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Calcium in PDB 3p7t: Radiation Damage Study of Thermolysin - 160K Structure A (0.1 Mgy)

Enzymatic activity of Radiation Damage Study of Thermolysin - 160K Structure A (0.1 Mgy)

All present enzymatic activity of Radiation Damage Study of Thermolysin - 160K Structure A (0.1 Mgy):
3.4.24.27;

Protein crystallography data

The structure of Radiation Damage Study of Thermolysin - 160K Structure A (0.1 Mgy), PDB code: 3p7t 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) 31.65 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.560, 93.560, 128.940, 90.00, 90.00, 120.00
R / Rfree (%) 14.6 / 20.4

Other elements in 3p7t:

The structure of Radiation Damage Study of Thermolysin - 160K Structure A (0.1 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 A (0.1 Mgy) (pdb code 3p7t). 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 A (0.1 Mgy), PDB code: 3p7t:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3p7t

Go back to Calcium Binding Sites List in 3p7t
Calcium binding site 1 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure A (0.1 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 A (0.1 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca317

b:8.3
occ:1.00
 O E:GLU187 2.3 7.9 1.0
OD2 E:ASP138 2.4 8.3 1.0
O E:HOH354 2.5 8.8 1.0
OD1 E:ASP185 2.5 8.3 1.0
OE2 E:GLU190 2.5 6.9 1.0
OE1 E:GLU190 2.6 4.8 1.0
OE1 E:GLU177 2.6 5.9 1.0
OE2 E:GLU177 2.8 8.5 1.0
CD E:GLU190 2.9 7.6 1.0
CD E:GLU177 3.0 8.4 1.0
C E:GLU187 3.4 9.2 1.0
CG E:ASP185 3.4 10.9 1.0
CG E:ASP138 3.4 7.3 1.0
OD2 E:ASP185 3.8 12.3 1.0
CA E:CA318 3.9 13.9 1.0
CB E:ASP138 4.0 5.2 1.0
O E:ASP185 4.1 10.1 1.0
N E:ILE188 4.2 8.6 1.0
N E:GLU187 4.3 9.7 1.0
CA E:ILE188 4.3 8.6 1.0
CG E:GLU190 4.4 7.7 1.0
CA E:GLU187 4.4 10.6 1.0
OD1 E:ASP138 4.4 8.6 1.0
N E:GLY189 4.4 7.7 1.0
O E:HOH358 4.5 11.1 1.0
CG E:GLU177 4.5 6.8 1.0
C E:ASP185 4.5 10.4 1.0
N E:ASP185 4.7 10.9 1.0
CB E:ASP185 4.7 10.3 1.0
C E:ILE188 4.8 8.9 1.0
CB E:GLU187 4.8 10.9 1.0
CA E:ASP185 4.9 10.4 1.0
CB E:GLU177 5.0 7.6 1.0
N E:GLU190 5.0 8.4 1.0

Calcium binding site 2 out of 4 in 3p7t

Go back to Calcium Binding Sites List in 3p7t
Calcium binding site 2 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure A (0.1 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 A (0.1 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:13.9
occ:1.00
 O E:HOH413 2.2 15.4 1.0
O E:ASN183 2.3 14.9 1.0
O E:HOH361 2.3 11.5 1.0
OE2 E:GLU190 2.4 6.9 1.0
OD2 E:ASP185 2.5 12.3 1.0
OE2 E:GLU177 2.5 8.5 1.0
CD E:GLU177 3.2 8.4 1.0
CG E:ASP185 3.4 10.9 1.0
CD E:GLU190 3.4 7.6 1.0
C E:ASN183 3.4 15.0 1.0
OE1 E:GLU177 3.7 5.9 1.0
OD1 E:ASP185 3.8 8.3 1.0
CA E:CA317 3.9 8.3 1.0
CG E:GLU190 3.9 7.7 1.0
OD2 E:ASP191 4.0 14.8 1.0
CA E:PRO184 4.1 12.2 1.0
O E:HOH506 4.1 21.0 1.0
OD1 E:ASP191 4.1 14.1 1.0
CB E:ASN183 4.2 17.6 1.0
CG E:GLU177 4.2 6.8 1.0
N E:ASP185 4.2 10.9 1.0
O E:LYS182 4.2 17.6 1.0
C E:PRO184 4.2 11.4 1.0
N E:PRO184 4.3 13.7 1.0
CG E:ASP191 4.4 12.9 1.0
OE1 E:GLU190 4.4 4.8 1.0
CA E:ASN183 4.4 16.7 1.0
CB E:ASP185 4.5 10.3 1.0
O E:PRO184 4.9 12.4 1.0
CA E:ASP185 5.0 10.4 1.0

Calcium binding site 3 out of 4 in 3p7t

Go back to Calcium Binding Sites List in 3p7t
Calcium binding site 3 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure A (0.1 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 A (0.1 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:8.3
occ:1.00
 O E:GLN61 2.3 6.7 1.0
O E:HOH430 2.4 9.1 1.0
OD1 E:ASP59 2.4 11.9 1.0
O E:HOH396 2.4 4.4 1.0
OD1 E:ASP57 2.4 9.2 1.0
O E:HOH420 2.5 7.6 1.0
OD2 E:ASP57 2.6 6.2 1.0
CG E:ASP57 2.9 8.3 1.0
CG E:ASP59 3.4 10.6 1.0
C E:GLN61 3.5 8.2 1.0
OD2 E:ASP59 3.8 9.6 1.0
N E:GLN61 4.0 8.8 1.0
O E:HOH422 4.1 11.6 1.0
CA E:GLN61 4.1 10.2 1.0
O E:HOH471 4.3 21.4 1.0
N E:ASP59 4.3 7.7 1.0
CB E:GLN61 4.4 9.8 1.0
CB E:ASP57 4.4 8.0 1.0
O E:HOH434 4.4 11.5 1.0
O E:HOH486 4.5 26.9 1.0
N E:PHE62 4.6 7.1 1.0
OD2 E:ASP67 4.6 7.0 1.0
O E:HOH364 4.6 6.8 1.0
CB E:ASP59 4.7 8.1 1.0
N E:ASN60 4.8 8.2 1.0
N E:ALA58 4.8 7.8 1.0
CA E:PHE62 4.8 7.7 1.0
CA E:ASP59 4.9 8.1 1.0
O E:HOH662 5.0 19.0 1.0

Calcium binding site 4 out of 4 in 3p7t

Go back to Calcium Binding Sites List in 3p7t
Calcium binding site 4 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure A (0.1 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 A (0.1 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:13.0
occ:1.00
 O E:ILE197 2.3 19.9 1.0
O E:HOH418 2.3 15.9 1.0
O E:HOH362 2.3 11.8 1.0
O E:TYR193 2.4 11.6 1.0
OG1 E:THR194 2.4 12.3 1.0
OD1 E:ASP200 2.4 11.0 1.0
O E:THR194 2.5 14.4 1.0
C E:THR194 3.3 14.6 1.0
C E:TYR193 3.4 11.6 1.0
C E:ILE197 3.5 20.9 1.0
CG E:ASP200 3.5 12.6 1.0
CB E:THR194 3.5 12.8 1.0
CA E:THR194 3.7 13.5 1.0
OD2 E:ASP200 3.8 11.4 1.0
N E:THR194 4.0 12.3 1.0
CA E:ILE197 4.1 20.9 1.0
N E:ILE197 4.2 22.3 1.0
CB E:ILE197 4.3 21.2 1.0
O E:ASP200 4.3 12.8 1.0
N E:PRO195 4.4 16.5 1.0
O E:HOH522 4.5 26.2 1.0
CD2 E:TYR193 4.5 8.5 1.0
O E:GLU190 4.5 9.5 1.0
N E:SER198 4.5 20.4 1.0
CA E:TYR193 4.6 10.8 1.0
CB E:TYR193 4.6 11.3 1.0
O E:HOH502 4.6 20.3 1.0
N E:ASP200 4.6 14.8 1.0
CG2 E:THR194 4.7 12.4 1.0
CA E:PRO195 4.8 18.2 1.0
CB E:ASP200 4.8 12.9 1.0
C E:ASP200 4.8 13.5 1.0
CA E:SER198 4.9 21.2 1.0
C E:PRO195 4.9 19.5 1.0
C E:SER198 4.9 19.8 1.0
N E:GLY199 5.0 19.1 1.0
O E:HOH414 5.0 29.1 1.0
CG E:TYR193 5.0 11.1 1.0
CA E:ASP200 5.0 13.5 1.0

Reference:

D.H.Juers, M.Weik. Radiation Damage Study of Thermolysin - 160K Structure A (0.1 Mgy) To Be Published.
Page generated: Tue Jul 8 15:23:01 2025

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