Calcium in PDB 5kxu: Structure Proteinase K Determined By Sacla

All present enzymatic activity of Structure Proteinase K Determined By Sacla:
3.4.21.64;

The structure of Structure Proteinase K Determined By Sacla, PDB code: 5kxu was solved by T.Masuda, M.Suzuki, S.Inoue, K.Numata, M.Sugahara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.15 / 1.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.500, 68.500, 108.400, 90.00, 90.00, 90.00
R / Rfree (%)	11.3 / 12.9

The binding sites of Calcium atom in the Structure Proteinase K Determined By Sacla (pdb code 5kxu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure Proteinase K Determined By Sacla, PDB code: 5kxu:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure Proteinase K Determined By Sacla


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure Proteinase K Determined By Sacla within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:13.7 occ:1.00 O A:PRO175 2.4 14.5 1.0 O A:HOH665 2.4 17.3 1.0 O A:VAL177 2.4 14.5 1.0 OD2 A:ASP200 2.4 13.8 1.0 O A:HOH679 2.4 15.3 1.0 O A:HOH707 2.4 17.8 1.0 O A:HOH765 2.5 18.9 1.0 OD1 A:ASP200 2.7 16.4 1.0 CG A:ASP200 2.9 13.8 1.0 C A:PRO175 3.5 13.5 1.0 C A:VAL177 3.7 13.3 1.0 HA A:PRO175 3.7 18.1 1.0 HA A:CYS178 3.7 14.9 1.0 H A:THR179 3.9 14.5 1.0 CA A:PRO175 4.2 15.1 1.0 H A:VAL177 4.2 16.4 1.0 N A:VAL177 4.2 13.7 1.0 O A:VAL198 4.4 16.5 1.0 CB A:ASP200 4.4 13.4 1.0 O A:HOH798 4.4 50.5 1.0 C A:SER176 4.5 14.3 1.0 HA A:SER176 4.5 17.1 1.0 N A:SER176 4.5 13.6 1.0 CA A:CYS178 4.5 12.4 1.0 N A:CYS178 4.5 12.4 1.0 O A:GLU174 4.6 14.0 1.0 CA A:VAL177 4.6 13.5 1.0 N A:THR179 4.6 12.1 1.0 O A:HOH809 4.7 43.9 1.0 HG22 A:VAL198 4.7 24.6 1.0 O A:HOH800 4.7 43.0 1.0 CA A:SER176 4.7 14.2 1.0 HB2 A:ASP200 4.7 16.0 1.0 HB3 A:ASP200 4.8 16.0 1.0 O A:HOH697 4.8 50.3 1.0 O A:HOH708 4.8 21.6 1.0 HB A:THR179 4.8 15.6 1.0 OG1 A:THR179 4.9 13.8 1.0 HB3 A:PRO175 4.9 22.3 1.0 O A:HOH804 4.9 56.9 1.0 HG1 A:THR179 4.9 16.6 1.0 O A:HOH631 5.0 45.1 1.0 SG A:CYS249 5.0 14.7 1.0

Calcium binding site 2 out of 2 in the Structure Proteinase K Determined By Sacla


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure Proteinase K Determined By Sacla within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:24.1 occ:1.00 O A:HOH688 2.3 25.6 1.0 O A:THR16 2.4 22.6 1.0 O A:HOH752 2.4 28.6 1.0 OD1 A:ASP260 2.4 23.6 1.0 O A:HOH722 2.4 29.4 1.0 O A:HOH782 2.4 26.9 1.0 OD2 A:ASP260 2.5 21.8 1.0 CG A:ASP260 2.8 21.9 1.0 C A:THR16 3.6 19.9 1.0 HG A:SER17 3.6 28.2 0.4 HB A:THR16 3.7 25.9 1.0 HA A:SER17 3.7 24.7 0.4 HA A:SER17 3.8 24.1 0.6 HH22 A:ARG12 3.9 21.5 1.0 HB3 A:ASN257 4.2 20.2 1.0 CB A:ASP260 4.3 20.2 1.0 O A:HOH653 4.3 52.0 1.0 OG A:SER17 4.3 23.5 0.4 O A:HOH746 4.3 26.3 0.2 HA A:THR16 4.4 23.0 1.0 CA A:THR16 4.4 19.2 1.0 N A:SER17 4.5 19.8 0.4 CB A:THR16 4.5 21.6 1.0 N A:SER17 4.5 19.0 0.6 OD1 A:ASN257 4.5 19.4 1.0 CA A:SER17 4.5 20.6 0.4 CA A:SER17 4.5 20.1 0.6 HB3 A:ASP260 4.5 24.2 1.0 HB3 A:SER17 4.6 26.3 0.6 NH2 A:ARG12 4.7 17.9 1.0 O A:HOH794 4.7 49.2 1.0 HB2 A:ASP260 4.8 24.2 1.0 HA A:ASP260 4.8 22.7 1.0 CG A:ASN257 4.8 17.7 1.0 HH21 A:ARG12 4.9 21.5 1.0 HD3 A:PRO18 4.9 25.1 1.0 CB A:ASN257 5.0 16.8 1.0

T.Masuda, M.Suzuki, S.Inoue, C.Song, T.Nakane, E.Nango, R.Tanaka, K.Tono, Y.Joti, T.Kameshima, T.Hatsui, M.Yabashi, B.Mikami, O.Nureki, K.Numata, S.Iwata, M.Sugahara. Atomic Resolution Structure of Serine Protease Proteinase K at Ambient Temperature. Sci Rep V. 7 45604 2017.
ISSN: ESSN 2045-2322
PubMed: 28361898
DOI: 10.1038/SREP45604