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Calcium in PDB 5t9k: Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin

Enzymatic activity of Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin

All present enzymatic activity of Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin:
3.4.24.27;

Protein crystallography data

The structure of Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin, PDB code: 5t9k was solved by M.Dong, B.J.Bahnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.58 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.715, 93.715, 131.235, 90.00, 90.00, 120.00
R / Rfree (%) 13.8 / 19.5

Other elements in 5t9k:

The structure of Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin (pdb code 5t9k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin, PDB code: 5t9k:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5t9k

Go back to Calcium Binding Sites List in 5t9k
Calcium binding site 1 out of 4 in the Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:22.1
occ:1.00
 O A:GLU187 2.3 20.3 1.0
OD1 A:ASP185 2.5 29.4 1.0
OD2 A:ASP138 2.5 20.3 1.0
OE2 A:GLU190 2.5 21.4 1.0
OE1 A:GLU177 2.5 21.3 1.0
OE1 A:GLU190 2.6 21.6 1.0
O A:HOH581 2.6 23.3 1.0
OE2 A:GLU177 2.7 22.8 1.0
CD A:GLU190 2.8 30.0 1.0
CD A:GLU177 3.0 21.7 1.0
C A:GLU187 3.4 21.9 1.0
CG A:ASP138 3.4 21.5 1.0
CG A:ASP185 3.5 28.6 1.0
CA A:CA402 3.7 39.0 1.0
OD2 A:ASP185 3.8 27.5 1.0
CB A:ASP138 4.0 20.0 1.0
O A:ASP185 4.2 23.9 1.0
N A:GLU187 4.2 30.7 1.0
N A:ILE188 4.3 20.8 1.0
CA A:GLU187 4.3 28.1 1.0
O A:HOH539 4.3 49.1 1.0
CA A:ILE188 4.3 17.7 1.0
CG A:GLU190 4.4 24.1 1.0
OD1 A:ASP138 4.4 23.0 1.0
N A:GLY189 4.4 24.9 1.0
CG A:GLU177 4.4 16.4 1.0
O A:HOH574 4.5 23.8 1.0
CB A:GLU187 4.6 22.4 1.0
C A:ASP185 4.6 25.0 1.0
N A:ASP185 4.7 20.9 1.0
CB A:ASP185 4.8 28.0 1.0
C A:ILE188 4.8 25.7 1.0
CB A:GLU177 5.0 20.2 1.0

Calcium binding site 2 out of 4 in 5t9k

Go back to Calcium Binding Sites List in 5t9k
Calcium binding site 2 out of 4 in the Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:39.0
occ:1.00
 OE2 A:GLU190 2.3 21.4 1.0
O A:HOH552 2.6 38.4 1.0
O A:ASN183 2.6 28.6 1.0
OE2 A:GLU177 2.6 22.8 1.0
OD2 A:ASP185 2.7 27.5 1.0
CD A:GLU177 3.3 21.7 1.0
CD A:GLU190 3.3 30.0 1.0
CG A:ASP185 3.4 28.6 1.0
O A:LYS182 3.6 33.8 0.5
OE1 A:GLU177 3.7 21.3 1.0
OD1 A:ASP185 3.7 29.4 1.0
CA A:CA401 3.7 22.1 1.0
C A:ASN183 3.7 32.6 1.0
CG A:GLU190 3.8 24.1 1.0
O A:HOH539 4.1 49.1 1.0
N A:ASP185 4.2 20.9 1.0
OD2 A:ASP191 4.2 25.9 1.0
OE1 A:GLU190 4.3 21.6 1.0
OD1 A:ASP191 4.3 27.4 1.0
CA A:PRO184 4.3 30.6 1.0
CG A:GLU177 4.3 16.4 1.0
CB A:ASN183 4.3 38.4 1.0
C A:PRO184 4.4 35.8 1.0
CB A:ASP185 4.5 28.0 1.0
N A:PRO184 4.5 32.6 1.0
CG A:ASP191 4.6 33.5 1.0
CA A:ASN183 4.7 35.5 1.0
C A:LYS182 4.8 28.7 0.5
CA A:ASP185 5.0 21.7 1.0

Calcium binding site 3 out of 4 in 5t9k

Go back to Calcium Binding Sites List in 5t9k
Calcium binding site 3 out of 4 in the Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:20.6
occ:1.00
 O A:HOH689 2.2 22.8 1.0
O A:GLN61 2.3 19.1 0.5
O A:GLN61 2.3 19.2 0.5
OD1 A:ASP57 2.4 23.7 1.0
O A:HOH559 2.4 18.0 1.0
OD1 A:ASP59 2.4 25.6 1.0
O A:HOH594 2.5 22.9 1.0
OD2 A:ASP57 2.5 19.9 1.0
CG A:ASP57 2.8 21.7 1.0
CG A:ASP59 3.4 30.2 1.0
C A:GLN61 3.5 20.3 0.5
C A:GLN61 3.5 20.3 0.5
OD2 A:ASP59 3.8 26.9 1.0
O A:HOH620 3.9 33.2 1.0
N A:GLN61 4.0 19.9 0.5
N A:GLN61 4.0 19.9 0.5
CA A:GLN61 4.2 21.9 0.5
CA A:GLN61 4.2 21.9 0.5
CB A:ASP57 4.4 19.0 1.0
N A:ASP59 4.4 21.8 1.0
CB A:GLN61 4.4 23.5 0.5
CB A:GLN61 4.4 23.6 0.5
N A:PHE62 4.5 20.5 1.0
O A:HOH519 4.6 17.3 1.0
OD2 A:ASP67 4.6 24.4 1.0
N A:ASN60 4.7 23.5 1.0
CA A:PHE62 4.7 20.2 1.0
CB A:ASP59 4.7 20.5 1.0
N A:ALA58 4.8 17.4 1.0
CA A:ASP59 4.9 20.2 1.0
C A:ASP59 4.9 24.4 1.0

Calcium binding site 4 out of 4 in 5t9k

Go back to Calcium Binding Sites List in 5t9k
Calcium binding site 4 out of 4 in the Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:29.4
occ:1.00
 OG1 A:THR194 2.3 26.1 1.0
O A:ILE197 2.3 41.8 1.0
OD1 A:ASP200 2.3 24.7 1.0
O A:HOH663 2.4 32.7 1.0
O A:THR194 2.4 27.8 1.0
O A:TYR193 2.4 23.9 1.0
O A:HOH521 2.5 27.7 1.0
C A:THR194 3.2 38.7 1.0
CG A:ASP200 3.3 24.4 1.0
C A:TYR193 3.4 28.4 1.0
CB A:THR194 3.4 38.1 1.0
C A:ILE197 3.5 48.5 1.0
OD2 A:ASP200 3.6 28.5 1.0
CA A:THR194 3.7 28.7 1.0
N A:THR194 3.9 22.9 1.0
N A:ILE197 4.2 51.0 1.0
CA A:ILE197 4.2 39.5 1.0
CB A:ILE197 4.3 41.7 1.0
N A:PRO195 4.3 30.3 1.0
O A:ASP200 4.5 29.8 1.0
N A:SER198 4.5 43.0 0.7
N A:SER198 4.6 43.1 0.3
O A:GLU190 4.6 24.0 1.0
CA A:TYR193 4.6 28.3 1.0
CG2 A:THR194 4.6 26.2 1.0
CA A:SER198 4.6 43.2 0.7
N A:ASP200 4.7 27.4 1.0
CA A:PRO195 4.7 39.9 1.0
CB A:ASP200 4.7 30.0 1.0
CB A:TYR193 4.7 25.2 1.0
CA A:SER198 4.7 43.1 0.3
O A:HOH683 4.8 49.4 1.0
C A:ASP200 4.8 26.1 1.0
CD2 A:TYR193 4.8 25.2 1.0
O A:HOH599 4.9 48.5 1.0
O A:HOH579 4.9 58.2 1.0
CA A:ASP200 5.0 28.7 1.0
C A:SER198 5.0 42.0 0.3

Reference:

M.Dong, B.J.Bahnson. Conformational Sampling Differences Across the Arrhenius Plot Biphasic Break Point at Ambient Temperature in the Enzyme Thermolysin To Be Published.
Page generated: Wed Jul 9 10:09:14 2025

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