Calcium in PDB 5ms4: Kallikrein-Related Peptidase 8 Leupeptin Inhibitor Complex

All present enzymatic activity of Kallikrein-Related Peptidase 8 Leupeptin Inhibitor Complex:
3.4.21.118;

The structure of Kallikrein-Related Peptidase 8 Leupeptin Inhibitor Complex, PDB code: 5ms4 was solved by M.Debela, V.Magdolen, W.Skala, W.Bode, H.Brandstetter, P.Goettig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.53 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.103, 46.045, 103.349, 90.00, 91.40, 90.00
R / Rfree (%)	21.2 / 25.9

The binding sites of Calcium atom in the Kallikrein-Related Peptidase 8 Leupeptin Inhibitor Complex (pdb code 5ms4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Kallikrein-Related Peptidase 8 Leupeptin Inhibitor Complex, PDB code: 5ms4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Kallikrein-Related Peptidase 8 Leupeptin Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Kallikrein-Related Peptidase 8 Leupeptin Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:15.0 occ:1.00 OE2 A:GLU80 2.3 6.3 1.0 O A:SER72 2.3 25.6 1.0 O A:ASN75 2.4 13.8 1.0 O A:HOH407 2.5 15.1 1.0 OD2 A:ASP77 2.5 10.4 1.0 OD1 A:ASP70 2.6 16.2 1.0 NH2 A:ARG66 2.9 13.9 1.0 C A:SER72 3.4 18.5 1.0 CD A:GLU80 3.5 5.1 1.0 CG A:ASP77 3.5 5.8 1.0 CG A:ASP70 3.6 14.8 1.0 C A:ASN75 3.6 12.5 1.0 N A:ASP77 3.7 12.4 1.0 N A:SER72 4.0 10.3 1.0 CG A:GLU80 4.1 6.6 1.0 CA A:LYS76 4.1 12.1 1.0 OD2 A:ASP70 4.1 21.4 1.0 CB A:ASP77 4.2 7.1 1.0 CZ A:ARG66 4.2 14.4 1.0 CA A:SER72 4.3 6.6 1.0 C A:LYS76 4.3 11.4 1.0 N A:LYS76 4.3 15.9 1.0 N A:LEU73 4.4 14.4 1.0 OD1 A:ASP77 4.4 14.0 1.0 OE1 A:GLU80 4.5 19.0 1.0 CA A:LEU73 4.5 8.3 1.0 N A:HIS71 4.5 10.9 1.0 O A:LEU73 4.6 24.7 1.0 N A:ASN75 4.6 20.1 1.0 CA A:ASP77 4.6 8.0 1.0 C A:LEU73 4.6 9.9 1.0 CB A:ASP70 4.6 10.4 1.0 CA A:ASN75 4.7 11.2 1.0 O D:HOH421 4.7 10.2 1.0 CB A:SER72 4.7 7.7 1.0 CA A:ASP70 4.8 7.0 1.0 NE A:ARG66 4.9 8.0 1.0 C A:HIS71 5.0 12.2 1.0

Calcium binding site 2 out of 4 in the Kallikrein-Related Peptidase 8 Leupeptin Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Kallikrein-Related Peptidase 8 Leupeptin Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:29.6 occ:1.00 OE2 B:GLU80 2.3 16.4 1.0 O B:SER72 2.3 16.6 1.0 OD1 B:ASP70 2.4 14.7 1.0 O B:HOH504 2.5 21.6 1.0 OD2 B:ASP77 2.5 22.6 1.0 O B:ASN75 2.6 22.3 1.0 OD2 B:ASP70 2.9 18.9 1.0 CG B:ASP70 2.9 12.6 1.0 CD B:GLU80 3.2 15.0 1.0 CG B:ASP77 3.3 22.7 1.0 CB B:ASP77 3.4 35.2 1.0 C B:SER72 3.5 11.3 1.0 C B:ASN75 3.8 32.8 1.0 CG B:GLU80 4.0 15.9 1.0 OE1 B:GLU80 4.0 25.4 1.0 O B:LYS76 4.1 25.4 1.0 N B:SER72 4.2 11.6 1.0 C B:LYS76 4.2 24.6 1.0 CB B:ASP70 4.3 8.5 1.0 N B:ASN75 4.3 11.2 1.0 O B:LEU73 4.4 15.1 1.0 CA B:SER72 4.4 6.1 1.0 C B:LEU73 4.4 11.2 1.0 N B:LEU73 4.4 10.1 1.0 CA B:LEU73 4.5 13.8 1.0 OD1 B:ASP77 4.5 20.6 1.0 CA B:ASP77 4.6 22.9 1.0 CA B:ASN75 4.6 15.7 1.0 N B:ASP77 4.7 19.6 1.0 N B:HIS71 4.7 9.2 1.0 N B:LYS76 4.7 33.4 1.0 CA B:LYS76 4.8 28.0 1.0 CB B:SER72 4.8 11.4 1.0 CA B:ASP70 4.8 7.2 1.0 N B:GLN74 4.9 9.0 1.0

Calcium binding site 3 out of 4 in the Kallikrein-Related Peptidase 8 Leupeptin Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Kallikrein-Related Peptidase 8 Leupeptin Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:24.3 occ:1.00 O C:SER72 2.2 17.7 1.0 OE2 C:GLU80 2.2 11.4 1.0 O C:ASN75 2.3 12.0 1.0 OD1 C:ASP70 2.4 11.1 1.0 OD2 C:ASP77 2.7 16.8 1.0 CG C:ASP70 3.1 6.4 1.0 OD2 C:ASP70 3.2 9.0 1.0 C C:SER72 3.3 11.6 1.0 CD C:GLU80 3.4 7.7 1.0 C C:ASN75 3.5 12.1 1.0 CG C:ASP77 3.7 9.3 1.0 O C:LEU73 3.7 17.2 1.0 CG C:GLU80 3.9 11.3 1.0 C C:LEU73 4.0 10.2 1.0 N C:SER72 4.0 10.1 1.0 NH2 C:ARG66 4.1 21.0 1.0 CA C:LEU73 4.1 8.2 1.0 N C:LEU73 4.1 10.3 1.0 O C:HOH468 4.2 13.2 1.0 CA C:SER72 4.2 5.9 1.0 CA C:LYS76 4.2 19.2 1.0 N C:ASN75 4.3 10.3 1.0 C C:LYS76 4.3 13.4 1.0 N C:LYS76 4.3 24.0 1.0 CB C:ASP70 4.3 6.2 1.0 CB C:ASP77 4.4 15.4 1.0 OE1 C:GLU80 4.4 15.3 1.0 O C:LYS76 4.5 17.0 1.0 N C:HIS71 4.5 5.9 1.0 CA C:ASN75 4.5 9.4 1.0 OD1 C:ASP77 4.6 14.8 1.0 CZ C:ARG66 4.6 20.1 1.0 CA C:ASP70 4.7 5.9 1.0 NE C:ARG66 4.7 9.4 1.0 N C:GLN74 4.7 9.7 1.0 N C:ASP77 4.8 10.8 1.0 CB C:SER72 4.8 14.3 1.0 C C:HIS71 4.9 7.2 1.0

Calcium binding site 4 out of 4 in the Kallikrein-Related Peptidase 8 Leupeptin Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Kallikrein-Related Peptidase 8 Leupeptin Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:49.2 occ:1.00 O D:SER72 2.3 22.0 1.0 O D:ASN75 2.5 29.0 1.0 OD2 D:ASP77 2.7 22.4 1.0 OD1 D:ASP70 2.8 22.2 1.0 OE2 D:GLU80 3.0 17.3 1.0 O D:HOH489 3.0 31.7 1.0 CG D:ASP70 3.5 14.2 1.0 OD2 D:ASP70 3.5 13.0 1.0 C D:SER72 3.6 19.9 1.0 NH2 D:ARG66 3.7 8.3 1.0 C D:ASN75 3.7 41.2 1.0 O D:LEU73 3.8 28.9 1.0 CD D:GLU80 3.9 28.6 1.0 C D:LEU73 4.0 29.2 1.0 CG D:ASP77 4.0 20.0 1.0 CG D:GLU80 4.0 19.7 1.0 N D:ASN75 4.0 37.7 1.0 CA D:LEU73 4.2 24.3 1.0 N D:LEU73 4.4 24.2 1.0 CA D:ASN75 4.5 43.9 1.0 N D:ASP77 4.5 45.5 1.0 C D:GLN74 4.5 30.3 1.0 N D:GLN74 4.6 24.0 1.0 CA D:SER72 4.6 11.9 1.0 CZ D:ARG66 4.6 7.8 1.0 N D:SER72 4.7 21.8 1.0 N D:LYS76 4.7 43.6 1.0 OD1 D:ASP77 4.8 27.4 1.0 O D:HOH500 4.8 17.9 1.0 CB D:ASP77 4.8 24.3 1.0 CA D:LYS76 4.9 36.5 1.0 CB D:ASP70 4.9 14.8 1.0 O D:GLN74 5.0 37.7 1.0 CB D:SER72 5.0 12.1 1.0

M.Debela, V.Magdolen, W.Skala, B.Elsasser, E.L.Schneider, C.S.Craik, M.L.Biniossek, O.Schilling, W.Bode, H.Brandstetter, P.Goettig. Structural Determinants of Specificity and Regulation of Activity in the Allosteric Loop Network of Human KLK8/Neuropsin. Sci Rep V. 8 10705 2018.
ISSN: ESSN 2045-2322
PubMed: 30013126
DOI: 10.1038/S41598-018-29058-6