Zinc in PDB 5ib9: Crystal Structure of Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1

The structure of Crystal Structure of Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1, PDB code: 5ib9 was solved by R.Tagawa, H.Nakano, K.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.80 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.180, 68.443, 76.589, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22.3

The binding sites of Zinc atom in the Crystal Structure of Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1 (pdb code 5ib9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1, PDB code: 5ib9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1


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 Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:15.3 occ:1.00 OD2 A:ASP240 1.8 14.3 1.0 NE2 A:HIS371 2.1 14.2 1.0 O2 A:BES1007 2.1 16.2 1.0 OE2 A:GLU273 2.1 13.8 1.0 O3 A:BES1007 2.4 33.3 1.0 OE1 A:GLU273 2.6 17.0 1.0 CD A:GLU273 2.6 11.4 1.0 CG A:ASP240 2.9 11.1 1.0 C2 A:BES1007 3.0 30.1 1.0 CE1 A:HIS371 3.0 21.7 1.0 C3 A:BES1007 3.0 31.4 1.0 CD2 A:HIS371 3.1 19.8 1.0 OD1 A:ASP240 3.3 11.9 1.0 C1 A:BES1007 3.4 28.0 1.0 ZN A:ZN1002 3.5 13.1 1.0 CE1 A:TYR370 3.9 30.8 1.0 N2 A:BES1007 3.9 29.7 1.0 O A:HOH1338 3.9 14.3 1.0 CG A:GLU273 4.1 15.1 1.0 ND1 A:HIS371 4.2 19.1 1.0 OE1 A:GLU272 4.2 14.4 1.0 CG A:HIS371 4.2 17.1 1.0 N1 A:BES1007 4.2 31.7 1.0 OH A:TYR370 4.2 34.1 1.0 CB A:ASP240 4.2 11.4 1.0 CE1 A:HIS228 4.5 10.3 1.0 CZ A:TYR370 4.5 31.2 1.0 NE2 A:HIS228 4.5 11.1 1.0 CG1 A:VAL232 4.6 16.2 1.0 O A:HOH1262 4.7 24.6 1.0 CD1 A:TYR370 4.8 28.2 1.0 C6 A:BES1007 4.9 33.2 1.0 C4 A:BES1007 4.9 32.5 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1


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 Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:13.1 occ:1.00 OD1 A:ASP240 2.0 11.9 1.0 NE2 A:HIS228 2.0 11.1 1.0 O2 A:BES1007 2.1 16.2 1.0 OD1 A:ASP301 2.1 14.7 1.0 OD2 A:ASP301 2.3 14.6 1.0 CG A:ASP301 2.6 13.5 1.0 N2 A:BES1007 2.6 29.7 1.0 CE1 A:HIS228 2.9 10.3 1.0 C2 A:BES1007 3.1 30.1 1.0 CD2 A:HIS228 3.1 11.1 1.0 CG A:ASP240 3.1 11.1 1.0 C1 A:BES1007 3.4 28.0 1.0 OD2 A:ASP240 3.5 14.3 1.0 ZN A:ZN1001 3.5 15.3 1.0 OE1 A:GLU272 3.9 14.4 1.0 OE2 A:GLU273 3.9 13.8 1.0 CB A:ASP241 4.0 10.1 1.0 ND1 A:HIS228 4.1 11.3 1.0 CB A:ASP301 4.1 12.1 1.0 CD A:GLU272 4.2 13.1 1.0 CG A:HIS228 4.2 9.0 1.0 OE2 A:GLU272 4.2 17.3 1.0 CB A:ASP240 4.3 11.4 1.0 C3 A:BES1007 4.4 31.4 1.0 CG A:ASP241 4.5 10.4 1.0 CA A:ASP240 4.5 10.4 1.0 C6 A:BES1007 4.6 33.2 1.0 OD2 A:ASP241 4.7 9.6 1.0 SD A:MET302 4.7 16.7 1.0 O3 A:BES1007 4.7 33.3 1.0 CD A:GLU273 4.7 11.4 1.0 CG A:MET302 4.7 11.8 1.0 C A:ASP240 4.8 11.8 1.0 OG A:SER346 4.8 11.8 1.0 CA A:ASP301 4.8 11.5 1.0 CA A:ASP241 4.9 9.2 1.0 N A:ASP241 5.0 10.8 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1


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 Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:16.4 occ:1.00 OD2 A:ASP386 1.8 17.9 1.0 O A:HOH1263 1.8 15.2 1.0 OD2 A:ASP390 2.0 13.0 1.0 O A:HOH1376 2.1 16.4 1.0 O A:HOH1483 2.4 19.6 1.0 O A:HOH1496 2.9 25.7 1.0 CG A:ASP390 2.9 14.1 1.0 CG A:ASP386 2.9 15.3 1.0 OD1 A:ASP390 3.1 14.9 1.0 OD1 A:ASP386 3.3 14.7 1.0 ZN A:ZN1004 3.4 15.2 1.0 O A:HOH1541 3.7 24.0 1.0 OG1 A:THR13 3.8 12.9 1.0 O A:HOH1391 4.0 20.6 1.0 O A:ASP386 4.1 12.8 1.0 O A:HOH1318 4.2 16.1 1.0 CB A:ASP390 4.2 12.3 1.0 O A:THR10 4.2 17.5 1.0 CB A:ASP386 4.2 13.8 1.0 O A:HOH1244 4.2 25.8 1.0 C A:ASP386 4.5 10.8 1.0 CB A:THR10 4.7 16.9 1.0 O A:HOH1234 4.8 16.3 1.0 O A:HOH1527 4.9 26.9 1.0 CA A:THR10 4.9 15.9 1.0 CA A:ASP386 5.0 12.5 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1


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 Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:15.2 occ:1.00 OD1 A:ASP386 2.0 14.7 1.0 O A:HOH1318 2.1 16.1 1.0 O A:HOH1263 2.1 15.2 1.0 O A:THR13 2.1 14.8 1.0 OG1 A:THR13 2.2 12.9 1.0 O A:HOH1234 2.2 16.3 1.0 CG A:ASP386 3.0 15.3 1.0 C A:THR13 3.1 14.9 1.0 CB A:THR13 3.2 11.7 1.0 OD2 A:ASP386 3.3 17.9 1.0 ZN A:ZN1003 3.4 16.4 1.0 CA A:THR13 3.5 14.2 1.0 O A:THR10 3.6 17.5 1.0 N A:THR13 3.7 13.0 1.0 O A:HOH1541 3.9 24.0 1.0 OD1 A:ASP390 4.1 14.9 1.0 O A:HOH1328 4.1 23.5 1.0 N A:ASP14 4.3 14.7 1.0 CB A:ASP386 4.4 13.8 1.0 O A:HOH1512 4.4 43.8 1.0 CG2 A:THR13 4.6 12.0 1.0 OD2 A:ASP390 4.6 13.0 1.0 C A:THR10 4.7 15.4 1.0 C A:ARG12 4.7 16.4 1.0 CG A:ASP390 4.8 14.1 1.0 CA A:ASP14 4.8 14.8 1.0 O A:HOH1590 5.0 44.0 1.0 O A:HOH1376 5.0 16.4 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1


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 Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:18.4 occ:1.00 O A:HOH1383 1.8 19.4 1.0 OE1 A:GLU383 2.0 15.6 1.0 CD A:GLU383 2.7 19.0 1.0 OE2 A:GLU383 2.8 26.5 1.0 O A:HOH1381 4.0 38.5 1.0 CG A:GLU383 4.1 16.9 1.0 CB A:GLU383 4.6 15.0 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1


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 Aminopeptidase Equipped with Pad From Aneurinibacillus Sp. Am-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:14.8 occ:1.00 NE2 A:HIS204 2.0 13.3 1.0 O A:HOH1493 2.1 38.7 1.0 O A:HOH1526 2.5 27.5 1.0 O A:HOH1488 2.8 21.1 1.0 CE1 A:HIS204 3.0 11.5 1.0 CD2 A:HIS204 3.1 12.2 1.0 O A:HOH1260 3.5 35.5 1.0 ND1 A:HIS204 4.1 11.9 1.0 CG A:HIS204 4.2 9.1 1.0 O A:HOH1684 4.2 38.0 1.0 O A:HOH1556 4.2 31.3 1.0 CG2 A:THR202 4.4 15.8 1.0 CB A:PRO59 4.5 9.6 1.0 CD1 A:LEU38 4.8 21.8 1.0

R.Tagawa, H.Nakano, K.Watanabe. Crystal Structure of Aminopeptidase To Be Published.