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Calcium in PDB 8sou: Proteinase K Multiconformer Model at 363K

Enzymatic activity of Proteinase K Multiconformer Model at 363K

All present enzymatic activity of Proteinase K Multiconformer Model at 363K:
3.4.21.64;

Protein crystallography data

The structure of Proteinase K Multiconformer Model at 363K, PDB code: 8sou was solved by S.Du, S.Wankowicz, F.Yabukarski, T.Doukov, D.Herschlag, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.58 / 1.54
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.458, 68.458, 104.967, 90, 90, 90
R / Rfree (%) 17.3 / 22.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Proteinase K Multiconformer Model at 363K (pdb code 8sou). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Proteinase K Multiconformer Model at 363K, PDB code: 8sou:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 8sou

Go back to Calcium Binding Sites List in 8sou
Calcium binding site 1 out of 3 in the Proteinase K Multiconformer Model at 363K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Proteinase K Multiconformer Model at 363K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:66.0
occ:0.42
CA A:CA302 0.0 66.0 0.4
O A:HOH440 0.4 35.8 0.2
O A:HOH440 0.6 33.3 0.4
O A:HOH491 2.5 60.7 1.0
O A:VAL177 2.9 19.8 0.2
HG A:CYS249 3.0 20.3 0.4
O A:PRO175 3.1 20.7 0.3
O A:PRO175 3.1 20.6 0.4
O A:PRO175 3.1 20.6 0.2
OD1 A:ASP200 3.1 16.3 0.4
O A:VAL177 3.3 16.2 0.4
HG A:CYS249 3.3 22.1 0.4
O A:VAL177 3.3 20.2 0.4
OD2 A:ASP200 3.4 14.5 0.2
OD2 A:ASP200 3.5 17.7 0.4
OD1 A:ASP200 3.5 19.4 0.4
O A:HOH472 3.6 42.1 0.4
CG A:ASP200 3.7 18.1 0.4
CA A:CA302 3.7 44.5 0.2
CG A:ASP200 3.8 15.5 0.4
CG A:ASP200 3.8 15.0 0.2
OD2 A:ASP200 3.9 15.4 0.4
SG A:CYS249 3.9 16.9 0.4
HB3 A:CYS249 4.0 19.0 0.4
HA A:CYS178 4.0 12.6 0.2
HA A:CYS178 4.0 18.1 0.4
OD1 A:ASP200 4.0 14.8 0.2
SG A:CYS249 4.0 21.3 0.2
C A:VAL177 4.1 16.2 0.4
HA A:SER176 4.1 23.7 1.0
HB3 A:CYS249 4.1 24.5 0.2
C A:VAL177 4.1 19.6 0.2
HA A:CYS178 4.1 24.2 0.3
C A:VAL177 4.1 20.3 0.4
SG A:CYS249 4.1 18.4 0.4
HB3 A:CYS249 4.2 21.8 0.4
O A:HOH472 4.2 36.0 0.4
C A:PRO175 4.2 20.4 0.3
C A:PRO175 4.3 20.3 0.4
C A:PRO175 4.3 20.3 0.2
C A:SER176 4.3 19.9 1.0
O A:SER176 4.3 22.6 1.0
CB A:CYS249 4.5 15.8 0.4
CA A:CA302 4.5 46.2 0.4
N A:VAL177 4.5 19.5 0.2
N A:VAL177 4.5 17.8 0.4
N A:VAL177 4.5 19.3 0.4
O A:HOH440 4.5 26.8 0.4
CA A:SER176 4.6 19.8 1.0
HB3 A:ASP200 4.6 18.9 0.2
CB A:CYS249 4.6 20.4 0.2
O A:HOH487 4.7 52.6 1.0
CB A:CYS249 4.7 18.2 0.4
O A:HOH472 4.7 15.5 0.2
N A:CYS178 4.7 15.8 0.4
CA A:CYS178 4.8 15.1 0.4
HB2 A:CYS249 4.8 19.0 0.4
HB3 A:ASP200 4.8 21.2 0.4
CA A:VAL177 4.8 19.8 0.2
CA A:CYS178 4.8 10.5 0.2
H A:VAL177 4.8 23.2 0.4
CB A:ASP200 4.8 15.8 0.2
H A:VAL177 4.8 21.4 0.4
N A:CYS178 4.8 20.3 0.3
H A:VAL177 4.8 23.4 0.2
CA A:VAL177 4.8 17.3 0.4
CB A:ASP200 4.9 17.6 0.4
CA A:CYS178 4.9 20.1 0.3
N A:SER176 4.9 19.5 1.0
CA A:VAL177 4.9 20.2 0.4
HA A:VAL177 4.9 23.8 0.2
N A:CYS178 4.9 9.1 0.2
HB2 A:CYS249 4.9 24.5 0.2
HB3 A:ASP200 5.0 17.6 0.4
O A:HOH461 5.0 32.6 1.0

Calcium binding site 2 out of 3 in 8sou

Go back to Calcium Binding Sites List in 8sou
Calcium binding site 2 out of 3 in the Proteinase K Multiconformer Model at 363K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Proteinase K Multiconformer Model at 363K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:46.2
occ:0.37
CA A:CA302 0.0 46.2 0.4
O A:HOH472 0.4 15.5 0.2
O A:HOH440 0.4 26.8 0.4
O A:GLU174 2.7 19.3 0.3
HG22 A:THR179 2.8 20.0 0.3
O A:GLU174 2.8 19.3 0.4
O A:VAL177 2.8 20.2 0.4
O A:VAL177 2.8 16.2 0.4
OG1 A:THR179 2.8 10.7 0.4
OG1 A:THR179 2.8 14.8 0.2
O A:GLU174 2.9 18.5 0.2
HG22 A:VAL198 2.9 25.2 0.4
HG22 A:VAL198 2.9 26.1 0.2
OD2 A:ASP200 2.9 17.7 0.4
OD2 A:ASP200 3.0 14.5 0.2
HG1 A:THR179 3.0 12.8 0.4
O A:HOH472 3.0 36.0 0.4
OD2 A:ASP200 3.1 15.4 0.4
O A:HOH472 3.1 42.1 0.4
HA A:PRO175 3.1 25.6 0.4
HA A:PRO175 3.2 25.4 0.2
HA A:PRO175 3.2 25.7 0.3
HG1 A:THR179 3.2 17.8 0.2
CA A:CA302 3.2 44.5 0.2
O A:VAL198 3.2 21.6 0.4
O A:VAL198 3.2 21.0 0.2
H A:THR179 3.3 15.5 0.2
HB A:THR179 3.3 11.6 0.4
O A:VAL198 3.3 19.3 0.4
HG21 A:THR179 3.5 20.0 0.3
H A:THR179 3.5 23.8 0.3
O A:VAL177 3.5 19.8 0.2
CG2 A:THR179 3.5 16.6 0.3
CB A:THR179 3.6 9.7 0.4
O A:PRO175 3.6 20.6 0.4
O A:PRO175 3.6 20.7 0.3
O A:PRO175 3.6 20.6 0.2
HB A:THR179 3.6 20.6 0.3
HB A:THR179 3.7 16.9 0.2
C A:VAL177 3.7 19.6 0.2
HG23 A:VAL177 3.7 26.5 0.4
CG2 A:VAL198 3.7 21.8 0.2
CG2 A:VAL198 3.7 21.0 0.4
HG23 A:VAL177 3.8 23.2 0.4
H A:THR179 3.8 15.0 0.4
HG23 A:VAL198 3.8 26.1 0.2
C A:VAL177 3.8 20.3 0.4
C A:GLU174 3.8 20.6 0.4
CA A:PRO175 3.8 21.4 0.4
C A:GLU174 3.8 19.8 0.3
HG22 A:VAL177 3.8 26.5 0.4
CB A:THR179 3.8 14.1 0.2
C A:VAL177 3.8 16.2 0.4
HG23 A:VAL198 3.8 25.2 0.4
CG A:ASP200 3.8 15.0 0.2
C A:PRO175 3.8 20.3 0.4
CA A:PRO175 3.9 21.2 0.2
CA A:PRO175 3.9 21.4 0.3
HG23 A:VAL177 3.9 25.0 0.2
C A:PRO175 3.9 20.4 0.3
C A:PRO175 3.9 20.3 0.2
C A:GLU174 3.9 19.9 0.2
N A:THR179 3.9 12.9 0.2
H A:VAL177 3.9 23.2 0.4
O A:ALA172 3.9 17.2 0.4
H A:VAL177 3.9 21.4 0.4
H A:VAL177 3.9 23.4 0.2
HB A:VAL198 3.9 23.7 0.4
O A:HOH440 4.0 33.3 0.4
HG22 A:VAL177 4.0 23.2 0.4
O A:ALA172 4.0 18.5 0.2
OD1 A:ASP200 4.0 14.8 0.2
CG A:ASP200 4.0 18.1 0.4
CG A:ASP200 4.0 15.5 0.4
N A:THR179 4.1 12.5 0.4
CB A:THR179 4.1 17.2 0.3
N A:THR179 4.1 19.8 0.3
HG21 A:VAL198 4.1 25.2 0.4
HG21 A:VAL198 4.1 26.1 0.2
HA A:CYS178 4.2 12.6 0.2
O A:HOH440 4.2 35.8 0.2
O A:ALA172 4.2 12.4 0.3
HG22 A:VAL177 4.2 25.0 0.2
HA A:CYS178 4.2 24.2 0.3
CG2 A:VAL177 4.2 22.1 0.4
OD1 A:ASP200 4.3 16.3 0.4
HG23 A:THR179 4.3 20.0 0.3
N A:PRO175 4.3 21.8 0.4
HA A:CYS178 4.3 18.1 0.4
N A:PRO175 4.3 21.4 0.3
CG2 A:VAL177 4.3 19.3 0.4
N A:PRO175 4.3 21.2 0.2
N A:VAL177 4.4 19.5 0.2
N A:VAL177 4.4 19.3 0.4
N A:VAL177 4.4 17.8 0.4
C A:VAL198 4.4 20.7 0.4
C A:VAL198 4.4 20.6 0.2
C A:VAL198 4.4 19.4 0.4
CA A:THR179 4.5 9.4 0.4
OD1 A:ASP200 4.5 19.4 0.4
CG2 A:VAL177 4.5 20.9 0.2
CA A:CA302 4.5 66.0 0.4
CA A:THR179 4.5 13.3 0.2
N A:CYS178 4.6 9.1 0.2
HG21 A:THR179 4.6 11.9 0.4
CA A:VAL177 4.6 19.8 0.2
CA A:VAL177 4.6 20.2 0.4
N A:CYS178 4.6 20.3 0.3
CA A:VAL177 4.7 17.3 0.4
C A:CYS178 4.7 14.2 0.4
HA A:VAL198 4.7 26.0 0.2
HA A:VAL198 4.7 26.3 0.4
CA A:CYS178 4.7 10.5 0.2
N A:CYS178 4.7 15.8 0.4
HA A:VAL198 4.7 24.8 0.4
C A:CYS178 4.7 11.7 0.2
CG2 A:THR179 4.7 9.9 0.4
N A:SER176 4.7 19.5 1.0
CA A:THR179 4.8 18.3 0.3
CA A:CYS178 4.8 20.1 0.3
CA A:CYS178 4.8 15.1 0.4
CB A:VAL198 4.8 19.8 0.4
HG13 A:VAL198 4.8 27.0 0.4
C A:CYS178 4.8 20.1 0.3
CB A:VAL198 4.9 21.7 0.4
CB A:VAL198 4.9 21.9 0.2
H A:GLU174 4.9 18.5 0.3
CA A:VAL198 4.9 20.7 0.4
CA A:VAL198 4.9 21.9 0.4
CA A:VAL198 4.9 21.6 0.2
HG13 A:VAL198 4.9 26.9 0.2
HA A:THR179 4.9 11.3 0.4
N A:GLU174 4.9 16.5 0.4
N A:GLU174 4.9 15.4 0.3
HG21 A:VAL177 4.9 26.5 0.4
HA A:THR179 5.0 15.9 0.2
CA A:GLU174 5.0 19.5 0.4
CA A:GLU174 5.0 18.1 0.3

Calcium binding site 3 out of 3 in 8sou

Go back to Calcium Binding Sites List in 8sou
Calcium binding site 3 out of 3 in the Proteinase K Multiconformer Model at 363K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Proteinase K Multiconformer Model at 363K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:44.5
occ:0.21
CA A:CA302 0.0 44.5 0.2
O A:HOH472 0.3 42.1 0.4
O A:HOH472 0.6 36.0 0.4
OD1 A:ASP200 2.4 14.8 0.2
OD1 A:ASP200 2.7 19.4 0.4
OD1 A:ASP200 3.0 16.3 0.4
O A:HOH440 3.0 26.8 0.4
O A:HOH472 3.2 15.5 0.2
OD2 A:ASP200 3.2 17.7 0.4
CG A:ASP200 3.2 15.0 0.2
CA A:CA302 3.2 46.2 0.4
O A:VAL198 3.3 19.3 0.4
CG A:ASP200 3.3 18.1 0.4
OD2 A:ASP200 3.3 14.5 0.2
O A:HOH440 3.4 33.3 0.4
O A:VAL198 3.4 21.0 0.2
O A:VAL198 3.4 21.6 0.4
HA A:PRO175 3.5 25.7 0.3
HA A:PRO175 3.5 25.6 0.4
HA A:PRO175 3.5 25.4 0.2
O A:PRO175 3.5 20.6 0.4
O A:PRO175 3.6 20.7 0.3
O A:PRO175 3.6 20.6 0.2
CG A:ASP200 3.6 15.5 0.4
O A:HOH480 3.7 48.3 1.0
HA A:VAL198 3.7 26.3 0.4
O A:HOH440 3.7 35.8 0.2
HA A:VAL198 3.7 26.0 0.2
HA A:VAL198 3.7 24.8 0.4
OD2 A:ASP200 3.7 15.4 0.4
CA A:CA302 3.7 66.0 0.4
HG22 A:VAL198 4.1 25.2 0.4
HG23 A:VAL198 4.1 25.2 0.4
C A:VAL198 4.1 19.4 0.4
HG23 A:VAL198 4.1 26.1 0.2
HG22 A:VAL198 4.1 26.1 0.2
C A:VAL198 4.2 20.6 0.2
C A:VAL198 4.2 20.7 0.4
CA A:PRO175 4.3 21.4 0.3
CA A:PRO175 4.3 21.4 0.4
CA A:PRO175 4.3 21.2 0.2
C A:PRO175 4.4 20.3 0.4
HB3 A:PRO175 4.4 24.9 0.4
HB3 A:PRO175 4.4 25.3 0.2
C A:PRO175 4.4 20.4 0.3
C A:PRO175 4.4 20.3 0.2
HB3 A:PRO175 4.4 25.7 0.3
CA A:VAL198 4.4 20.7 0.4
CA A:VAL198 4.4 21.9 0.4
CA A:VAL198 4.4 21.6 0.2
CG2 A:VAL198 4.5 21.0 0.4
CG2 A:VAL198 4.6 21.8 0.2
HG22 A:THR179 4.6 20.0 0.3
CB A:ASP200 4.6 15.8 0.2
O A:VAL177 4.6 16.2 0.4
O A:VAL177 4.7 20.2 0.4
O A:SER197 4.7 23.6 1.0
HB A:VAL198 4.7 23.7 0.4
CB A:ASP200 4.7 17.6 0.4
HA A:ASP200 4.8 17.3 0.4
O A:LEU199 4.8 19.6 1.0
HA A:ASP200 4.8 20.1 0.4
CB A:PRO175 4.9 20.7 0.4
CB A:PRO175 4.9 21.1 0.2
CB A:PRO175 4.9 21.4 0.3
HA A:ASP200 4.9 18.8 0.2
O A:VAL177 4.9 19.8 0.2
HB3 A:ASP200 4.9 18.9 0.2
CB A:ASP200 5.0 14.6 0.4
C A:LEU199 5.0 17.3 1.0

Reference:

S.Du, S.Wankowicz, F.Yabukarski, T.Doukov, D.Herschlag, J.S.Fraser. Refinement of Multiconformer Ensemble Models From Multi-Temperature X-Ray Diffraction Data Methods Enzymol. 2023.
ISSN: ISSN 0076-6879
DOI: 10.1016/BS.MIE.2023.06.009
Page generated: Thu Dec 28 01:47:42 2023

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