 CE1 C:HIS252 3.2 31.7 1.0 ZN C:ZN411 3.5 56.9 1.0 OE2 C:GLU259 3.9 40.0 1.0 O C:ASP250 3.9 28.9 1.0 CB C:ASP250 4.0 27.8 1.0 CG C:GLU267 4.2 24.8 1.0 CG C:HIS252 4.3 25.5 1.0 ND1 C:HIS252 4.3 30.8 1.0 OD2 C:ASP225 4.4 31.4 1.0 CD2 C:TRP47 4.4 32.3 1.0 C C:ASP250 4.4 26.5 1.0 CG C:TRP47 4.5 30.1 1.0 CA C:ASP250 4.5 26.4 1.0 O C:HOH2024 4.7 42.1 1.0 CE2 C:TRP47 4.7 31.0 1.0 CE3 C:TRP47 4.7 31.2 1.0 CD1 C:TRP47 4.7 32.6 1.0 CB C:TRP47 4.8 29.6 1.0 CA C:GLY264 4.9 32.4 1.0 CD C:GLU259 4.9 40.6 1.0 NE1 C:TRP47 4.9 32.1 1.0 CB C:ALA265 4.9 27.0 1.0 N C:GLY264 4.9 30.1 1.0

Zinc binding site 7 out of 16 in the Gamma Lactamase From Delftia Acidovorans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Gamma Lactamase From Delftia Acidovorans within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn411 b:55.8 occ:1.00 OD2 D:ASP250 2.2 32.1 1.0 OD2 D:ASP225 2.2 31.3 1.0 OD1 D:ASN223 2.3 25.5 1.0 O D:HOH2269 2.4 23.4 1.0 OD1 D:ASP225 2.6 22.1 1.0 CG D:ASP225 2.8 28.0 1.0 CG D:ASN223 3.0 25.2 1.0 ND2 D:ASN223 3.0 20.5 1.0 CG D:ASP250 3.1 21.4 1.0 ZN D:ZN412 3.4 38.4 1.0 OD1 D:ASP250 3.6 34.4 1.0 NE2 D:HIS70 3.8 38.2 1.0 OE1 D:GLU259 4.1 38.4 1.0 O D:GLY153 4.2 32.2 1.0 CE1 D:HIS252 4.2 31.4 1.0 NE2 D:HIS252 4.2 30.6 1.0 CB D:ASP225 4.3 22.2 1.0 C D:GLY153 4.3 30.0 1.0 CA D:GLY153 4.3 26.8 1.0 CB D:ASP250 4.4 28.0 1.0 CB D:ASN223 4.4 20.8 1.0 CD2 D:HIS70 4.5 40.9 1.0 OD2 C:ASP367 4.5 37.1 1.0 OD1 C:ASP367 4.6 36.6 1.0 OE2 D:GLU259 4.6 39.5 1.0 CE1 D:HIS70 4.6 41.8 1.0 CD D:GLU259 4.8 40.3 1.0 CG C:ASP367 4.9 38.1 1.0 CA D:ASP225 4.9 26.7 1.0 CA D:ASN223 4.9 24.6 1.0 N D:LEU154 5.0 31.0 1.0 N D:ASP225 5.0 25.2 1.0

Zinc binding site 8 out of 16 in the Gamma Lactamase From Delftia Acidovorans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Gamma Lactamase From Delftia Acidovorans within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn412 b:38.4 occ:1.00 OD1 D:ASP250 1.9 34.4 1.0 OE2 D:GLU267 2.1 24.2 1.0 NE2 D:HIS252 2.1 30.6 1.0 OE1 D:GLU267 2.6 29.1 1.0 CG D:ASP250 2.6 21.4 1.0 CD D:GLU267 2.7 29.2 1.0 OD2 D:ASP250 2.8 32.1 1.0 O D:HOH2269 2.9 23.4 1.0 CD2 D:HIS252 3.1 21.2 1.0 CE1 D:HIS252 3.2 31.4 1.0 ZN D:ZN411 3.4 55.8 1.0 O D:ASP250 3.8 28.3 1.0 OE2 D:GLU259 3.9 39.5 1.0 CB D:ASP250 4.0 28.0 1.0 CG D:GLU267 4.2 24.8 1.0 CG D:HIS252 4.2 25.2 1.0 ND1 D:HIS252 4.3 30.1 1.0 OD2 D:ASP225 4.4 31.3 1.0 C D:ASP250 4.4 26.2 1.0 CA D:ASP250 4.4 26.1 1.0 CD2 D:TRP47 4.5 32.5 1.0 CG D:TRP47 4.5 30.1 1.0 O D:HOH2195 4.7 30.1 1.0 CD1 D:TRP47 4.8 32.5 1.0 CE2 D:TRP47 4.8 31.0 1.0 CE3 D:TRP47 4.8 31.2 1.0 CA D:GLY264 4.9 32.2 1.0 CD D:GLU259 4.9 40.3 1.0 CB D:TRP47 4.9 29.6 1.0 CB D:ALA265 4.9 26.9 1.0 NE1 D:TRP47 5.0 31.9 1.0 N D:GLY264 5.0 29.9 1.0

Zinc binding site 9 out of 16 in the Gamma Lactamase From Delftia Acidovorans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Gamma Lactamase From Delftia Acidovorans within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn411 b:61.8 occ:1.00 OD2 E:ASP250 2.1 32.2 1.0 OD1 E:ASN223 2.1 25.6 1.0 OD2 E:ASP225 2.2 31.4 1.0 O E:HOH2249 2.4 30.8 1.0 OD1 E:ASP225 2.7 22.8 1.0 CG E:ASP225 2.8 27.9 1.0 CG E:ASN223 2.9 25.3 1.0 ND2 E:ASN223 3.1 20.5 1.0 CG E:ASP250 3.2 21.7 1.0 ZN E:ZN412 3.5 46.2 1.0 OD1 E:ASP250 3.7 35.0 1.0 NE2 E:HIS70 3.8 38.0 1.0 O E:GLY153 4.1 32.3 1.0 OE1 E:GLU259 4.2 38.4 1.0 C E:GLY153 4.2 30.1 1.0 CB E:ASP225 4.3 22.4 1.0 CE1 E:HIS252 4.3 31.5 1.0 CA E:GLY153 4.3 26.9 1.0 NE2 E:HIS252 4.3 30.2 1.0 CB E:ASN223 4.3 21.2 1.0 CB E:ASP250 4.4 28.1 1.0 OD1 G:ASP367 4.5 37.0 1.0 CD2 E:HIS70 4.5 40.9 1.0 OD2 G:ASP367 4.5 37.0 1.0 OE2 E:GLU259 4.6 39.5 1.0 CE1 E:HIS70 4.6 41.8 1.0 CA E:ASN223 4.8 24.6 1.0 CD E:GLU259 4.8 40.6 1.0 CG G:ASP367 4.9 38.1 1.0 CA E:ASP225 4.9 26.8 1.0 N E:ASP225 4.9 25.6 1.0 N E:LEU154 4.9 30.9 1.0 C E:ASN223 5.0 25.5 1.0 CB E:LEU154 5.0 30.5 1.0

Zinc binding site 10 out of 16 in the Gamma Lactamase From Delftia Acidovorans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Gamma Lactamase From Delftia Acidovorans within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn412 b:46.2 occ:1.00 OD1 E:ASP250 1.9 35.0 1.0 OE2 E:GLU267 2.0 25.1 1.0 NE2 E:HIS252 2.1 30.2 1.0 CD E:GLU267 2.7 29.5 1.0 CG E:ASP250 2.7 21.7 1.0 OE1 E:GLU267 2.7 29.2 1.0 O E:HOH2249 2.9 30.8 1.0 OD2 E:ASP250 2.9 32.2 1.0 CD2 E:HIS252 3.1 20.9 1.0 CE1 E:HIS252 3.1 31.5 1.0 ZN E:ZN411 3.5 61.8 1.0 OE2 E:GLU259 3.7 39.5 1.0 O E:ASP250 3.9 28.9 1.0 CB E:ASP250 4.1 28.1 1.0 CG E:GLU267 4.2 25.0 1.0 ND1 E:HIS252 4.2 30.5 1.0 CG E:HIS252 4.2 25.3 1.0 OD2 E:ASP225 4.3 31.4 1.0 C E:ASP250 4.5 26.2 1.0 CA E:ASP250 4.5 26.3 1.0 CD2 E:TRP47 4.5 32.4 1.0 CG E:TRP47 4.6 30.0 1.0 O E:HOH2182 4.7 29.0 1.0 CD E:GLU259 4.8 40.6 1.0 CA E:GLY264 4.8 32.1 1.0 CE2 E:TRP47 4.8 31.1 1.0 CB E:ALA265 4.8 26.7 1.0 CD1 E:TRP47 4.8 32.6 1.0 CE3 E:TRP47 4.8 31.3 1.0 N E:GLY264 4.9 29.9 1.0 CB E:TRP47 4.9 29.7 1.0 NE1 E:TRP47 5.0 32.0 1.0

M.N.Isupov, K.Line, I.S.Gonsalvez, P.Gange-Harris, M.Lanzotti, V.Saneei, J.A.Littlechild. The Structure of Gamma Lactamase From Delftia Acidovorans To Be Published.