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Calcium in PDB 3dyb: Proteinase K- Digalacturonic Acid Complex

Enzymatic activity of Proteinase K- Digalacturonic Acid Complex

All present enzymatic activity of Proteinase K- Digalacturonic Acid Complex:
3.4.21.64;

Protein crystallography data

The structure of Proteinase K- Digalacturonic Acid Complex, PDB code: 3dyb was solved by S.B.Larson, J.S.Day, A.Mcpherson, R.Cudney, C.Nguyen, Center For High-Throughput Structural Biology (Chtsb), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.36 / 1.32
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.720, 67.720, 101.890, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 20.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Proteinase K- Digalacturonic Acid Complex (pdb code 3dyb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Proteinase K- Digalacturonic Acid Complex, PDB code: 3dyb:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3dyb

Go back to Calcium Binding Sites List in 3dyb
Calcium binding site 1 out of 2 in the Proteinase K- Digalacturonic Acid Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Proteinase K- Digalacturonic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca300

b:6.8
occ:0.10
O A:HOH608 1.6 26.5 0.9
O A:HOH608 2.3 5.5 0.1
O A:HOH507 2.3 7.6 0.1
OD2 A:ASP200 2.4 14.0 1.0
O A:VAL177 2.4 15.7 1.0
O A:HOH594 2.4 39.8 1.0
O A:HOH507 2.4 19.1 0.9
O A:PRO175 2.5 13.2 1.0
O A:HOH693 2.6 50.0 1.0
OD1 A:ASP200 2.8 19.6 1.0
CG A:ASP200 2.9 15.0 1.0
C A:PRO175 3.5 14.2 1.0
C A:VAL177 3.6 13.8 1.0
HA A:CYS178 3.6 11.7 1.0
HA A:PRO175 3.8 14.9 1.0
H A:THR179 3.8 10.8 1.0
H A:VAL177 4.1 12.2 1.0
O A:HOH742 4.1 50.6 1.0
N A:VAL177 4.2 12.1 1.0
O A:HOH814 4.2 28.6 0.5
CA A:PRO175 4.2 14.9 1.0
O A:GLU174 4.3 11.5 1.0
CB A:ASP200 4.4 13.3 1.0
CA A:CYS178 4.4 11.6 1.0
O A:VAL198 4.4 14.1 1.0
C A:SER176 4.5 13.1 1.0
N A:CYS178 4.5 10.6 1.0
N A:SER176 4.5 13.1 1.0
O A:HOH710 4.5 33.5 1.0
N A:THR179 4.5 10.7 1.0
CA A:VAL177 4.5 12.2 1.0
HA A:SER176 4.5 13.3 1.0
HB2 A:ASP200 4.6 13.0 1.0
HB3 A:ASP200 4.7 13.0 1.0
CA A:SER176 4.8 12.8 1.0
HB A:THR179 4.8 12.4 1.0
HG21 A:VAL198 4.8 20.9 1.0
SG A:CYS249 4.8 13.6 1.0
O A:HOH672 4.8 21.6 0.5
OG1 A:THR179 4.9 13.2 1.0

Calcium binding site 2 out of 2 in 3dyb

Go back to Calcium Binding Sites List in 3dyb
Calcium binding site 2 out of 2 in the Proteinase K- Digalacturonic Acid Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Proteinase K- Digalacturonic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:33.1
occ:1.00
OH A:TYR195 2.3 19.3 1.0
O A:HOH650 2.3 27.3 1.0
O A:HOH638 2.4 22.1 1.0
O A:HOH654 2.4 25.4 1.0
O A:ASN163 2.4 14.3 1.0
O A:HOH569 2.4 22.8 1.0
HH A:TYR195 2.8 18.3 1.0
HE2 A:TYR195 3.0 15.9 1.0
HA A:ALA164 3.1 13.8 1.0
O A:HOH605 3.2 36.0 1.0
CZ A:TYR195 3.3 16.0 1.0
CE2 A:TYR195 3.5 17.2 1.0
C A:ASN163 3.6 13.9 1.0
O A:HOH617 3.8 35.6 1.0
CA A:ALA164 4.0 13.5 1.0
OD1 A:ASN163 4.1 14.5 1.0
CG A:ASN163 4.2 13.6 1.0
N A:ALA164 4.2 14.1 1.0
O A:HOH554 4.3 28.6 1.0
ND2 A:ASN163 4.3 14.4 1.0
O A:HOH840 4.3 29.9 1.0
HD21 A:ASN163 4.3 14.1 1.0
HB1 A:ALA164 4.5 14.6 1.0
HB3 A:ASN163 4.5 12.2 1.0
CE1 A:TYR195 4.6 15.0 1.0
HD22 A:ASN163 4.6 14.1 1.0
CB A:ASN163 4.7 11.8 1.0
CA A:ASN163 4.7 12.0 1.0
CB A:ALA164 4.8 15.7 1.0
O A:HOH586 4.8 16.2 0.6
CD2 A:TYR195 4.9 12.9 1.0
HE1 A:TYR195 4.9 15.2 1.0
HB2 A:ALA164 4.9 14.6 1.0
C A:ALA164 4.9 13.2 1.0

Reference:

S.B.Larson, J.S.Day, C.Nguyen, R.Cudney, A.Mcpherson. High-Resolution Structure of Proteinase K Cocrystallized with Digalacturonic Acid. Acta Crystallogr.,Sect.F V. 65 192 2009.
ISSN: ESSN 1744-3091
PubMed: 19255463
DOI: 10.1107/S1744309109002218
Page generated: Sat Dec 12 04:09:30 2020

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