Zinc in PDB 8j9c: Crystal Structure of M61 Peptidase (Apo-Form) From Xanthomonas Campestris

The structure of Crystal Structure of M61 Peptidase (Apo-Form) From Xanthomonas Campestris, PDB code: 8j9c was solved by P.Yadav, A.Kumar, 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)	47.26 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.842, 94.512, 144.495, 90, 104.17, 90
R / Rfree (%)	15.4 / 18.9

The structure of Crystal Structure of M61 Peptidase (Apo-Form) From Xanthomonas Campestris also contains other interesting chemical elements:

Sodium

(Na)

5 atoms

The binding sites of Zinc atom in the Crystal Structure of M61 Peptidase (Apo-Form) From Xanthomonas Campestris (pdb code 8j9c). 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 (Apo-Form) From Xanthomonas Campestris, PDB code: 8j9c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of M61 Peptidase (Apo-Form) 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 (Apo-Form) From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:23.7 occ:1.00 OE1 A:GLU342 2.0 24.1 1.0 O A:HOH1042 2.2 23.1 1.0 NE2 A:HIS308 2.3 24.9 1.0 NE2 A:HIS312 2.3 24.3 1.0 CD A:GLU342 2.8 26.7 1.0 OE2 A:GLU342 3.0 28.0 1.0 CD2 A:HIS308 3.0 23.6 1.0 CD2 A:HIS312 3.0 21.2 1.0 O A:HOH820 3.1 36.6 1.0 CE1 A:HIS308 3.4 23.6 1.0 CE1 A:HIS312 3.4 21.4 1.0 CE1 A:TYR414 3.9 29.8 1.0 O A:HOH804 4.0 24.8 1.0 OH A:TYR414 4.1 29.1 1.0 OE1 A:GLU279 4.2 21.5 1.0 CG A:GLU342 4.3 23.4 1.0 CG A:HIS308 4.3 21.4 1.0 CG A:HIS312 4.3 21.2 1.0 OE2 A:GLU309 4.3 34.3 1.0 OE1 A:GLU309 4.3 34.0 1.0 ND1 A:HIS308 4.4 22.3 1.0 ND1 A:HIS312 4.4 21.9 1.0 CG2 A:THR345 4.5 18.0 1.0 CZ A:TYR414 4.5 29.2 1.0 CD A:GLU309 4.7 31.7 1.0 CB A:GLU342 4.7 20.1 1.0 CD A:GLU279 4.7 23.4 1.0 O A:HOH1155 4.9 31.0 1.0 CA A:GLU342 4.9 24.3 1.0 OE2 A:GLU279 4.9 20.3 1.0 CD1 A:TYR414 5.0 25.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of M61 Peptidase (Apo-Form) 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 (Apo-Form) From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:27.1 occ:1.00 OE1 B:GLU342 2.0 27.4 1.0 O B:HOH1014 2.2 25.5 1.0 NE2 B:HIS308 2.3 24.8 1.0 NE2 B:HIS312 2.3 21.9 1.0 O B:HOH804 2.7 36.1 1.0 CD B:GLU342 2.8 29.1 1.0 OE2 B:GLU342 2.9 30.5 1.0 CD2 B:HIS312 3.0 21.0 1.0 CD2 B:HIS308 3.0 21.3 1.0 CE1 B:HIS308 3.4 24.4 1.0 CE1 B:HIS312 3.4 22.8 1.0 OH B:TYR414 3.9 30.7 1.0 CE1 B:TYR414 3.9 27.6 1.0 O B:HOH806 4.0 29.3 1.0 OE1 B:GLU279 4.2 24.5 1.0 CG B:HIS308 4.3 22.4 1.0 CG B:HIS312 4.3 26.3 1.0 CG B:GLU342 4.3 28.4 1.0 CZ B:TYR414 4.4 29.4 1.0 ND1 B:HIS308 4.4 27.1 1.0 ND1 B:HIS312 4.4 22.6 1.0 OE2 B:GLU309 4.4 32.0 1.0 OE1 B:GLU309 4.5 31.0 1.0 CG2 B:THR345 4.5 20.6 1.0 O B:HOH1146 4.6 34.4 1.0 CD B:GLU279 4.7 27.4 1.0 CB B:GLU342 4.8 23.4 1.0 CD B:GLU309 4.8 30.8 1.0 OE2 B:GLU279 4.9 25.1 1.0 CA B:GLU342 4.9 25.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of M61 Peptidase (Apo-Form) 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 (Apo-Form) From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:32.8 occ:1.00 OE1 C:GLU342 2.0 30.5 1.0 O C:HOH943 2.2 33.3 1.0 NE2 C:HIS312 2.3 32.5 1.0 NE2 C:HIS308 2.3 36.0 1.0 CD C:GLU342 2.8 36.5 1.0 OE2 C:GLU342 2.9 33.2 1.0 CD2 C:HIS308 3.0 33.4 1.0 CD2 C:HIS312 3.0 32.6 1.0 O C:HOH848 3.2 37.8 1.0 CE1 C:HIS312 3.4 32.8 1.0 CE1 C:HIS308 3.4 36.1 1.0 O C:HOH805 3.9 32.4 1.0 CE1 C:TYR414 4.0 35.6 1.0 OH C:TYR414 4.1 40.3 1.0 OE1 C:GLU309 4.1 43.0 1.0 OE1 C:GLU279 4.1 27.4 1.0 OE2 C:GLU309 4.2 40.6 1.0 CG C:HIS308 4.3 36.3 1.0 CG C:GLU342 4.3 32.9 1.0 CG C:HIS312 4.3 31.7 1.0 ND1 C:HIS308 4.4 37.6 1.0 ND1 C:HIS312 4.4 30.1 1.0 CG2 C:THR345 4.5 30.4 1.0 CZ C:TYR414 4.5 36.5 1.0 CD C:GLU309 4.5 39.9 1.0 CD C:GLU279 4.7 35.4 1.0 CB C:GLU342 4.8 31.2 1.0 OE2 C:GLU279 4.8 33.4 1.0 O C:HOH970 4.9 38.0 1.0 CA C:GLU342 4.9 31.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of M61 Peptidase (Apo-Form) 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 (Apo-Form) From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:29.1 occ:1.00 OE1 D:GLU342 2.0 24.7 1.0 O D:HOH1011 2.2 30.4 1.0 NE2 D:HIS312 2.3 24.5 1.0 NE2 D:HIS308 2.3 30.5 1.0 CD D:GLU342 2.8 31.9 1.0 O D:HOH839 2.8 38.6 1.0 OE2 D:GLU342 2.9 29.9 1.0 CD2 D:HIS308 3.1 25.8 1.0 CD2 D:HIS312 3.1 25.0 1.0 CE1 D:HIS312 3.4 25.2 1.0 CE1 D:HIS308 3.4 30.3 1.0 O D:HOH811 3.7 30.0 1.0 CE1 D:TYR414 4.0 31.4 1.0 OH D:TYR414 4.1 36.4 1.0 OE1 D:GLU279 4.2 25.1 1.0 CG D:GLU342 4.2 27.2 1.0 CG D:HIS308 4.3 30.7 1.0 CG D:HIS312 4.3 24.9 1.0 ND1 D:HIS312 4.4 24.5 1.0 ND1 D:HIS308 4.4 27.9 1.0 CG2 D:THR345 4.4 24.1 1.0 OE1 D:GLU309 4.4 33.6 1.0 CZ D:TYR414 4.5 32.4 1.0 O D:HOH1108 4.5 32.7 1.0 OE2 D:GLU309 4.6 38.9 1.0 CD D:GLU279 4.7 27.9 1.0 CB D:GLU342 4.7 26.4 1.0 CD D:GLU309 4.8 34.1 1.0 OE2 D:GLU279 4.9 27.3 1.0 CA D:GLU342 4.9 26.2 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