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Calcium in PDB 3p7p: Radiation Damage Study of Thermolysin - 100K Structure A (0.1 Mgy)

Enzymatic activity of Radiation Damage Study of Thermolysin - 100K Structure A (0.1 Mgy)

All present enzymatic activity of Radiation Damage Study of Thermolysin - 100K Structure A (0.1 Mgy):
3.4.24.27;

Protein crystallography data

The structure of Radiation Damage Study of Thermolysin - 100K Structure A (0.1 Mgy), PDB code: 3p7p 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) 80.85 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.220, 93.220, 128.610, 90.00, 90.00, 120.00
R / Rfree (%) 14.9 / 21.1

Other elements in 3p7p:

The structure of Radiation Damage Study of Thermolysin - 100K 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 - 100K Structure A (0.1 Mgy) (pdb code 3p7p). 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 A (0.1 Mgy), PDB code: 3p7p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3p7p

Go back to Calcium Binding Sites List in 3p7p
Calcium binding site 1 out of 4 in the Radiation Damage Study of Thermolysin - 100K 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 - 100K Structure A (0.1 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca317

b:8.2
occ:1.00
 O E:GLU187 2.2 7.2 1.0
OD2 E:ASP138 2.4 10.2 1.0
OD1 E:ASP185 2.5 9.4 1.0
O E:HOH350 2.5 6.8 1.0
OE2 E:GLU190 2.5 6.4 1.0
OE1 E:GLU190 2.5 4.5 1.0
OE1 E:GLU177 2.6 5.1 1.0
OE2 E:GLU177 2.8 7.0 1.0
CD E:GLU190 2.9 7.4 1.0
CD E:GLU177 3.1 7.4 1.0
C E:GLU187 3.4 8.8 1.0
CG E:ASP185 3.4 10.8 1.0
CG E:ASP138 3.5 7.2 1.0
OD2 E:ASP185 3.8 12.6 1.0
CA E:CA318 3.9 12.2 1.0
CB E:ASP138 4.0 4.9 1.0
O E:ASP185 4.1 9.7 1.0
N E:ILE188 4.2 8.1 1.0
CA E:ILE188 4.3 8.0 1.0
N E:GLU187 4.3 9.3 1.0
CA E:GLU187 4.3 10.3 1.0
CG E:GLU190 4.4 6.0 1.0
OD1 E:ASP138 4.4 8.2 1.0
N E:GLY189 4.4 7.0 1.0
O E:HOH354 4.5 11.3 1.0
C E:ASP185 4.5 10.0 1.0
CG E:GLU177 4.5 6.0 1.0
CB E:GLU187 4.7 10.5 1.0
N E:ASP185 4.7 10.1 1.0
CB E:ASP185 4.7 10.0 1.0
C E:ILE188 4.8 8.2 1.0
CA E:ASP185 4.9 9.9 1.0
CB E:GLU177 5.0 7.2 1.0

Calcium binding site 2 out of 4 in 3p7p

Go back to Calcium Binding Sites List in 3p7p
Calcium binding site 2 out of 4 in the Radiation Damage Study of Thermolysin - 100K 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 - 100K Structure A (0.1 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:12.2
occ:1.00
 O E:HOH409 2.2 12.7 1.0
O E:ASN183 2.3 13.0 1.0
O E:HOH357 2.3 8.7 1.0
OE2 E:GLU190 2.4 6.4 1.0
OE2 E:GLU177 2.5 7.0 1.0
OD2 E:ASP185 2.5 12.6 1.0
CD E:GLU177 3.2 7.4 1.0
CG E:ASP185 3.4 10.8 1.0
CD E:GLU190 3.4 7.4 1.0
C E:ASN183 3.5 13.6 1.0
OE1 E:GLU177 3.7 5.1 1.0
OD1 E:ASP185 3.8 9.4 1.0
CG E:GLU190 3.9 6.0 1.0
CA E:CA317 3.9 8.2 1.0
OD2 E:ASP191 4.0 11.9 1.0
CA E:PRO184 4.1 11.0 1.0
O E:HOH501 4.1 16.8 1.0
CB E:ASN183 4.2 16.1 1.0
CG E:GLU177 4.2 6.0 1.0
O E:LYS182 4.2 17.1 1.0
N E:ASP185 4.2 10.1 1.0
C E:PRO184 4.2 10.4 1.0
OD1 E:ASP191 4.3 10.9 1.0
N E:PRO184 4.3 12.3 1.0
OE1 E:GLU190 4.4 4.5 1.0
CA E:ASN183 4.4 15.3 1.0
CG E:ASP191 4.5 10.5 1.0
CB E:ASP185 4.5 10.0 1.0
O E:PRO184 4.8 11.4 1.0
O E:HOH518 4.9 22.0 1.0
CA E:ASP185 5.0 9.9 1.0

Calcium binding site 3 out of 4 in 3p7p

Go back to Calcium Binding Sites List in 3p7p
Calcium binding site 3 out of 4 in the Radiation Damage Study of Thermolysin - 100K 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 - 100K Structure A (0.1 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:8.6
occ:1.00
 O E:GLN61 2.3 6.3 1.0
O E:HOH426 2.4 6.8 1.0
OD1 E:ASP57 2.4 9.9 1.0
O E:HOH392 2.4 4.0 1.0
OD1 E:ASP59 2.4 11.9 1.0
O E:HOH416 2.5 8.4 1.0
OD2 E:ASP57 2.6 5.6 1.0
CG E:ASP57 2.9 7.8 1.0
CG E:ASP59 3.4 10.0 1.0
C E:GLN61 3.4 7.8 1.0
OD2 E:ASP59 3.8 10.1 1.0
N E:GLN61 3.9 8.4 1.0
O E:HOH418 4.1 9.3 1.0
CA E:GLN61 4.1 9.9 1.0
CB E:GLN61 4.3 9.3 1.0
N E:ASP59 4.4 7.1 1.0
CB E:ASP57 4.4 7.5 1.0
O E:HOH430 4.4 9.6 1.0
O E:HOH467 4.4 19.8 1.0
N E:PHE62 4.5 6.8 1.0
O E:HOH481 4.6 24.0 1.0
OD2 E:ASP67 4.6 6.6 1.0
O E:HOH360 4.6 6.5 1.0
CB E:ASP59 4.7 7.5 1.0
N E:ALA58 4.7 6.8 1.0
N E:ASN60 4.7 7.6 1.0
CA E:PHE62 4.8 7.4 1.0
CA E:ASP59 4.9 7.5 1.0

Calcium binding site 4 out of 4 in 3p7p

Go back to Calcium Binding Sites List in 3p7p
Calcium binding site 4 out of 4 in the Radiation Damage Study of Thermolysin - 100K 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 - 100K Structure A (0.1 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:11.5
occ:1.00
 O E:ILE197 2.3 18.7 1.0
O E:HOH358 2.3 9.5 1.0
O E:HOH414 2.3 14.1 1.0
O E:TYR193 2.4 10.5 1.0
OG1 E:THR194 2.4 10.3 1.0
OD1 E:ASP200 2.5 10.1 1.0
O E:THR194 2.5 13.1 1.0
C E:THR194 3.3 12.9 1.0
C E:TYR193 3.4 10.3 1.0
C E:ILE197 3.4 19.2 1.0
CG E:ASP200 3.5 12.3 1.0
CB E:THR194 3.5 10.8 1.0
CA E:THR194 3.7 11.6 1.0
OD2 E:ASP200 3.9 11.1 1.0
N E:THR194 4.0 10.7 1.0
CA E:ILE197 4.1 19.1 1.0
N E:ILE197 4.2 20.6 1.0
CB E:ILE197 4.2 19.4 1.0
O E:ASP200 4.3 12.5 1.0
N E:PRO195 4.4 14.6 1.0
O E:HOH651 4.4 27.6 1.0
O E:GLU190 4.5 8.5 1.0
N E:SER198 4.5 18.6 1.0
O E:HOH517 4.5 25.3 1.0
CA E:TYR193 4.5 10.1 1.0
CD2 E:TYR193 4.6 7.7 1.0
O E:HOH497 4.6 17.9 1.0
CB E:TYR193 4.6 10.7 1.0
N E:ASP200 4.7 14.1 1.0
CA E:PRO195 4.7 16.3 1.0
CG2 E:THR194 4.8 10.4 1.0
O E:HOH410 4.8 24.3 1.0
CB E:ASP200 4.8 12.6 1.0
CA E:SER198 4.8 19.0 1.0
C E:ASP200 4.9 13.1 1.0
C E:PRO195 4.9 18.0 1.0
C E:SER198 4.9 17.8 1.0
N E:GLY199 4.9 17.4 1.0
CG2 E:ILE197 5.0 18.6 1.0
CG E:TYR193 5.0 10.0 1.0

Reference:

D.H.Juers, M.Weik. Radiation Damage Study of Thermolysin - 100K Structure A (0.1 Mgy) To Be Published.
Page generated: Sat Jul 13 16:35:00 2024

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