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Calcium in PDB 6sel: Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator.

Enzymatic activity of Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator.

All present enzymatic activity of Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator.:
3.4.24.27;

Protein crystallography data

The structure of Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator., PDB code: 6sel was solved by J.Sandy, J.Sanchez-Weatherby, H.Mikolajek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.02 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.558, 93.558, 130.591, 90.00, 90.00, 120.00
R / Rfree (%) 12.9 / 16.9

Other elements in 6sel:

The structure of Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator. also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator. (pdb code 6sel). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator., PDB code: 6sel:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6sel

Go back to Calcium Binding Sites List in 6sel
Calcium binding site 1 out of 5 in the Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:20.1
occ:1.00
 O A:GLU187 2.4 17.5 1.0
OD2 A:ASP138 2.4 19.7 1.0
OE2 A:GLU190 2.5 19.9 1.0
OE1 A:GLU177 2.5 20.5 1.0
O A:HOH573 2.5 18.8 1.0
OE1 A:GLU190 2.5 19.4 1.0
OD1 A:ASP185 2.6 23.1 1.0
OE2 A:GLU177 2.8 22.0 1.0
CD A:GLU190 2.8 20.9 1.0
CD A:GLU177 3.0 21.9 1.0
CG A:ASP138 3.4 18.0 1.0
C A:GLU187 3.4 21.8 1.0
CG A:ASP185 3.5 25.0 1.0
HB3 A:ASP138 3.6 20.6 1.0
HA A:ILE188 3.7 22.2 1.0
H A:GLU187 3.7 27.1 1.0
H A:GLY189 3.8 22.2 1.0
OD2 A:ASP185 3.8 23.9 1.0
CA A:CA405 3.8 29.5 1.0
HB2 A:GLU187 3.9 28.1 1.0
CB A:ASP138 4.0 17.2 1.0
H A:GLU190 4.1 23.2 1.0
H A:ASP185 4.2 29.7 1.0
N A:GLU187 4.2 22.6 1.0
O A:ASP185 4.2 22.8 1.0
OD1 A:ASP138 4.2 18.8 1.0
HB2 A:ASP138 4.2 20.6 1.0
N A:ILE188 4.3 18.9 1.0
CA A:GLU187 4.3 25.1 1.0
O A:HOH580 4.3 34.3 1.0
CG A:GLU190 4.3 20.7 1.0
HD13 A:ILE188 4.4 26.1 1.0
CA A:ILE188 4.4 18.5 1.0
N A:GLY189 4.4 18.5 1.0
O A:HOH551 4.4 20.5 1.0
CG A:GLU177 4.4 22.1 1.0
CB A:GLU187 4.6 23.4 1.0
HG3 A:GLU190 4.6 24.8 1.0
C A:ASP185 4.7 22.5 1.0
HB2 A:GLU177 4.7 24.6 1.0
HG2 A:GLU190 4.8 24.8 1.0
C A:ILE188 4.8 19.0 1.0
N A:ASP185 4.8 24.8 1.0
HB3 A:GLU177 4.8 24.6 1.0
CB A:ASP185 4.8 24.2 1.0
HG2 A:GLU177 4.9 26.5 1.0
HA A:THR174 4.9 24.3 1.0
HB3 A:GLU190 4.9 23.9 1.0
HG3 A:GLU177 4.9 26.5 1.0
N A:GLU190 4.9 19.4 1.0
CB A:GLU177 4.9 20.5 1.0

Calcium binding site 2 out of 5 in 6sel

Go back to Calcium Binding Sites List in 6sel
Calcium binding site 2 out of 5 in the Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:29.5
occ:1.00
 OE2 A:GLU190 2.3 19.9 1.0
O A:ASN183 2.4 26.7 1.0
OD2 A:ASP185 2.4 23.9 1.0
O A:HOH514 2.5 31.0 1.0
O A:HOH548 2.6 29.7 1.0
OE2 A:GLU177 2.6 22.0 1.0
CD A:GLU190 3.3 20.9 1.0
CD A:GLU177 3.3 21.9 1.0
CG A:ASP185 3.3 25.0 1.0
HG3 A:GLU190 3.5 24.8 1.0
C A:ASN183 3.5 28.2 1.0
HB2 A:ASN183 3.6 47.0 1.0
HA A:PRO184 3.7 29.7 1.0
OE1 A:GLU177 3.8 20.5 1.0
OD1 A:ASP185 3.8 23.1 1.0
CG A:GLU190 3.8 20.7 1.0
CA A:CA404 3.8 20.1 1.0
HG2 A:GLU190 3.8 24.8 1.0
HB3 A:ASN183 3.9 47.0 1.0
H A:ASP185 4.0 29.7 1.0
O A:LYS182 4.1 36.3 1.0
CB A:ASN183 4.1 39.1 1.0
N A:ASP185 4.2 24.8 1.0
OD2 A:ASP191 4.2 25.1 1.0
HG2 A:GLU177 4.2 26.5 1.0
CA A:PRO184 4.2 24.8 1.0
OD1 A:ASP191 4.2 25.0 1.0
CG A:GLU177 4.3 22.1 1.0
OE1 A:GLU190 4.3 19.4 1.0
C A:PRO184 4.3 26.6 1.0
N A:PRO184 4.3 27.8 1.0
HB3 A:ASP185 4.4 29.0 1.0
HG3 A:GLU177 4.4 26.5 1.0
CB A:ASP185 4.4 24.2 1.0
O A:HOH580 4.5 34.3 1.0
CA A:ASN183 4.5 37.7 1.0
CG A:ASP191 4.6 24.8 1.0
CA A:ASP185 5.0 24.5 1.0
O A:PRO184 5.0 28.4 1.0

Calcium binding site 3 out of 5 in 6sel

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Calcium binding site 3 out of 5 in the Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:19.9
occ:1.00
 O A:GLN61 2.2 17.7 1.0
O A:HOH645 2.3 21.8 1.0
OD1 A:ASP59 2.4 24.3 1.0
OD1 A:ASP57 2.4 20.0 1.0
O A:HOH555 2.4 18.5 1.0
O A:HOH571 2.5 20.2 1.0
OD2 A:ASP57 2.6 18.7 1.0
CG A:ASP57 2.8 20.0 1.0
H A:GLN61 3.3 23.9 1.0
CG A:ASP59 3.4 25.2 1.0
C A:GLN61 3.4 20.2 1.0
H A:ASP59 3.6 26.8 1.0
OD2 A:ASP59 3.7 25.9 1.0
HB2 A:GLN61 3.8 30.4 1.0
O A:HOH626 4.0 24.6 1.0
N A:GLN61 4.0 19.9 1.0
HA A:PHE62 4.0 28.9 1.0
CA A:GLN61 4.2 23.8 1.0
H A:ALA58 4.3 23.3 1.0
CB A:ASP57 4.4 20.3 1.0
N A:ASP59 4.4 22.4 1.0
H A:ASN60 4.4 27.5 1.0
CB A:GLN61 4.4 25.3 1.0
N A:PHE62 4.5 17.9 1.0
OD2 A:ASP67 4.6 20.6 1.0
CB A:ASP59 4.6 23.9 1.0
N A:ASN60 4.7 22.9 1.0
O A:HOH509 4.7 16.3 1.0
HB2 A:ASP57 4.7 24.4 1.0
CA A:PHE62 4.7 24.1 1.0
H A:PHE63 4.8 23.9 1.0
HB3 A:ASP57 4.8 24.4 1.0
N A:ALA58 4.8 19.4 1.0
CA A:ASP59 4.9 21.0 1.0
HA A:ASP57 4.9 21.4 1.0
C A:ASP59 4.9 24.0 1.0

Calcium binding site 4 out of 5 in 6sel

Go back to Calcium Binding Sites List in 6sel
Calcium binding site 4 out of 5 in the Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:85.7
occ:1.00
 O A:HOH664 2.9 28.2 1.0
HH12 A:ARG35 3.0 32.7 1.0
O A:HOH622 3.2 20.5 1.0
HD21 A:ASN21 3.3 31.0 1.0
HH22 A:ARG35 3.3 29.2 1.0
HE2 A:TYR75 3.5 32.8 1.0
HD22 A:ASN21 3.6 31.0 1.0
ND2 A:ASN21 3.6 25.8 1.0
O A:HOH658 3.6 36.1 1.0
HD2 A:TYR75 3.6 30.2 1.0
O A:HOH696 3.6 50.5 1.0
HA A:ILE20 3.7 25.7 1.0
O A:ASN19 3.8 25.1 1.0
NH1 A:ARG35 3.8 27.2 1.0
CE2 A:TYR75 3.9 27.3 1.0
CD2 A:TYR75 4.0 25.1 1.0
NH2 A:ARG35 4.1 24.4 1.0
O A:HOH660 4.1 45.6 1.0
H A:ASN21 4.2 22.9 1.0
O A:HOH687 4.3 42.5 1.0
HH11 A:ARG35 4.4 32.7 1.0
CZ A:ARG35 4.4 23.1 1.0
CG A:ASN21 4.4 24.6 1.0
CA A:ILE20 4.7 21.4 1.0
C A:ASN19 4.7 24.3 1.0
HA A:TYR75 4.7 20.4 1.0
N A:ASN21 4.8 19.1 1.0
HH21 A:ARG35 4.8 29.2 1.0
CZ A:TYR75 4.9 27.9 1.0
HH A:TYR75 4.9 38.2 1.0
O A:HOH610 4.9 22.7 1.0
OD1 A:ASN21 4.9 25.5 1.0
HG22 A:ILE20 4.9 26.4 1.0

Calcium binding site 5 out of 5 in 6sel

Go back to Calcium Binding Sites List in 6sel
Calcium binding site 5 out of 5 in the Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:28.6
occ:1.00
 O A:HOH649 2.3 31.5 1.0
OG1 A:THR194 2.3 25.6 1.0
O A:ILE197 2.3 37.7 1.0
O A:THR194 2.4 29.1 1.0
OD1 A:ASP200 2.4 28.1 1.0
O A:TYR193 2.4 24.5 1.0
O A:HOH525 2.6 21.4 1.0
C A:THR194 3.2 30.8 1.0
C A:TYR193 3.3 25.4 1.0
CG A:ASP200 3.4 25.7 1.0
CB A:THR194 3.4 28.5 1.0
H A:ILE197 3.5 49.5 1.0
C A:ILE197 3.5 40.6 1.0
CA A:THR194 3.6 27.8 1.0
HB A:ILE197 3.7 47.8 1.0
OD2 A:ASP200 3.7 26.8 1.0
HB A:THR194 3.7 34.3 1.0
N A:THR194 3.8 24.0 1.0
H A:ASP200 4.0 36.5 1.0
HA A:SER198 4.1 49.2 1.0
HB3 A:TYR193 4.1 31.4 1.0
N A:ILE197 4.2 41.3 1.0
N A:PRO195 4.2 27.7 1.0
CA A:ILE197 4.2 38.1 1.0
HA A:PRO195 4.2 39.0 1.0
HD2 A:TYR193 4.3 33.6 1.0
CB A:ILE197 4.4 39.8 1.0
HG22 A:ILE197 4.4 46.7 1.0
O A:ASP200 4.5 24.0 1.0
N A:SER198 4.5 38.2 1.0
CA A:TYR193 4.6 23.5 1.0
HA A:THR194 4.6 33.4 1.0
O A:HOH513 4.6 43.4 1.0
O A:GLU190 4.6 20.3 1.0
CA A:PRO195 4.6 32.5 1.0
CG2 A:THR194 4.6 26.4 1.0
H A:THR194 4.7 28.9 1.0
CA A:SER198 4.7 41.0 1.0
HG21 A:THR194 4.7 31.6 1.0
N A:ASP200 4.7 30.4 1.0
CB A:ASP200 4.7 26.1 1.0
CB A:TYR193 4.7 26.1 1.0
C A:ASP200 4.8 24.6 1.0
CD2 A:TYR193 4.8 28.0 1.0
HG23 A:THR194 4.9 31.6 1.0
C A:PRO195 4.9 36.2 1.0
H A:TYR193 4.9 25.9 1.0
O A:HOH646 4.9 43.0 1.0
CG2 A:ILE197 5.0 38.9 1.0
C A:SER198 5.0 33.4 1.0

Reference:

J.Sandy, J.Sanchez-Weatherby, H.Mikolajek. Multicrystal Structure of Thermolysin at Room Temperature Using A Multilayer Monochromator. To Be Published.
Page generated: Wed Jul 9 17:48:52 2025

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