Zinc in PDB 8j9d: Crystal Structure of M61 Peptidase (Bestatin-Bound) From Xanthomonas Campestris

The structure of Crystal Structure of M61 Peptidase (Bestatin-Bound) From Xanthomonas Campestris, PDB code: 8j9d was solved by P.Yadav, A.Kumar, B.S.Kulkarni, S.N.Jamdar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.36 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.008, 95.196, 144.489, 90, 104.47, 90
R / Rfree (%)	17.1 / 19.1

The binding sites of Zinc atom in the Crystal Structure of M61 Peptidase (Bestatin-Bound) From Xanthomonas Campestris (pdb code 8j9d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of M61 Peptidase (Bestatin-Bound) From Xanthomonas Campestris, PDB code: 8j9d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of M61 Peptidase (Bestatin-Bound) From Xanthomonas Campestris


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 M61 Peptidase (Bestatin-Bound) From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:15.5 occ:1.00 O2 A:BES702 1.8 20.1 1.0 OE1 A:GLU342 2.0 16.4 1.0 NE2 A:HIS308 2.0 16.8 1.0 NE2 A:HIS312 2.1 16.8 1.0 O3 A:BES702 2.8 26.5 1.0 CD2 A:HIS308 2.9 16.3 1.0 CD A:GLU342 2.9 16.5 1.0 C2 A:BES702 2.9 25.4 1.0 CD2 A:HIS312 3.0 18.0 1.0 OE2 A:GLU342 3.1 16.5 1.0 CE1 A:HIS308 3.1 16.5 1.0 CE1 A:HIS312 3.2 13.5 1.0 C3 A:BES702 3.2 27.9 1.0 C1 A:BES702 3.6 25.7 1.0 N2 A:BES702 3.9 24.7 1.0 OE1 A:GLU309 3.9 19.3 1.0 CG A:HIS308 4.1 15.9 1.0 CE1 A:TYR414 4.1 15.7 1.0 OH A:TYR414 4.1 15.8 1.0 ND1 A:HIS308 4.2 16.2 1.0 CG A:HIS312 4.2 13.6 1.0 ND1 A:HIS312 4.2 13.6 1.0 CG A:GLU342 4.3 15.8 1.0 CG2 A:THR345 4.4 13.8 1.0 OE2 A:GLU309 4.4 19.0 1.0 OE1 A:GLU279 4.5 14.9 1.0 CZ A:TYR414 4.5 15.8 1.0 CD A:GLU309 4.5 18.8 1.0 N1 A:BES702 4.6 30.7 1.0 CB A:GLU342 4.7 14.6 1.0 CA A:GLU342 4.8 14.8 1.0 CD A:GLU279 4.9 14.6 1.0 CB A:THR345 5.0 14.1 1.0 OE2 A:GLU279 5.0 14.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of M61 Peptidase (Bestatin-Bound) From Xanthomonas Campestris


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 M61 Peptidase (Bestatin-Bound) From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:15.1 occ:1.00 O2 B:BES702 1.9 21.4 1.0 OE1 B:GLU342 2.0 17.2 1.0 NE2 B:HIS308 2.0 17.5 1.0 NE2 B:HIS312 2.1 17.2 1.0 O3 B:BES702 2.8 24.8 1.0 CD B:GLU342 2.9 16.3 1.0 CD2 B:HIS308 2.9 16.4 1.0 C2 B:BES702 2.9 23.2 1.0 CD2 B:HIS312 3.1 16.0 1.0 OE2 B:GLU342 3.1 15.9 1.0 CE1 B:HIS308 3.1 16.9 1.0 CE1 B:HIS312 3.1 16.1 1.0 C3 B:BES702 3.2 26.0 1.0 C1 B:BES702 3.5 23.2 1.0 N2 B:BES702 3.8 22.8 1.0 OE1 B:GLU309 4.0 16.3 1.0 OH B:TYR414 4.1 16.5 1.0 CG B:HIS308 4.1 16.3 1.0 CE1 B:TYR414 4.1 17.3 1.0 ND1 B:HIS308 4.1 16.8 1.0 ND1 B:HIS312 4.2 16.3 1.0 CG B:HIS312 4.2 16.2 1.0 CG B:GLU342 4.3 16.0 1.0 CG2 B:THR345 4.5 14.1 1.0 CZ B:TYR414 4.5 17.1 1.0 OE2 B:GLU279 4.5 14.4 1.0 OE2 B:GLU309 4.5 16.3 1.0 N1 B:BES702 4.6 29.4 1.0 CD B:GLU309 4.6 16.4 1.0 CB B:GLU342 4.7 15.4 1.0 CA B:GLU342 4.8 15.5 1.0 CD B:GLU279 4.9 14.8 1.0 C6 B:BES702 5.0 23.9 1.0 OE1 B:GLU279 5.0 14.8 1.0 CB B:THR345 5.0 15.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of M61 Peptidase (Bestatin-Bound) From Xanthomonas Campestris


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 M61 Peptidase (Bestatin-Bound) From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:19.1 occ:1.00 O2 C:BES702 1.9 23.7 1.0 OE1 C:GLU342 2.0 18.5 1.0 NE2 C:HIS308 2.0 20.1 1.0 NE2 C:HIS312 2.1 19.8 1.0 O3 C:BES702 2.8 30.3 1.0 CD C:GLU342 2.8 18.0 1.0 CD2 C:HIS308 2.9 20.0 1.0 C2 C:BES702 2.9 27.2 1.0 CD2 C:HIS312 3.0 19.5 1.0 OE2 C:GLU342 3.0 17.8 1.0 CE1 C:HIS312 3.1 19.6 1.0 CE1 C:HIS308 3.1 19.9 1.0 C3 C:BES702 3.2 30.5 1.0 C1 C:BES702 3.5 28.2 1.0 N2 C:BES702 3.8 27.7 1.0 OE2 C:GLU309 4.0 21.1 1.0 CG C:HIS308 4.1 20.1 1.0 OH C:TYR414 4.1 20.9 1.0 CE1 C:TYR414 4.1 20.6 1.0 ND1 C:HIS308 4.2 20.0 1.0 ND1 C:HIS312 4.2 19.7 1.0 CG C:HIS312 4.2 19.6 1.0 CG C:GLU342 4.3 17.9 1.0 CG2 C:THR345 4.4 19.6 1.0 OE1 C:GLU309 4.4 21.4 1.0 OE1 C:GLU279 4.5 17.8 1.0 CZ C:TYR414 4.5 20.6 1.0 CD C:GLU309 4.6 21.1 1.0 N1 C:BES702 4.6 33.5 1.0 CB C:GLU342 4.7 17.4 1.0 CA C:GLU342 4.8 17.4 1.0 CD C:GLU279 4.9 18.0 1.0 OE2 C:GLU279 4.9 18.1 1.0 CB C:THR345 4.9 19.4 1.0 C6 C:BES702 5.0 29.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of M61 Peptidase (Bestatin-Bound) From Xanthomonas Campestris


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 M61 Peptidase (Bestatin-Bound) From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:19.9 occ:1.00 O2 D:BES702 1.9 22.2 1.0 OE1 D:GLU342 2.0 17.5 1.0 NE2 D:HIS308 2.0 17.9 1.0 NE2 D:HIS312 2.1 17.3 1.0 O3 D:BES702 2.8 28.1 1.0 CD D:GLU342 2.8 17.4 1.0 CD2 D:HIS308 2.8 18.5 1.0 C2 D:BES702 2.9 25.0 1.0 OE2 D:GLU342 3.0 17.2 1.0 CD2 D:HIS312 3.1 17.6 1.0 CE1 D:HIS308 3.2 18.6 1.0 CE1 D:HIS312 3.2 17.6 1.0 C3 D:BES702 3.2 27.8 1.0 C1 D:BES702 3.5 24.6 1.0 N2 D:BES702 3.8 24.0 1.0 OE1 D:GLU309 4.0 19.7 1.0 CG D:HIS308 4.1 18.4 1.0 OH D:TYR414 4.1 17.9 1.0 CE1 D:TYR414 4.1 18.3 1.0 ND1 D:HIS308 4.2 18.5 1.0 CG D:HIS312 4.2 17.9 1.0 ND1 D:HIS312 4.3 17.9 1.0 CG D:GLU342 4.3 17.2 1.0 CG2 D:THR345 4.4 17.6 1.0 OE2 D:GLU309 4.5 19.6 1.0 OE1 D:GLU279 4.5 18.2 1.0 CZ D:TYR414 4.5 18.1 1.0 N1 D:BES702 4.6 30.4 1.0 CD D:GLU309 4.6 19.5 1.0 CB D:GLU342 4.7 17.4 1.0 CA D:GLU342 4.8 17.8 1.0 CD D:GLU279 4.9 18.4 1.0 C6 D:BES702 5.0 24.9 1.0 CB D:THR345 5.0 18.5 1.0

S.N.Jamdar, P.Yadav, B.S.Kulkarni, A.Kumar, R.D.Makde. Crystal Structure of A Newly Identified M61 Family Aminopeptidase with Broad Substrate Specificity That Is Solely Responsible For Recycling Acidic Amino Acids. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 38646733
DOI: 10.1111/FEBS.17133