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Calcium in PDB 3p7q: Radiation Damage Study of Thermolysin - 100K Structure B (2.5 Mgy)

Enzymatic activity of Radiation Damage Study of Thermolysin - 100K Structure B (2.5 Mgy)

All present enzymatic activity of Radiation Damage Study of Thermolysin - 100K Structure B (2.5 Mgy):
3.4.24.27;

Protein crystallography data

The structure of Radiation Damage Study of Thermolysin - 100K Structure B (2.5 Mgy), PDB code: 3p7q 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) 31.58 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.260, 93.260, 128.690, 90.00, 90.00, 120.00
R / Rfree (%) 14.6 / 20.5

Other elements in 3p7q:

The structure of Radiation Damage Study of Thermolysin - 100K Structure B (2.5 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 - 100K Structure B (2.5 Mgy) (pdb code 3p7q). 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 - 100K Structure B (2.5 Mgy), PDB code: 3p7q:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3p7q

Go back to Calcium Binding Sites List in 3p7q
Calcium binding site 1 out of 4 in the Radiation Damage Study of Thermolysin - 100K Structure B (2.5 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 - 100K Structure B (2.5 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca317

b:9.9
occ:1.00
 O E:GLU187 2.2 8.4 1.0
OD2 E:ASP138 2.4 13.7 1.0
O E:HOH336 2.4 9.1 1.0
OD1 E:ASP185 2.5 10.8 1.0
OE2 E:GLU190 2.5 9.9 1.0
OE1 E:GLU190 2.6 8.1 1.0
OE1 E:GLU177 2.6 9.0 1.0
OE2 E:GLU177 2.8 8.8 1.0
CD E:GLU190 2.9 10.1 1.0
CD E:GLU177 3.0 9.8 1.0
C E:GLU187 3.4 10.2 1.0
CG E:ASP185 3.4 12.4 1.0
CG E:ASP138 3.5 10.8 1.0
OD2 E:ASP185 3.7 14.8 1.0
CA E:CA318 3.9 14.4 1.0
CB E:ASP138 4.0 7.5 1.0
O E:ASP185 4.1 10.6 1.0
N E:ILE188 4.2 9.4 1.0
N E:GLU187 4.3 10.9 1.0
CA E:ILE188 4.3 9.6 1.0
CA E:GLU187 4.3 11.7 1.0
CG E:GLU190 4.4 8.7 1.0
O E:HOH340 4.4 15.4 1.0
N E:GLY189 4.4 8.9 1.0
OD1 E:ASP138 4.4 12.7 1.0
C E:ASP185 4.5 11.3 1.0
CG E:GLU177 4.5 7.8 1.0
N E:ASP185 4.7 11.5 1.0
CB E:ASP185 4.7 11.3 1.0
CB E:GLU187 4.8 11.9 1.0
C E:ILE188 4.8 9.9 1.0
CA E:ASP185 4.9 11.3 1.0
CB E:GLU177 5.0 8.1 1.0
N E:GLU190 5.0 9.9 1.0

Calcium binding site 2 out of 4 in 3p7q

Go back to Calcium Binding Sites List in 3p7q
Calcium binding site 2 out of 4 in the Radiation Damage Study of Thermolysin - 100K Structure B (2.5 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 - 100K Structure B (2.5 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:14.4
occ:1.00
 O E:HOH395 2.2 16.4 1.0
O E:ASN183 2.3 15.1 1.0
O E:HOH343 2.3 14.7 1.0
OE2 E:GLU190 2.4 9.9 1.0
OE2 E:GLU177 2.5 8.8 1.0
OD2 E:ASP185 2.5 14.8 1.0
CD E:GLU177 3.2 9.8 1.0
CG E:ASP185 3.4 12.4 1.0
CD E:GLU190 3.4 10.1 1.0
C E:ASN183 3.5 15.6 1.0
OE1 E:GLU177 3.7 9.0 1.0
OD1 E:ASP185 3.8 10.8 1.0
CG E:GLU190 3.9 8.7 1.0
CA E:CA317 3.9 9.9 1.0
OD2 E:ASP191 4.0 17.1 1.0
CA E:PRO184 4.0 12.7 1.0
CG E:GLU177 4.2 7.8 1.0
O E:LYS182 4.2 19.8 1.0
O E:HOH490 4.2 21.2 1.0
CB E:ASN183 4.2 18.4 1.0
OD1 E:ASP191 4.2 16.7 1.0
N E:ASP185 4.2 11.5 1.0
C E:PRO184 4.2 12.0 1.0
N E:PRO184 4.3 14.2 1.0
OE1 E:GLU190 4.4 8.1 1.0
CG E:ASP191 4.4 14.4 1.0
CB E:ASP185 4.5 11.3 1.0
CA E:ASN183 4.5 17.6 1.0
O E:PRO184 4.9 12.8 1.0
O E:HOH507 5.0 27.4 1.0
CA E:ASP185 5.0 11.3 1.0

Calcium binding site 3 out of 4 in 3p7q

Go back to Calcium Binding Sites List in 3p7q
Calcium binding site 3 out of 4 in the Radiation Damage Study of Thermolysin - 100K Structure B (2.5 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 - 100K Structure B (2.5 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:9.7
occ:1.00
 O E:GLN61 2.3 7.5 1.0
O E:HOH412 2.3 9.1 1.0
O E:HOH378 2.4 6.7 1.0
OD1 E:ASP57 2.4 10.1 1.0
OD1 E:ASP59 2.4 15.1 1.0
O E:HOH402 2.5 10.6 1.0
OD2 E:ASP57 2.6 7.5 1.0
CG E:ASP57 2.9 8.4 1.0
CG E:ASP59 3.4 12.3 1.0
C E:GLN61 3.4 8.9 1.0
OD2 E:ASP59 3.8 13.1 1.0
N E:GLN61 4.0 9.3 1.0
O E:HOH404 4.0 12.4 1.0
CA E:GLN61 4.1 10.8 1.0
CB E:GLN61 4.4 10.6 1.0
N E:ASP59 4.4 8.4 1.0
CB E:ASP57 4.4 8.6 1.0
O E:HOH455 4.4 20.1 1.0
O E:HOH416 4.4 12.4 1.0
N E:PHE62 4.5 7.9 1.0
O E:HOH470 4.6 29.1 1.0
OD2 E:ASP67 4.6 8.8 1.0
O E:HOH346 4.6 7.8 1.0
CB E:ASP59 4.7 9.2 1.0
N E:ASN60 4.8 8.5 1.0
N E:ALA58 4.8 8.1 1.0
CA E:PHE62 4.8 8.3 1.0
CA E:ASP59 4.9 8.8 1.0

Calcium binding site 4 out of 4 in 3p7q

Go back to Calcium Binding Sites List in 3p7q
Calcium binding site 4 out of 4 in the Radiation Damage Study of Thermolysin - 100K Structure B (2.5 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 - 100K Structure B (2.5 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:12.7
occ:1.00
 O E:HOH400 2.3 17.0 1.0
O E:ILE197 2.3 20.7 1.0
O E:HOH344 2.3 12.0 1.0
OG1 E:THR194 2.4 12.0 1.0
O E:TYR193 2.4 12.4 1.0
O E:THR194 2.5 15.3 1.0
OD1 E:ASP200 2.5 12.2 1.0
C E:THR194 3.3 15.2 1.0
C E:TYR193 3.4 12.5 1.0
C E:ILE197 3.5 21.2 1.0
CB E:THR194 3.5 12.8 1.0
CG E:ASP200 3.5 14.6 1.0
CA E:THR194 3.7 13.7 1.0
OD2 E:ASP200 3.9 14.3 1.0
N E:THR194 4.0 12.8 1.0
CA E:ILE197 4.2 21.2 1.0
N E:ILE197 4.2 22.7 1.0
CB E:ILE197 4.3 21.3 1.0
O E:ASP200 4.3 14.2 1.0
N E:PRO195 4.4 16.9 1.0
O E:HOH506 4.5 25.9 1.0
O E:HOH634 4.5 29.1 1.0
N E:SER198 4.5 20.6 1.0
O E:GLU190 4.5 10.2 1.0
O E:HOH486 4.6 20.4 1.0
CA E:TYR193 4.6 12.1 1.0
CD2 E:TYR193 4.6 9.9 1.0
CB E:TYR193 4.6 12.7 1.0
N E:ASP200 4.7 16.2 1.0
CA E:PRO195 4.7 18.5 1.0
CG2 E:THR194 4.7 12.8 1.0
O E:HOH396 4.8 27.8 1.0
CA E:SER198 4.8 21.0 1.0
CB E:ASP200 4.8 14.5 1.0
C E:ASP200 4.9 14.9 1.0
C E:PRO195 4.9 20.0 1.0
C E:SER198 4.9 19.9 1.0
N E:GLY199 4.9 19.8 1.0

Reference:

D.H.Juers, M.Weik. Radiation Damage Study of Thermolysin - 100K Structure B (2.5 Mgy) To Be Published.
Page generated: Tue Jul 8 15:21:56 2025

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