Calcium in PDB 3wqb: Crystal Structure of Aeromonas Sobria Serine Protease (Asp) and the Chaperone (ORF2) Complex

The structure of Crystal Structure of Aeromonas Sobria Serine Protease (Asp) and the Chaperone (ORF2) Complex, PDB code: 3wqb was solved by H.Kobayashi, T.Yoshida, T.Miyakawa, R.Kato, M.Tashiro, H.Yamanaka, M.Tanokura, H.Tsuge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.74 / 1.41
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	152.062, 152.062, 51.625, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 20.7

The binding sites of Calcium atom in the Crystal Structure of Aeromonas Sobria Serine Protease (Asp) and the Chaperone (ORF2) Complex (pdb code 3wqb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Aeromonas Sobria Serine Protease (Asp) and the Chaperone (ORF2) Complex, PDB code: 3wqb:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Aeromonas Sobria Serine Protease (Asp) and the Chaperone (ORF2) Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Aeromonas Sobria Serine Protease (Asp) and the Chaperone (ORF2) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:12.1 occ:1.00 O A:VAL126 2.3 12.6 1.0 O A:ILE130 2.3 13.6 1.0 O A:THR132 2.4 11.7 1.0 OD1 A:ASN29 2.4 13.7 1.0 OD1 A:ASN128 2.4 12.5 1.0 OD1 A:ASP87 2.4 12.8 1.0 OD2 A:ASP87 2.5 12.4 1.0 CG A:ASP87 2.8 12.3 1.0 CG A:ASN128 3.4 13.1 1.0 CG A:ASN29 3.4 12.9 1.0 C A:VAL126 3.5 12.2 1.0 C A:THR132 3.5 11.3 1.0 C A:ILE130 3.5 13.3 1.0 N A:THR132 3.7 12.0 1.0 ND2 A:ASN128 3.9 13.8 1.0 N A:ASN128 4.0 14.1 1.0 C A:GLY131 4.0 12.3 1.0 CB A:ASN29 4.1 13.3 1.0 CA A:THR132 4.2 11.4 1.0 N A:VAL126 4.3 11.7 1.0 CB A:ASP87 4.3 12.3 1.0 CA A:GLY131 4.4 12.4 1.0 CG1 A:ILE130 4.4 14.9 1.0 CA A:VAL126 4.4 12.4 1.0 N A:ILE130 4.4 14.5 1.0 N A:GLY131 4.4 12.7 1.0 N A:ASP127 4.5 13.0 1.0 CA A:ILE130 4.5 14.1 1.0 ND2 A:ASN29 4.5 12.6 1.0 CA A:ASP127 4.6 13.9 1.0 N A:LYS133 4.6 11.3 1.0 O A:GLY131 4.6 12.7 1.0 CB A:ASN128 4.6 14.2 1.0 CA A:ASN128 4.7 14.0 1.0 C A:ASP127 4.7 14.1 1.0 C A:ASN128 4.7 14.7 1.0 CB A:VAL126 4.8 12.3 1.0 C A:ALA125 4.8 11.2 1.0 CA A:LYS133 4.8 11.3 1.0 O A:ASN128 4.9 15.3 1.0 CA A:ASN29 4.9 13.9 1.0 CB A:ALA125 5.0 10.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Aeromonas Sobria Serine Protease (Asp) and the Chaperone (ORF2) Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Aeromonas Sobria Serine Protease (Asp) and the Chaperone (ORF2) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:13.5 occ:1.00 OD1 A:ASP454 2.3 15.1 1.0 O A:ALA555 2.3 13.6 1.0 OD2 A:ASP488 2.3 13.4 1.0 OD1 A:ASN579 2.4 17.4 1.0 OD1 A:ASN578 2.4 15.7 1.0 OD2 A:ASP553 2.5 14.1 1.0 OD1 A:ASP553 2.6 13.6 1.0 CG A:ASP553 2.9 12.5 1.0 CG A:ASP488 3.3 13.0 1.0 CG A:ASP454 3.4 14.9 1.0 CG A:ASN579 3.5 17.6 1.0 CG A:ASN578 3.5 17.1 1.0 C A:ALA555 3.5 13.9 1.0 CB A:ASP488 3.9 11.7 1.0 ND2 A:ASN578 4.0 17.4 1.0 ND2 A:ASN579 4.0 17.6 1.0 OD2 A:ASP454 4.1 15.8 1.0 NH2 A:ARG485 4.2 14.1 1.0 CA A:ASN556 4.3 16.3 1.0 OD1 A:ASP488 4.3 13.9 1.0 N A:ASN556 4.4 14.7 1.0 CB A:ASP553 4.4 12.2 1.0 CB A:ASP454 4.4 14.4 1.0 N A:ASN579 4.5 18.2 1.0 CE1 A:HIS483 4.5 14.4 1.0 NE2 A:HIS483 4.5 14.0 1.0 CA A:ASP454 4.5 14.2 1.0 N A:ALA555 4.5 12.6 1.0 CA A:ALA555 4.6 13.1 1.0 N A:VAL455 4.6 13.6 1.0 NE A:ARG485 4.6 13.5 1.0 CB A:ASN579 4.8 18.2 1.0 CB A:ASN556 4.8 16.6 1.0 CB A:ASN578 4.8 17.9 1.0 CZ A:ARG485 4.9 13.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Aeromonas Sobria Serine Protease (Asp) and the Chaperone (ORF2) Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Aeromonas Sobria Serine Protease (Asp) and the Chaperone (ORF2) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:15.7 occ:1.00 O A:MET303 2.3 13.1 1.0 O A:CYS326 2.4 13.4 1.0 O A:GLY300 2.4 14.2 1.0 O A:LEU298 2.4 12.8 1.0 OD2 A:ASP297 2.4 10.7 1.0 O A:ASN306 2.5 12.5 1.0 C A:MET303 3.5 12.6 1.0 CG A:ASP297 3.5 11.1 1.0 C A:CYS326 3.6 13.8 1.0 C A:GLY300 3.6 14.0 1.0 C A:ASN306 3.6 12.1 1.0 C A:LEU298 3.6 12.3 1.0 CB A:CYS326 3.7 14.9 1.0 N A:GLY300 4.0 14.0 1.0 CB A:ASP297 4.0 11.3 1.0 C A:PRO299 4.1 14.2 1.0 CA A:GLY304 4.2 11.8 1.0 CB A:ASN306 4.2 11.8 1.0 N A:GLY304 4.3 12.1 1.0 CA A:ASN306 4.3 12.0 1.0 CA A:CYS326 4.3 14.6 1.0 N A:ASN306 4.4 11.9 1.0 O A:PRO299 4.4 14.8 1.0 CA A:GLY300 4.4 13.8 1.0 N A:LEU298 4.5 11.4 1.0 CA A:PRO299 4.5 13.8 1.0 N A:MET303 4.5 13.1 1.0 OD1 A:ASP297 4.5 12.1 1.0 CA A:MET303 4.5 12.4 1.0 CA A:LEU298 4.5 11.7 1.0 N A:PRO299 4.5 13.4 1.0 N A:CYS301 4.5 14.6 1.0 N A:ASP327 4.6 12.9 1.0 CA A:CYS301 4.6 15.1 1.0 N A:ARG307 4.7 13.1 1.0 C A:GLY304 4.7 11.3 1.0 O A:SER325 4.7 15.8 1.0 CB A:LEU298 4.8 12.1 1.0 CA A:ASP327 4.8 12.6 1.0 C A:ASP297 4.8 11.6 1.0 CG A:ASN306 4.9 11.5 1.0 CB A:ARG307 4.9 13.7 1.0 CA A:ARG307 4.9 13.6 1.0 CB A:MET303 4.9 12.5 1.0

H.Kobayashi, T.Yoshida, T.Miyakawa, M.Tashiro, K.Okamoto, H.Yamanaka, M.Tanokura, H.Tsuge. Structural Basis For Action of the External Chaperone For A Propeptide-Deficient Serine Protease From Aeromonas Sobria J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.622852