Zinc in PDB 2ek8: Aminopeptidase From Aneurinibacillus Sp. Strain Am-1

The structure of Aminopeptidase From Aneurinibacillus Sp. Strain Am-1, PDB code: 2ek8 was solved by M.Akioka, H.Nakano, K.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.85 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.624, 68.618, 76.841, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 23.8

The binding sites of Zinc atom in the Aminopeptidase From Aneurinibacillus Sp. Strain Am-1 (pdb code 2ek8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Aminopeptidase From Aneurinibacillus Sp. Strain Am-1, PDB code: 2ek8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Aminopeptidase From Aneurinibacillus Sp. Strain Am-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Aminopeptidase From Aneurinibacillus Sp. Strain Am-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:20.0 occ:1.00 OD2 A:ASP240 2.0 17.3 1.0 OE2 A:GLU273 2.1 18.1 1.0 NE2 A:HIS371 2.1 24.3 1.0 O A:HOH2379 2.3 23.8 1.0 OE1 A:GLU273 2.6 18.1 1.0 CD A:GLU273 2.7 13.3 1.0 CG A:ASP240 3.0 17.3 1.0 CD2 A:HIS371 3.1 22.3 1.0 CE1 A:HIS371 3.1 23.8 1.0 OD1 A:ASP240 3.2 17.5 1.0 ZN A:ZN1002 3.5 17.6 1.0 CE1 A:TYR370 3.8 25.1 1.0 O A:HOH2125 3.9 26.9 1.0 O A:HOH2009 3.9 15.3 1.0 OH A:TYR370 4.1 24.4 1.0 CG A:GLU273 4.2 15.9 1.0 ND1 A:HIS371 4.2 24.5 1.0 CG A:HIS371 4.2 22.1 1.0 CB A:ASP240 4.3 14.1 1.0 CZ A:TYR370 4.3 24.8 1.0 O A:HOH2388 4.3 50.9 1.0 OE1 A:GLU272 4.4 14.8 1.0 CG1 A:VAL232 4.6 18.5 1.0 CE1 A:HIS228 4.6 10.6 1.0 NE2 A:HIS228 4.6 12.3 1.0 CD1 A:TYR370 4.8 24.0 1.0 O A:HOH2113 4.8 26.1 1.0

Zinc binding site 2 out of 6 in the Aminopeptidase From Aneurinibacillus Sp. Strain Am-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Aminopeptidase From Aneurinibacillus Sp. Strain Am-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:17.6 occ:1.00 OD1 A:ASP240 2.0 17.5 1.0 O A:HOH2379 2.0 23.8 1.0 NE2 A:HIS228 2.1 12.3 1.0 OD1 A:ASP301 2.1 15.2 1.0 OD2 A:ASP301 2.4 13.4 1.0 CG A:ASP301 2.6 15.0 1.0 CE1 A:HIS228 3.1 10.6 1.0 CG A:ASP240 3.1 17.3 1.0 CD2 A:HIS228 3.1 12.2 1.0 OD2 A:ASP240 3.5 17.3 1.0 ZN A:ZN1001 3.5 20.0 1.0 CB A:ASP241 3.9 11.2 1.0 OE2 A:GLU273 3.9 18.1 1.0 OE1 A:GLU272 4.0 14.8 1.0 O A:HOH2388 4.0 50.9 1.0 CB A:ASP301 4.1 13.1 1.0 ND1 A:HIS228 4.2 12.6 1.0 CG A:HIS228 4.2 11.4 1.0 CD A:GLU272 4.2 16.5 1.0 OE2 A:GLU272 4.3 19.4 1.0 CB A:ASP240 4.3 14.1 1.0 CG A:ASP241 4.4 11.4 1.0 CE A:MET302 4.5 21.7 1.0 CG A:MET302 4.5 15.6 1.0 CA A:ASP240 4.6 14.7 1.0 OD2 A:ASP241 4.6 11.0 1.0 CD A:GLU273 4.7 13.3 1.0 O A:HOH2125 4.7 26.9 1.0 SD A:MET302 4.7 17.8 1.0 C A:ASP240 4.8 13.7 1.0 CA A:ASP301 4.8 13.0 1.0 CA A:ASP241 4.8 11.6 1.0 N A:ASP241 4.9 12.3 1.0 OG A:SER346 5.0 15.6 1.0

Zinc binding site 3 out of 6 in the Aminopeptidase From Aneurinibacillus Sp. Strain Am-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Aminopeptidase From Aneurinibacillus Sp. Strain Am-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:21.5 occ:1.00 O A:HOH2321 1.8 16.4 1.0 OD2 A:ASP390 2.0 15.4 1.0 OD2 A:ASP386 2.0 19.4 1.0 CG A:ASP390 2.8 13.0 1.0 CG A:ASP386 2.9 16.3 1.0 OD1 A:ASP390 3.0 14.0 1.0 OD1 A:ASP386 3.1 17.3 1.0 ZN A:ZN1004 3.3 20.5 1.0 OG1 A:THR13 3.8 14.4 1.0 O A:HOH2073 3.9 22.9 1.0 O A:ASP386 4.1 15.5 1.0 O A:HOH2029 4.2 16.9 1.0 O A:THR10 4.2 20.1 1.0 CB A:ASP390 4.2 11.3 1.0 CB A:ASP386 4.2 15.4 1.0 O A:HOH2031 4.2 22.3 1.0 O A:HOH2381 4.4 28.1 1.0 C A:ASP386 4.5 15.4 1.0 O A:HOH2405 4.7 29.9 1.0 CB A:THR10 4.8 20.0 1.0 O A:HOH2107 4.8 20.2 1.0 O A:HOH2291 4.8 47.0 1.0 CA A:THR10 4.9 18.9 1.0 CA A:ASP386 4.9 14.7 1.0

Zinc binding site 4 out of 6 in the Aminopeptidase From Aneurinibacillus Sp. Strain Am-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Aminopeptidase From Aneurinibacillus Sp. Strain Am-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:20.5 occ:1.00 OD1 A:ASP386 2.0 17.3 1.0 O A:THR13 2.1 16.7 1.0 OG1 A:THR13 2.2 14.4 1.0 O A:HOH2321 2.2 16.4 1.0 O A:HOH2029 2.2 16.9 1.0 O A:HOH2107 2.3 20.2 1.0 CG A:ASP386 3.1 16.3 1.0 CB A:THR13 3.1 16.8 1.0 C A:THR13 3.1 16.8 1.0 ZN A:ZN1003 3.3 21.5 1.0 OD2 A:ASP386 3.4 19.4 1.0 CA A:THR13 3.5 17.1 1.0 O A:THR10 3.6 20.1 1.0 N A:THR13 3.8 17.7 1.0 OD1 A:ASP390 4.0 14.0 1.0 O A:HOH2495 4.2 28.1 1.0 O A:HOH2380 4.3 39.6 1.0 N A:ASP14 4.3 16.5 1.0 CB A:ASP386 4.4 15.4 1.0 O A:HOH2291 4.4 47.0 1.0 CG2 A:THR13 4.5 14.9 1.0 C A:THR10 4.6 19.4 1.0 OD2 A:ASP390 4.7 15.4 1.0 O A:HOH2238 4.7 41.2 1.0 CG A:ASP390 4.7 13.0 1.0 C A:ARG12 4.8 19.1 1.0 CA A:ASP14 4.9 16.9 1.0 N A:ALA15 5.0 15.3 1.0

Zinc binding site 5 out of 6 in the Aminopeptidase From Aneurinibacillus Sp. Strain Am-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Aminopeptidase From Aneurinibacillus Sp. Strain Am-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:20.1 occ:1.00 NE2 A:HIS204 2.0 16.4 1.0 O A:HOH2512 2.7 22.4 1.0 CD2 A:HIS204 2.8 10.8 1.0 CE1 A:HIS204 3.2 14.7 1.0 CG A:HIS204 4.1 12.9 1.0 ND1 A:HIS204 4.2 13.9 1.0 CG2 A:THR202 4.4 15.6 1.0 CB A:PRO59 4.5 14.4 1.0 CD1 A:LEU38 4.9 20.9 1.0

Zinc binding site 6 out of 6 in the Aminopeptidase From Aneurinibacillus Sp. Strain Am-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Aminopeptidase From Aneurinibacillus Sp. Strain Am-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:23.9 occ:1.00 OE1 A:GLU383 2.0 19.5 1.0 CD A:GLU383 2.7 20.5 1.0 OE2 A:GLU383 2.7 23.4 1.0 O A:HOH2143 3.8 35.3 1.0 CG A:GLU383 4.1 17.8 1.0 CB A:GLU383 4.6 16.1 1.0

M.Akioka, H.Nakano, Y.Tsujimoto, H.Matsui, T.Nakatsu, H.Kato, K.Watanabe. Structural Characterization of A Novel Bacterial Aminopeptidase with An Apical Domain From Aneurinibacillus Sp. Strain Am-1 To Be Published.