Calcium in PDB 1wme: Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.50 Angstrom, 293 K)

The structure of Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.50 Angstrom, 293 K), PDB code: 1wme was solved by T.Nonaka, M.Fujihashi, A.Kita, K.Saeki, S.Ito, K.Horikoshi, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.00 / 1.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	43.539, 110.386, 168.960, 90.00, 90.00, 90.00
R / Rfree (%)	12.6 / 16.2

The binding sites of Calcium atom in the Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.50 Angstrom, 293 K) (pdb code 1wme). 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 Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.50 Angstrom, 293 K), PDB code: 1wme:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.50 Angstrom, 293 K)


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 Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.50 Angstrom, 293 K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:15.5 occ:1.00 OD1 A:ASP197 2.3 17.8 1.0 O A:SER194 2.3 17.2 1.0 O A:HOH2176 2.4 21.9 1.0 O A:HOH2177 2.4 18.3 1.0 OE2 A:GLU186 2.4 14.6 1.0 OE1 A:GLU186 2.5 15.9 1.0 ND1 A:HIS201 2.5 16.9 1.0 CD A:GLU186 2.8 14.2 1.0 CE1 A:HIS201 3.2 20.2 1.0 CG A:ASP197 3.4 17.1 1.0 C A:SER194 3.5 15.7 1.0 CG A:HIS201 3.7 17.7 1.0 OD2 A:ASP197 3.8 22.1 1.0 CB A:HIS201 4.1 15.9 1.0 CA A:SER194 4.2 17.2 1.0 CG A:GLU186 4.3 14.1 1.0 N A:ASP197 4.3 13.1 1.0 CB A:SER194 4.5 20.0 1.0 N A:ASN198 4.5 12.5 1.0 NE2 A:HIS201 4.5 23.2 1.0 N A:TYR195 4.5 15.2 1.0 O A:HOH2042 4.5 23.5 1.0 O A:HOH2102 4.6 43.6 1.0 CA A:TYR195 4.6 14.8 1.0 CB A:ASP197 4.6 13.8 1.0 C A:TYR195 4.7 14.2 1.0 CD2 A:HIS201 4.7 21.3 1.0 O A:HOH2187 4.7 48.8 1.0 N A:ALA196 4.8 14.3 1.0 CA A:ASP197 4.8 12.6 1.0 CB A:ASN198 4.8 14.7 1.0 C A:ASP197 4.9 11.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.50 Angstrom, 293 K)


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 Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.50 Angstrom, 293 K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:21.6 occ:1.00 OD1 A:ASP391 2.2 23.9 1.0 O A:THR386 2.4 25.5 1.0 OD1 A:ASP384 2.4 22.6 1.0 O A:HOH2178 2.4 22.4 1.0 O A:PRO388 2.4 23.5 1.0 OD1 A:ASN392 2.5 26.0 1.0 OD2 A:ASP384 2.5 20.3 1.0 OG1 A:THR386 2.7 25.1 1.0 CG A:ASP384 2.8 20.1 1.0 C A:THR386 3.4 24.6 1.0 CG A:ASP391 3.4 25.2 1.0 CG A:ASN392 3.5 24.1 1.0 C A:PRO388 3.6 23.8 1.0 OD2 A:ASP391 3.8 24.1 1.0 CB A:THR386 3.8 25.3 1.0 CA A:THR386 4.0 24.1 1.0 N A:THR386 4.1 23.1 1.0 CB A:ASN392 4.1 21.5 1.0 N A:ASN392 4.1 21.5 1.0 O A:HOH2117 4.2 38.8 1.0 CA A:TYR389 4.2 20.8 1.0 CB A:ASP384 4.3 17.8 1.0 C A:SER387 4.4 26.2 1.0 N A:TYR389 4.4 21.4 1.0 N A:ASP391 4.4 23.7 1.0 N A:SER387 4.4 27.1 1.0 N A:PRO388 4.4 25.8 1.0 ND2 A:ASN392 4.6 27.9 1.0 CB A:ASP391 4.6 24.9 1.0 C A:TYR389 4.6 20.3 1.0 CA A:PRO388 4.6 25.0 1.0 C A:ASP391 4.7 23.8 1.0 O A:SER387 4.7 34.8 1.0 CA A:SER387 4.7 27.7 1.0 N A:ASN390 4.7 21.4 1.0 CA A:ASP391 4.8 24.4 1.0 CA A:ASN392 4.8 20.8 1.0 CD A:PRO388 4.9 28.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.50 Angstrom, 293 K)


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 Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.50 Angstrom, 293 K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:15.0 occ:1.00 OE2 A:GLU400 2.2 15.5 1.0 OD1 A:ASP367 2.3 18.6 1.0 OD1 A:ASP369 2.3 17.8 1.0 O A:ASP394 2.3 17.5 1.0 O A:LEU368 2.4 15.8 1.0 O A:HOH2179 2.4 16.7 1.0 C A:LEU368 3.4 14.3 1.0 CD A:GLU400 3.4 14.0 1.0 CG A:ASP367 3.4 15.7 1.0 CG A:ASP369 3.4 16.9 1.0 C A:ASP394 3.5 17.2 1.0 CA A:ASP369 3.9 14.5 1.0 OD2 A:ASP367 3.9 19.0 1.0 O A:HOH2034 4.0 25.0 1.0 N A:ASP369 4.0 14.3 1.0 OE1 A:GLU400 4.2 16.0 1.0 N A:LEU368 4.2 14.6 1.0 CB A:ASP369 4.2 16.3 1.0 CB A:ASP394 4.3 16.2 1.0 OD1 A:ASP394 4.3 17.2 1.0 CA A:ASP394 4.4 16.9 1.0 O A:HOH2025 4.4 20.4 1.0 OD2 A:ASP369 4.4 19.4 1.0 CG A:GLU400 4.4 15.9 1.0 N A:GLY395 4.4 16.7 1.0 CH2 A:TRP351 4.4 15.4 1.0 CA A:LEU368 4.4 14.6 1.0 CA A:GLY395 4.5 17.8 1.0 C A:ASP367 4.6 15.2 1.0 N A:ASP394 4.7 18.5 1.0 CB A:ASP367 4.7 15.7 1.0 CG A:ASP394 4.8 15.3 1.0 CA A:ASP367 4.8 15.1 1.0 O A:ASN397 4.8 16.5 1.0 CZ2 A:TRP351 4.9 15.2 1.0

T.Nonaka, M.Fujihashi, A.Kita, K.Saeki, S.Ito, K.Horikoshi, K.Miki. The Crystal Structure of An Oxidatively Stable Subtilisin-Like Alkaline Serine Protease, Kp-43, with A C-Terminal {Beta}-Barrel Domain J.Biol.Chem. V. 279 47344 2004.
ISSN: ISSN 0021-9258
PubMed: 15342641
DOI: 10.1074/JBC.M409089200