Calcium in PDB 5kxv: Structure Proteinase K at 0.98 Angstroms

All present enzymatic activity of Structure Proteinase K at 0.98 Angstroms:
3.4.21.64;

The structure of Structure Proteinase K at 0.98 Angstroms, PDB code: 5kxv 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)	16.89 / 0.98
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.577, 67.577, 107.140, 90.00, 90.00, 90.00
R / Rfree (%)	10 / 11.4

The binding sites of Calcium atom in the Structure Proteinase K at 0.98 Angstroms (pdb code 5kxv). 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 at 0.98 Angstroms, PDB code: 5kxv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure Proteinase K at 0.98 Angstroms


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 at 0.98 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:5.7 occ:0.99 O A:PRO175 2.4 6.2 0.6 O A:VAL177 2.4 6.3 1.0 O A:HOH534 2.4 6.5 1.0 O2 A:GOL303 2.4 10.9 1.0 O A:HOH492 2.4 8.1 1.0 O A:PRO175 2.4 5.7 0.4 OD2 A:ASP200 2.4 6.3 1.0 O3 A:GOL303 2.5 10.1 1.0 OD1 A:ASP200 2.6 7.6 1.0 CG A:ASP200 2.9 6.2 1.0 C2 A:GOL303 3.3 14.3 1.0 C3 A:GOL303 3.4 13.2 1.0 H2 A:GOL303 3.4 17.1 1.0 C A:PRO175 3.5 6.1 0.6 C A:PRO175 3.5 6.0 0.4 O A:HOH414 3.6 9.1 0.4 C A:VAL177 3.6 5.3 1.0 HA A:CYS178 3.7 6.1 1.0 HA A:PRO175 3.7 8.1 0.4 H31 A:GOL303 3.8 15.8 1.0 HA A:PRO175 3.8 8.6 0.6 H A:THR179 3.9 5.7 1.0 H A:VAL177 4.1 6.7 1.0 N A:VAL177 4.2 5.6 1.0 CA A:PRO175 4.2 6.7 0.4 CA A:PRO175 4.3 7.2 0.6 O A:VAL198 4.3 7.5 1.0 H32 A:GOL303 4.3 15.8 1.0 CB A:ASP200 4.4 6.3 1.0 HA A:SER176 4.4 7.1 1.0 C A:SER176 4.4 5.9 1.0 N A:SER176 4.5 5.9 1.0 CA A:CYS178 4.5 5.0 1.0 N A:CYS178 4.5 5.0 1.0 O A:GLU174 4.5 5.8 1.0 CA A:VAL177 4.6 5.5 1.0 O A:HOH756 4.6 17.5 1.0 O A:HOH488 4.6 31.2 1.0 N A:THR179 4.6 4.8 1.0 HG22 A:VAL198 4.6 10.0 1.0 C1 A:GOL303 4.7 16.9 1.0 CA A:SER176 4.7 5.9 1.0 O A:HOH588 4.7 9.8 1.0 HB2 A:ASP200 4.7 7.6 1.0 O A:HOH584 4.7 19.1 0.7 HB3 A:ASP200 4.8 7.6 1.0 OG1 A:THR179 4.8 5.4 1.0 HB A:THR179 4.8 6.1 1.0 HG1 A:THR179 4.9 6.5 1.0 O A:HOH419 4.9 37.7 1.0 SG A:CYS249 5.0 8.8 1.0 HB2 A:PRO175 5.0 9.1 0.4 HG23 A:VAL198 5.0 10.0 1.0

Calcium binding site 2 out of 2 in the Structure Proteinase K at 0.98 Angstroms


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 at 0.98 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:11.8 occ:0.68 O A:THR16 2.4 12.8 1.0 O A:HOH688 2.4 20.2 1.0 O A:HOH647 2.4 25.7 1.0 O A:HOH567 2.4 18.4 1.0 OD1 A:ASP260 2.4 15.5 1.0 OD2 A:ASP260 2.5 14.7 1.0 O A:HOH698 2.5 22.9 0.7 O A:HOH698 2.6 19.4 0.3 CG A:ASP260 2.8 14.5 1.0 C A:THR16 3.6 10.8 1.0 HB A:THR16 3.7 13.5 1.0 HA A:SER17 3.8 12.9 1.0 HH22 A:ARG12 3.9 11.6 1.0 O A:HOH477 4.2 27.4 1.0 HB3 A:ASN257 4.3 11.8 1.0 CB A:ASP260 4.3 14.1 1.0 O A:HOH673 4.4 43.6 1.0 HA A:THR16 4.4 12.0 1.0 CA A:THR16 4.4 10.0 1.0 CB A:THR16 4.5 11.3 1.0 N A:SER17 4.5 10.4 1.0 OD1 A:ASN257 4.5 10.9 1.0 CA A:SER17 4.5 10.7 1.0 HB3 A:ASP260 4.6 16.9 1.0 NH2 A:ARG12 4.6 9.6 1.0 HB3 A:SER17 4.7 14.4 1.0 HA A:ASP260 4.7 16.0 1.0 HB2 A:ASP260 4.7 16.9 1.0 HH21 A:ARG12 4.8 11.6 1.0 O A:HOH819 4.8 46.3 1.0 HD3 A:PRO18 4.8 12.9 1.0 CG A:ASN257 4.8 10.3 1.0 O A:HOH428 4.9 16.6 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