Sodium 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:

Zinc

(Zn)

4 atoms

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of M61 Peptidase (Apo-Form) From Xanthomonas Campestris, PDB code: 8j9c:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of M61 Peptidase (Apo-Form) From Xanthomonas Campestris


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na703 b:25.0 occ:1.00 O A:HOH1134 2.2 27.2 1.0 O A:HOH972 2.4 30.7 1.0 OD2 A:ASP198 2.4 31.3 1.0 OD1 A:ASP454 2.4 40.7 1.0 O A:HOH1217 2.4 31.0 1.0 O A:HOH1113 2.6 38.7 1.0 CG A:ASP198 3.4 32.9 1.0 OD1 A:ASP198 3.6 29.0 1.0 CG A:ASP454 3.6 37.6 1.0 OD2 A:ASP195 4.3 28.0 1.0 OD2 A:ASP454 4.3 42.0 1.0 OD2 A:ASP197 4.4 32.4 1.0 O A:HOH1236 4.4 31.8 1.0 O A:TRP453 4.5 30.9 1.0 O A:HOH1230 4.5 35.5 1.0 OD1 A:ASP197 4.5 27.4 1.0 CA A:ASP454 4.7 27.4 1.0 CB A:ASP454 4.7 32.3 1.0 CB A:ASP198 4.7 24.9 1.0 CZ3 A:TRP453 4.7 29.4 1.0 O A:HOH1196 4.8 34.0 1.0 CE3 A:TRP453 4.9 30.2 1.0 CG A:ASP197 4.9 28.0 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of M61 Peptidase (Apo-Form) From Xanthomonas Campestris


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na702 b:32.9 occ:1.00 O B:HOH1019 2.4 31.8 1.0 O B:HOH877 2.4 29.1 1.0 OD2 B:ASP198 2.5 36.0 1.0 O B:HOH993 2.6 41.8 1.0 O B:HOH1249 2.7 51.6 1.0 O B:HOH1204 3.1 46.8 1.0 CG B:ASP198 3.3 32.2 1.0 OD1 B:ASP198 3.6 27.3 1.0 OD2 B:ASP195 4.1 30.1 1.0 OD2 B:ASP197 4.2 30.6 1.0 O B:HOH1043 4.3 32.6 1.0 OD1 B:ASP197 4.3 25.0 1.0 CG B:ASP197 4.7 26.1 1.0 CB B:ASP198 4.7 23.5 1.0 O B:TRP453 4.7 31.4 1.0 NE1 B:TRP453 4.7 36.3 1.0 CB B:ASP195 4.9 23.4 1.0 O B:HOH1111 4.9 37.1 1.0 CA B:ASP454 4.9 35.2 1.0 CG B:ASP195 5.0 29.9 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of M61 Peptidase (Apo-Form) From Xanthomonas Campestris


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na702 b:47.0 occ:1.00 O C:HOH952 2.3 39.7 1.0 O C:HOH869 2.5 37.9 1.0 O C:HOH974 2.6 53.8 1.0 OD1 C:ASP454 2.6 45.3 0.5 OD2 C:ASP198 2.7 44.3 1.0 CG C:ASP198 3.6 35.9 1.0 CG C:ASP454 3.7 45.6 0.5 OD1 C:ASP198 3.8 36.1 1.0 OD2 C:ASP195 4.2 42.4 1.0 OD1 C:ASP197 4.2 40.8 1.0 OD2 C:ASP454 4.4 45.5 0.5 O C:HOH1073 4.6 39.3 1.0 O C:TRP453 4.8 38.8 1.0 CA C:ASP454 4.8 41.6 0.5 CB C:ASP454 4.8 44.3 0.5 CA C:ASP454 4.8 41.6 0.5 OD2 C:ASP197 4.8 37.8 1.0 CZ3 C:TRP453 4.8 40.7 1.0 CB C:ASP454 4.9 44.3 0.5 CB C:ASP198 4.9 31.6 1.0 CG C:ASP197 4.9 34.6 1.0 CE3 C:TRP453 5.0 39.5 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of M61 Peptidase (Apo-Form) From Xanthomonas Campestris


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na702 b:41.5 occ:1.00 O D:HOH1024 2.4 34.4 1.0 O D:HOH1005 2.4 38.1 1.0 O D:HOH1238 2.5 41.0 1.0 O D:HOH1186 2.5 49.3 1.0 OD2 D:ASP198 2.6 34.3 1.0 CG D:ASP198 3.5 31.9 1.0 OD1 D:ASP198 3.7 32.9 1.0 OD2 D:ASP195 4.3 32.4 1.0 OD2 D:ASP197 4.4 36.8 1.0 O D:HOH1104 4.5 34.5 1.0 O D:TRP453 4.6 33.8 1.0 CZ3 D:TRP453 4.7 32.7 1.0 OD1 D:ASP197 4.7 26.2 1.0 CA D:ASP454 4.8 37.9 1.0 CE3 D:TRP453 4.9 32.4 1.0 CB D:ASP198 4.9 25.8 1.0 CG D:ASP197 4.9 29.5 1.0 CB D:ASP454 5.0 38.6 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of M61 Peptidase (Apo-Form) From Xanthomonas Campestris


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of M61 Peptidase (Apo-Form) From Xanthomonas Campestris within 5.0Å range: probe atom residue distance (Å) B Occ D:Na703 b:45.5 occ:1.00 O A:HOH881 2.3 32.9 1.0 O A:HOH1250 2.8 29.6 1.0 O D:TRP97 2.9 21.5 1.0 O D:HOH1179 3.0 31.0 1.0 O D:HOH1177 3.1 26.1 1.0 CG2 A:THR386 3.9 23.5 1.0 N D:TRP97 3.9 24.3 1.0 C D:TRP97 4.0 23.0 1.0 CD2 D:TRP97 4.0 21.1 1.0 CE2 D:TRP97 4.1 21.1 1.0 O A:HOH1117 4.2 32.6 1.0 CG D:TRP97 4.3 22.1 1.0 CE3 D:TRP97 4.3 21.4 1.0 O A:HOH1128 4.4 30.3 1.0 NE1 D:TRP97 4.4 21.8 1.0 CA D:TRP97 4.5 22.9 1.0 CZ2 D:TRP97 4.5 20.1 1.0 CD1 D:TRP97 4.5 24.6 1.0 OG1 A:THR386 4.6 20.7 1.0 CZ3 D:TRP97 4.7 23.1 1.0 CH2 D:TRP97 4.8 22.2 1.0 C D:PRO96 4.8 23.2 1.0 CB D:PRO96 4.8 26.0 1.0 CA D:PRO96 4.8 24.9 1.0 CE1 A:HIS486 4.9 25.0 1.0 O A:TRP384 4.9 22.3 1.0 CB A:THR386 4.9 21.0 1.0 CB D:TRP97 5.0 20.6 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