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Calcium in PDB 3p7u: Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy)

Enzymatic activity of Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy)

All present enzymatic activity of Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy):
3.4.24.27;

Protein crystallography data

The structure of Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy), PDB code: 3p7u was solved by D.H.Juers, M.Weik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.67 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.750, 93.750, 128.840, 90.00, 90.00, 120.00
R / Rfree (%) 14.5 / 20

Other elements in 3p7u:

The structure of Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy) (pdb code 3p7u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy), PDB code: 3p7u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3p7u

Go back to Calcium Binding Sites List in 3p7u
Calcium binding site 1 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca317

b:12.5
occ:1.00
 O E:GLU187 2.2 11.2 1.0
OD2 E:ASP138 2.4 15.2 1.0
OD1 E:ASP185 2.4 15.8 1.0
O E:HOH334 2.4 12.7 1.0
OE2 E:GLU190 2.5 12.8 1.0
OE1 E:GLU177 2.5 15.0 1.0
OE1 E:GLU190 2.7 11.0 1.0
OE2 E:GLU177 2.8 16.1 1.0
CD E:GLU190 2.9 14.4 1.0
CD E:GLU177 3.0 14.8 1.0
C E:GLU187 3.4 13.0 1.0
CG E:ASP185 3.4 16.5 1.0
CG E:ASP138 3.5 14.3 1.0
OD2 E:ASP185 3.8 19.3 1.0
CA E:CA318 3.8 24.2 1.0
CB E:ASP138 4.0 10.4 1.0
O E:ASP185 4.1 14.3 1.0
N E:ILE188 4.2 12.2 1.0
CA E:ILE188 4.3 13.5 1.0
N E:GLU187 4.3 13.3 1.0
CA E:GLU187 4.3 13.8 1.0
CG E:GLU190 4.4 13.3 1.0
N E:GLY189 4.4 13.5 1.0
OD1 E:ASP138 4.4 15.8 1.0
CG E:GLU177 4.5 11.9 1.0
O E:HOH338 4.5 17.6 1.0
C E:ASP185 4.6 14.9 1.0
CB E:GLU187 4.7 13.9 1.0
N E:ASP185 4.7 15.7 1.0
CB E:ASP185 4.7 15.3 1.0
C E:ILE188 4.8 13.9 1.0
CB E:GLU177 5.0 11.6 1.0
CA E:ASP185 5.0 15.1 1.0
N E:GLU190 5.0 14.1 1.0

Calcium binding site 2 out of 4 in 3p7u

Go back to Calcium Binding Sites List in 3p7u
Calcium binding site 2 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:24.2
occ:1.00
 O E:HOH393 2.1 25.3 1.0
O E:ASN183 2.3 23.1 1.0
O E:HOH341 2.3 26.5 1.0
OE2 E:GLU190 2.4 12.8 1.0
OE2 E:GLU177 2.5 16.1 1.0
OD2 E:ASP185 2.6 19.3 1.0
CD E:GLU177 3.2 14.8 1.0
CG E:ASP185 3.4 16.5 1.0
CD E:GLU190 3.4 14.4 1.0
C E:ASN183 3.5 23.2 1.0
OE1 E:GLU177 3.7 15.0 1.0
OD1 E:ASP185 3.7 15.8 1.0
CA E:CA317 3.8 12.5 1.0
CG E:GLU190 3.9 13.3 1.0
OD2 E:ASP191 4.0 24.9 1.0
CA E:PRO184 4.1 18.2 1.0
OD1 E:ASP191 4.1 23.0 1.0
CG E:GLU177 4.2 11.9 1.0
N E:ASP185 4.2 15.7 1.0
O E:HOH485 4.3 28.3 1.0
C E:PRO184 4.3 17.0 1.0
O E:LYS182 4.3 28.1 1.0
N E:PRO184 4.3 20.6 1.0
CB E:ASN183 4.3 26.7 1.0
CG E:ASP191 4.4 21.1 1.0
OE1 E:GLU190 4.5 11.0 1.0
CB E:ASP185 4.5 15.3 1.0
CA E:ASN183 4.5 25.5 1.0
O E:PRO184 4.9 16.3 1.0

Calcium binding site 3 out of 4 in 3p7u

Go back to Calcium Binding Sites List in 3p7u
Calcium binding site 3 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:13.3
occ:1.00
 O E:GLN61 2.3 10.1 1.0
OD1 E:ASP57 2.3 10.3 1.0
O E:HOH409 2.4 15.1 1.0
O E:HOH399 2.4 14.9 1.0
OD1 E:ASP59 2.4 20.3 1.0
O E:HOH376 2.4 13.2 1.0
OD2 E:ASP57 2.6 9.2 1.0
CG E:ASP57 2.8 10.8 1.0
C E:GLN61 3.4 11.5 1.0
CG E:ASP59 3.4 17.1 1.0
OD2 E:ASP59 3.8 18.6 1.0
N E:GLN61 4.0 12.0 1.0
O E:HOH401 4.0 16.8 1.0
CA E:GLN61 4.1 13.9 1.0
CB E:ASP57 4.3 10.2 1.0
CB E:GLN61 4.3 13.5 1.0
N E:ASP59 4.3 11.8 1.0
O E:HOH450 4.3 24.4 1.0
O E:HOH344 4.5 10.0 1.0
O E:HOH413 4.5 16.3 1.0
O E:HOH465 4.5 31.4 1.0
N E:PHE62 4.5 10.2 1.0
OD2 E:ASP67 4.7 11.6 1.0
CB E:ASP59 4.7 12.8 1.0
CA E:PHE62 4.8 10.6 1.0
N E:ASN60 4.8 11.6 1.0
N E:ALA58 4.8 10.3 1.0
CA E:ASP59 4.8 12.5 1.0
C E:ASP59 5.0 12.1 1.0

Calcium binding site 4 out of 4 in 3p7u

Go back to Calcium Binding Sites List in 3p7u
Calcium binding site 4 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:20.3
occ:1.00
 O E:ILE197 2.3 31.5 1.0
O E:HOH397 2.3 23.1 1.0
OG1 E:THR194 2.4 23.0 1.0
OD1 E:ASP200 2.4 16.6 1.0
O E:TYR193 2.4 20.8 1.0
O E:HOH342 2.4 19.2 1.0
O E:THR194 2.5 27.0 1.0
C E:THR194 3.3 26.7 1.0
C E:TYR193 3.4 20.6 1.0
CG E:ASP200 3.4 19.9 1.0
C E:ILE197 3.5 32.2 1.0
CB E:THR194 3.5 24.1 1.0
CA E:THR194 3.7 24.7 1.0
OD2 E:ASP200 3.8 20.3 1.0
N E:THR194 4.0 22.8 1.0
N E:ILE197 4.2 33.9 1.0
CA E:ILE197 4.2 32.7 1.0
CB E:ILE197 4.3 33.1 1.0
N E:PRO195 4.4 28.9 1.0
O E:ASP200 4.4 21.8 1.0
O E:HOH500 4.4 39.6 1.0
O E:GLU190 4.5 15.3 1.0
N E:SER198 4.6 31.7 1.0
N E:ASP200 4.6 23.8 1.0
CD2 E:TYR193 4.6 17.2 1.0
O E:HOH481 4.6 30.2 1.0
CA E:TYR193 4.6 19.5 1.0
CG2 E:THR194 4.7 24.8 1.0
CB E:ASP200 4.7 21.4 1.0
CB E:TYR193 4.8 19.6 1.0
CA E:PRO195 4.8 30.5 1.0
CA E:SER198 4.8 31.8 1.0
O E:HOH394 4.8 36.0 1.0
C E:ASP200 4.9 21.9 1.0
C E:SER198 4.9 30.3 1.0
CA E:ASP200 4.9 22.1 1.0
N E:GLY199 5.0 29.1 1.0
CG2 E:ILE197 5.0 31.5 1.0

Reference:

D.H.Juers, M.Weik. Radiation Damage Study of Thermolysin - 160K Structure B (2.4 Mgy) To Be Published.
Page generated: Tue Jul 8 15:23:02 2025

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