Calcium in PDB 1wmf: Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (Oxidized Form, 1.73 Angstrom)

The structure of Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (Oxidized Form, 1.73 Angstrom), PDB code: 1wmf 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)	20.00 / 1.73
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	42.917, 109.153, 167.164, 90.00, 90.00, 90.00
R / Rfree (%)	14.2 / 21.2

The binding sites of Calcium atom in the Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (Oxidized Form, 1.73 Angstrom) (pdb code 1wmf). 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 (Oxidized Form, 1.73 Angstrom), PDB code: 1wmf:
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 (Oxidized Form, 1.73 Angstrom)


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 (Oxidized Form, 1.73 Angstrom) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:15.4 occ:1.00 O A:SER194 2.2 16.4 1.0 O A:HOH3002 2.4 19.1 1.0 OD1 A:ASP197 2.4 15.9 1.0 OE2 A:GLU186 2.4 14.8 1.0 O A:HOH3001 2.4 16.9 1.0 OE1 A:GLU186 2.4 14.5 1.0 ND1 A:HIS201 2.6 19.2 1.0 CD A:GLU186 2.8 13.6 1.0 CE1 A:HIS201 3.3 20.7 1.0 C A:SER194 3.4 16.3 1.0 CG A:ASP197 3.5 15.2 1.0 CG A:HIS201 3.8 18.1 1.0 OD2 A:ASP197 3.9 16.6 1.0 CA A:SER194 4.1 17.4 1.0 CB A:HIS201 4.2 15.7 1.0 CG A:GLU186 4.3 13.2 1.0 N A:ASP197 4.4 13.9 1.0 CB A:SER194 4.4 19.3 1.0 O A:HOH3130 4.5 35.4 1.0 N A:TYR195 4.5 15.8 1.0 N A:ASN198 4.5 13.2 1.0 O A:HOH3054 4.5 21.4 1.0 NE2 A:HIS201 4.5 22.2 1.0 CA A:TYR195 4.6 16.4 1.0 O A:HOH3196 4.6 37.0 1.0 CB A:ASP197 4.7 14.9 1.0 C A:TYR195 4.7 14.9 1.0 CB A:ASN198 4.7 12.2 1.0 CD2 A:HIS201 4.8 20.9 1.0 N A:ALA196 4.8 13.5 1.0 CA A:ASP197 4.9 13.3 1.0 C A:ASP197 4.9 12.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (Oxidized Form, 1.73 Angstrom)


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 (Oxidized Form, 1.73 Angstrom) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:22.6 occ:1.00 OD1 A:ASN392 2.3 25.2 1.0 OD1 A:ASP391 2.3 22.3 1.0 O A:THR386 2.4 21.8 1.0 OD1 A:ASP384 2.4 20.9 1.0 O A:HOH3003 2.4 17.5 1.0 O A:PRO388 2.4 21.1 1.0 OD2 A:ASP384 2.5 19.2 1.0 OG1 A:THR386 2.5 21.9 1.0 CG A:ASP384 2.8 19.4 1.0 C A:THR386 3.4 22.4 1.0 CG A:ASN392 3.4 23.7 1.0 CG A:ASP391 3.4 22.3 1.0 C A:PRO388 3.6 22.4 1.0 CB A:THR386 3.7 22.0 1.0 OD2 A:ASP391 3.9 19.1 1.0 CA A:THR386 3.9 22.3 1.0 O A:HOH3240 4.0 36.2 1.0 N A:THR386 4.1 22.8 1.0 CA A:TYR389 4.1 23.6 1.0 CB A:ASN392 4.2 21.4 1.0 O A:HOH3160 4.2 43.6 1.0 N A:ASN392 4.3 22.2 1.0 CB A:ASP384 4.3 18.1 1.0 N A:TYR389 4.3 23.7 1.0 N A:ASP391 4.3 22.8 1.0 N A:PRO388 4.3 26.6 1.0 C A:SER387 4.3 26.6 1.0 ND2 A:ASN392 4.4 25.0 1.0 N A:SER387 4.5 24.2 1.0 O A:HOH3176 4.5 29.0 1.0 C A:TYR389 4.5 20.6 1.0 CA A:PRO388 4.6 24.9 1.0 O A:SER387 4.6 29.2 1.0 N A:ASN390 4.7 20.8 1.0 CB A:ASP391 4.7 21.9 1.0 CA A:SER387 4.7 25.3 1.0 C A:ASP391 4.8 22.1 1.0 CD A:PRO388 4.8 27.0 1.0 CA A:ASP391 4.8 23.4 1.0 CA A:ASN392 4.9 21.1 1.0 CG2 A:THR386 4.9 23.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Alkaline Serine Protease Kp-43 From Bacillus Sp. Ksm-KP43 (Oxidized Form, 1.73 Angstrom)


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 (Oxidized Form, 1.73 Angstrom) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:15.3 occ:1.00 OE2 A:GLU400 2.2 13.3 1.0 OD1 A:ASP369 2.3 15.4 1.0 OD1 A:ASP367 2.3 17.6 1.0 O A:ASP394 2.3 15.0 1.0 O A:LEU368 2.4 13.6 1.0 O A:HOH3004 2.4 16.4 1.0 C A:LEU368 3.3 13.4 1.0 CD A:GLU400 3.3 12.6 1.0 CG A:ASP367 3.5 16.6 1.0 C A:ASP394 3.5 16.0 1.0 CG A:ASP369 3.5 14.7 1.0 CA A:ASP369 3.8 13.7 1.0 N A:ASP369 3.9 14.6 1.0 OD2 A:ASP367 4.0 19.3 1.0 O A:HOH3170 4.0 22.1 1.0 OE1 A:GLU400 4.1 14.1 1.0 N A:LEU368 4.2 15.3 1.0 CB A:ASP369 4.2 14.1 1.0 CG A:GLU400 4.3 12.8 1.0 O A:HOH3053 4.3 18.1 1.0 CB A:ASP394 4.3 14.8 1.0 CA A:ASP394 4.3 15.9 1.0 N A:GLY395 4.4 15.6 1.0 OD2 A:ASP369 4.4 17.6 1.0 CA A:LEU368 4.4 13.7 1.0 OD1 A:ASP394 4.4 15.4 1.0 CH2 A:TRP351 4.5 14.7 1.0 CA A:GLY395 4.6 16.3 1.0 C A:ASP367 4.6 15.3 1.0 N A:ASP394 4.6 18.6 1.0 CB A:ASP367 4.7 15.0 1.0 CG A:ASP394 4.8 15.2 1.0 CA A:ASP367 4.8 15.2 1.0 O A:ASN397 4.8 14.9 1.0 CZ2 A:TRP351 5.0 14.8 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