Zinc in PDB 2ek9: Aminopeptidase From Aneurinibacillus Sp. Strain Am-1 with Bestatin

The structure of Aminopeptidase From Aneurinibacillus Sp. Strain Am-1 with Bestatin, PDB code: 2ek9 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)	15.00 / 1.97
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.813, 68.678, 77.044, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 21.9

The binding sites of Zinc atom in the Aminopeptidase From Aneurinibacillus Sp. Strain Am-1 with Bestatin (pdb code 2ek9). 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 with Bestatin, PDB code: 2ek9:
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 with Bestatin


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 with Bestatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:19.5 occ:1.00 OD2 A:ASP240 2.1 13.4 1.0 O2 A:BES2001 2.1 24.2 1.0 OE2 A:GLU273 2.2 18.5 1.0 O3 A:BES2001 2.2 25.8 1.0 NE2 A:HIS371 2.2 19.6 1.0 OE1 A:GLU273 2.4 19.1 1.0 CD A:GLU273 2.6 17.3 1.0 C3 A:BES2001 2.9 27.8 1.0 C2 A:BES2001 3.0 27.2 1.0 CG A:ASP240 3.1 14.7 1.0 CD2 A:HIS371 3.2 19.1 1.0 CE1 A:HIS371 3.2 21.3 1.0 OD1 A:ASP240 3.3 14.1 1.0 ZN A:ZN1002 3.5 17.4 1.0 N2 A:BES2001 3.6 26.9 1.0 CE1 A:TYR370 3.8 28.1 1.0 C1 A:BES2001 3.9 28.0 1.0 O A:HOH3072 3.9 12.4 1.0 CG A:GLU273 4.1 15.1 1.0 N1 A:BES2001 4.2 27.7 1.0 OE1 A:GLU272 4.2 14.9 1.0 ND1 A:HIS371 4.3 18.3 1.0 CG A:HIS371 4.3 20.1 1.0 OH A:TYR370 4.3 29.3 1.0 CB A:ASP240 4.4 13.7 1.0 NE2 A:HIS228 4.5 14.5 1.0 CZ A:TYR370 4.5 27.4 1.0 CG1 A:VAL232 4.6 16.9 1.0 CE1 A:HIS228 4.6 11.3 1.0 CD1 A:TYR370 4.7 25.5 1.0 O A:HOH3120 4.7 29.0 1.0 C6 A:BES2001 4.8 31.4 1.0 C4 A:BES2001 4.9 29.7 1.0

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


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 with Bestatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:17.4 occ:1.00 O2 A:BES2001 1.7 24.2 1.0 OD1 A:ASP240 2.0 14.1 1.0 OD1 A:ASP301 2.2 12.7 1.0 NE2 A:HIS228 2.2 14.5 1.0 OD2 A:ASP301 2.3 13.2 1.0 CG A:ASP301 2.6 12.1 1.0 C2 A:BES2001 2.7 27.2 1.0 CG A:ASP240 3.0 14.7 1.0 N2 A:BES2001 3.1 26.9 1.0 C1 A:BES2001 3.1 28.0 1.0 CD2 A:HIS228 3.2 11.6 1.0 CE1 A:HIS228 3.3 11.3 1.0 OD2 A:ASP240 3.4 13.4 1.0 ZN A:ZN1001 3.5 19.5 1.0 OE1 A:GLU272 3.9 14.9 1.0 C3 A:BES2001 4.0 27.8 1.0 OE2 A:GLU273 4.0 18.5 1.0 CB A:ASP241 4.1 12.4 1.0 CB A:ASP301 4.1 12.3 1.0 OE2 A:GLU272 4.2 15.4 1.0 CD A:GLU272 4.2 15.3 1.0 CB A:ASP240 4.3 13.7 1.0 CG A:HIS228 4.3 13.6 1.0 ND1 A:HIS228 4.3 14.3 1.0 O3 A:BES2001 4.4 25.8 1.0 CG A:ASP241 4.6 12.6 1.0 CA A:ASP240 4.6 13.3 1.0 SD A:MET302 4.6 16.5 1.0 C6 A:BES2001 4.6 31.4 1.0 CG A:MET302 4.7 13.0 1.0 CD A:GLU273 4.8 17.3 1.0 OD2 A:ASP241 4.8 11.4 1.0 C A:ASP240 4.9 12.8 1.0 CA A:ASP301 4.9 11.6 1.0 OG A:SER346 5.0 14.5 1.0

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


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 with Bestatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:21.2 occ:1.00 OD2 A:ASP390 2.0 15.5 1.0 OD2 A:ASP386 2.0 16.2 1.0 O A:HOH3247 2.1 17.5 1.0 CG A:ASP390 2.8 13.5 1.0 CG A:ASP386 2.9 15.4 1.0 OD1 A:ASP390 3.0 14.5 1.0 OD1 A:ASP386 3.2 13.9 1.0 ZN A:ZN1004 3.3 19.7 1.0 O A:HOH3163 3.6 20.7 1.0 O A:HOH3170 3.7 21.4 1.0 OG1 A:THR13 3.8 16.0 1.0 O A:ASP386 4.1 13.8 1.0 O A:HOH3043 4.2 23.7 1.0 O A:HOH3354 4.2 18.8 1.0 O A:HOH3250 4.2 29.1 1.0 CB A:ASP386 4.2 14.6 1.0 CB A:ASP390 4.3 13.9 1.0 O A:THR10 4.3 18.1 1.0 C A:ASP386 4.5 13.6 1.0 O A:HOH3200 4.5 43.2 1.0 O A:HOH3338 4.6 11.0 1.0 CB A:THR10 4.8 18.9 1.0 O A:HOH3228 4.9 38.5 1.0 O A:HOH3060 4.9 21.1 1.0 CA A:ASP386 4.9 14.3 1.0 CA A:THR10 4.9 18.0 1.0 CB A:THR13 5.0 16.2 1.0 N A:ASN387 5.0 14.0 1.0

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


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 with Bestatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:19.7 occ:1.00 OD1 A:ASP386 2.0 13.9 1.0 O A:THR13 2.1 18.6 1.0 O A:HOH3338 2.1 11.0 1.0 O A:HOH3354 2.2 18.8 1.0 OG1 A:THR13 2.2 16.0 1.0 CG A:ASP386 3.1 15.4 1.0 CB A:THR13 3.1 16.2 1.0 C A:THR13 3.1 17.1 1.0 ZN A:ZN1003 3.3 21.2 1.0 CA A:THR13 3.4 17.2 1.0 OD2 A:ASP386 3.4 16.2 1.0 O A:THR10 3.6 18.1 1.0 N A:THR13 3.8 17.1 1.0 O A:HOH3163 3.9 20.7 1.0 OD1 A:ASP390 4.0 14.5 1.0 O A:HOH3030 4.1 27.0 1.0 O A:HOH3121 4.2 39.9 1.0 N A:ASP14 4.3 17.0 1.0 CB A:ASP386 4.4 14.6 1.0 O A:HOH3228 4.4 38.5 1.0 CG2 A:THR13 4.4 15.7 1.0 C A:THR10 4.6 18.5 1.0 OD2 A:ASP390 4.7 15.5 1.0 CG A:ASP390 4.8 13.5 1.0 C A:ARG12 4.8 18.4 1.0 CA A:ASP14 4.9 17.2 1.0 O A:HOH3200 4.9 43.2 1.0 O A:HOH3226 4.9 47.2 1.0

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


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 with Bestatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:24.4 occ:1.00 OE1 A:GLU383 2.0 17.9 1.0 O A:HOH3240 2.1 23.8 1.0 CD A:GLU383 2.7 16.4 1.0 OE2 A:GLU383 2.9 21.1 1.0 O A:HOH3498 3.2 40.1 1.0 O A:HOH3144 3.8 37.9 1.0 CG A:GLU383 4.2 16.3 1.0 CB A:GLU383 4.7 15.8 1.0

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


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 with Bestatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:21.2 occ:1.00 NE2 A:HIS204 2.0 15.7 1.0 O A:HOH3029 2.7 21.0 1.0 CD2 A:HIS204 2.9 10.7 1.0 CE1 A:HIS204 3.1 12.8 1.0 O A:HOH3210 3.3 31.3 1.0 CG A:HIS204 4.1 12.7 1.0 ND1 A:HIS204 4.2 14.4 1.0 CG2 A:THR202 4.4 16.0 1.0 CB A:PRO59 4.5 14.0 1.0 CD1 A:LEU38 5.0 20.0 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.