Zinc in PDB 3a3n: Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two C-Terminal Residues

The structure of Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two C-Terminal Residues, PDB code: 3a3n was solved by S.Tanaka, H.Matsumura, Y.Koga, K.Takano, S.Kanaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.86 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.732, 68.468, 73.704, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 23.1

The structure of Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two C-Terminal Residues also contains other interesting chemical elements:

Calcium

(Ca)

7 atoms

The binding sites of Zinc atom in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two C-Terminal Residues (pdb code 3a3n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two C-Terminal Residues, PDB code: 3a3n:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two C-Terminal Residues


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 Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two C-Terminal Residues within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn399 b:48.2 occ:1.00 NE2 A:HIS153 2.3 30.9 1.0 O B:HOH145 2.5 40.4 1.0 O B:HOH106 2.5 32.8 1.0 O A:HOH465 2.8 20.6 1.0 CD2 A:HIS153 3.1 27.2 1.0 O B:HOH159 3.2 27.9 1.0 CE1 A:HIS153 3.4 28.6 1.0 CB A:ALA324 3.9 19.6 1.0 CG A:HIS153 4.3 27.6 1.0 ND1 A:HIS153 4.4 25.6 1.0 OXT B:VAL67 4.4 43.2 1.0 O A:SER234 4.4 20.9 1.0 ND2 A:ASN264 4.8 30.7 1.0 O B:HOH144 4.9 34.1 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two C-Terminal Residues


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 Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two C-Terminal Residues within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn68 b:43.0 occ:1.00 OD2 B:ASP42 2.1 35.3 1.0 NE2 B:HIS28 2.1 32.4 1.0 O B:HOH79 2.2 31.1 1.0 O B:HOH70 2.5 25.1 1.0 CE1 B:HIS28 2.8 35.6 1.0 CG B:ASP42 3.1 34.6 1.0 CD2 B:HIS28 3.3 32.7 1.0 CB B:ASP42 3.4 34.3 1.0 ND1 B:HIS28 4.0 36.5 1.0 NH2 B:ARG7 4.1 24.8 1.0 OD1 B:ASP42 4.2 32.1 1.0 CG B:HIS28 4.3 35.3 1.0 CG2 B:VAL30 4.5 30.2 1.0 CA B:ASP42 4.9 34.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two C-Terminal Residues


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 Complex Between Sa-Subtilisin and Tk-Propeptide with Deletion of the Two C-Terminal Residues within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn69 b:38.8 occ:1.00 NE2 B:HIS64 1.9 23.8 1.0 OD1 A:ASP241 2.1 33.0 1.0 O A:HOH443 2.4 36.6 1.0 CG A:ASP241 2.7 32.0 1.0 OD2 A:ASP241 2.7 31.4 1.0 CD2 B:HIS64 2.8 25.9 1.0 CE1 B:HIS64 3.0 25.0 1.0 O B:PHE62 3.4 28.6 1.0 O B:HOH107 3.4 29.6 1.0 CG B:HIS64 4.0 26.0 1.0 ND1 B:HIS64 4.0 25.8 1.0 CB A:ASP241 4.1 29.5 1.0 O A:ASP240 4.2 30.4 1.0 N B:PHE62 4.2 29.6 1.0 C B:PHE62 4.3 28.9 1.0 CB A:ALA239 4.5 26.1 1.0 O B:HOH102 4.6 33.2 1.0 CA B:PHE62 4.7 29.0 1.0 O A:HOH14 4.7 32.0 1.0 C A:ASP240 4.8 30.0 1.0 OH A:TYR243 4.8 27.6 1.0 CA A:ASP241 4.8 30.4 1.0 CB B:PHE62 4.9 29.7 1.0 CE1 A:TYR243 5.0 29.0 1.0 CB B:GLU61 5.0 29.7 1.0

S.Tanaka, H.Matsumura, Y.Koga, K.Takano, S.Kanaya. Identification of the Interactions Critical For Propeptide-Catalyzed Folding of Tk-Subtilisin J.Mol.Biol. V. 394 306 2009.
ISSN: ISSN 0022-2836
PubMed: 19766655
DOI: 10.1016/J.JMB.2009.09.028