Calcium in PDB 1wmd: Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.30 Angstrom, 100 K)

The structure of Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.30 Angstrom, 100 K), PDB code: 1wmd 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)	100.00 / 1.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	42.840, 109.036, 166.912, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 16.9

The binding sites of Calcium atom in the Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.30 Angstrom, 100 K) (pdb code 1wmd). 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 (1.30 Angstrom, 100 K), PDB code: 1wmd:
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 (1.30 Angstrom, 100 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 (1.30 Angstrom, 100 K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:11.8 occ:1.00 O A:SER194 2.3 12.3 1.0 O A:HOH3002 2.4 17.0 1.0 OD1 A:ASP197 2.4 12.4 1.0 O A:HOH3001 2.4 14.5 1.0 OE1 A:GLU186 2.4 11.7 1.0 OE2 A:GLU186 2.4 10.1 1.0 ND1 A:HIS201 2.5 14.6 1.0 CD A:GLU186 2.8 10.0 1.0 CE1 A:HIS201 3.4 15.4 1.0 CG A:ASP197 3.4 11.8 1.0 C A:SER194 3.4 12.3 1.0 CG A:HIS201 3.7 16.1 1.0 OD2 A:ASP197 3.9 14.9 1.0 CA A:SER194 4.2 13.5 1.0 CB A:HIS201 4.2 13.9 1.0 CG A:GLU186 4.3 10.5 1.0 N A:ASP197 4.3 10.0 1.0 O A:HOH3322 4.4 31.9 1.0 O A:HOH3242 4.4 28.1 1.0 CB A:SER194 4.4 15.5 1.0 N A:TYR195 4.5 11.8 1.0 O A:HOH3010 4.5 16.3 1.0 N A:ASN198 4.5 9.5 1.0 O A:HOH3397 4.6 44.9 1.0 CA A:TYR195 4.6 11.6 1.0 NE2 A:HIS201 4.6 18.1 1.0 C A:TYR195 4.6 10.8 1.0 CB A:ASP197 4.7 11.0 1.0 CD2 A:HIS201 4.7 17.7 1.0 CB A:ASN198 4.7 9.9 1.0 O A:HOH3193 4.8 39.0 1.0 N A:ALA196 4.8 10.8 1.0 CA A:ASP197 4.9 9.9 1.0 C A:ASP197 4.9 9.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.30 Angstrom, 100 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 (1.30 Angstrom, 100 K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:15.9 occ:1.00 O A:THR386 2.3 17.5 1.0 OD1 A:ASP391 2.3 16.1 1.0 OD1 A:ASP384 2.4 17.8 1.0 O A:HOH3003 2.4 17.7 1.0 OD1 A:ASN392 2.4 16.5 1.0 O A:PRO388 2.5 16.2 1.0 OD2 A:ASP384 2.5 15.2 1.0 OG1 A:THR386 2.6 17.2 1.0 CG A:ASP384 2.8 14.7 1.0 C A:THR386 3.3 16.4 1.0 CG A:ASP391 3.4 15.3 1.0 CG A:ASN392 3.5 16.8 1.0 C A:PRO388 3.6 18.5 1.0 CB A:THR386 3.7 15.9 1.0 OD2 A:ASP391 3.8 15.1 1.0 O A:HOH3311 3.9 42.6 1.0 CA A:THR386 3.9 16.6 1.0 N A:THR386 4.0 16.2 1.0 CB A:ASN392 4.2 16.3 1.0 N A:ASN392 4.2 15.4 1.0 CA A:TYR389 4.2 16.3 1.0 CB A:ASP384 4.3 13.9 1.0 C A:SER387 4.3 19.8 1.0 N A:ASP391 4.3 15.1 1.0 N A:TYR389 4.4 17.9 1.0 N A:PRO388 4.4 21.2 1.0 N A:SER387 4.4 18.4 1.0 ND2 A:ASN392 4.5 21.2 1.0 CA A:PRO388 4.6 19.6 1.0 CB A:ASP391 4.6 15.1 1.0 C A:TYR389 4.6 15.2 1.0 O A:SER387 4.7 24.5 1.0 CA A:SER387 4.7 17.2 1.0 C A:ASP391 4.7 16.9 1.0 N A:ASN390 4.7 15.8 1.0 CA A:ASP391 4.8 14.6 1.0 CA A:ASN392 4.9 14.2 1.0 CD A:PRO388 4.9 23.0 1.0 CG2 A:THR386 5.0 18.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (1.30 Angstrom, 100 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 (1.30 Angstrom, 100 K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:11.4 occ:1.00 OE2 A:GLU400 2.3 11.2 1.0 OD1 A:ASP369 2.3 12.7 1.0 OD1 A:ASP367 2.3 13.8 1.0 O A:ASP394 2.3 13.2 1.0 O A:LEU368 2.4 11.5 1.0 O A:HOH3004 2.4 11.3 1.0 C A:LEU368 3.3 9.9 1.0 CD A:GLU400 3.4 11.2 1.0 CG A:ASP367 3.4 12.0 1.0 C A:ASP394 3.5 13.7 1.0 CG A:ASP369 3.5 12.1 1.0 CA A:ASP369 3.9 11.0 1.0 OD2 A:ASP367 3.9 13.2 1.0 O A:HOH3121 3.9 17.6 1.0 N A:ASP369 3.9 10.8 1.0 N A:LEU368 4.2 11.0 1.0 CB A:ASP394 4.2 11.9 1.0 OE1 A:GLU400 4.2 11.9 1.0 CB A:ASP369 4.2 11.7 1.0 CA A:ASP394 4.3 13.8 1.0 O A:HOH3030 4.3 16.1 1.0 CG A:GLU400 4.4 10.3 1.0 OD1 A:ASP394 4.4 11.6 1.0 N A:GLY395 4.4 14.0 1.0 CA A:LEU368 4.4 10.3 1.0 OD2 A:ASP369 4.4 14.8 1.0 CH2 A:TRP351 4.4 11.2 1.0 C A:ASP367 4.5 10.5 1.0 CA A:GLY395 4.5 13.7 1.0 N A:ASP394 4.6 14.0 1.0 CB A:ASP367 4.7 12.1 1.0 O A:ASN397 4.7 11.4 1.0 CA A:ASP367 4.8 10.7 1.0 CG A:ASP394 4.8 11.7 1.0 CZ2 A:TRP351 5.0 10.1 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