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Calcium in PDB 3p7s: Radiation Damage Study of Thermolysin - 100K Structure D (7.2 Mgy)

Enzymatic activity of Radiation Damage Study of Thermolysin - 100K Structure D (7.2 Mgy)

All present enzymatic activity of Radiation Damage Study of Thermolysin - 100K Structure D (7.2 Mgy):
3.4.24.27;

Protein crystallography data

The structure of Radiation Damage Study of Thermolysin - 100K Structure D (7.2 Mgy), PDB code: 3p7s 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) 34.24 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.350, 93.350, 128.780, 90.00, 90.00, 120.00
R / Rfree (%) 14.6 / 20.2

Other elements in 3p7s:

The structure of Radiation Damage Study of Thermolysin - 100K Structure D (7.2 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 D (7.2 Mgy) (pdb code 3p7s). 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 D (7.2 Mgy), PDB code: 3p7s:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3p7s

Go back to Calcium Binding Sites List in 3p7s
Calcium binding site 1 out of 4 in the Radiation Damage Study of Thermolysin - 100K Structure D (7.2 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 D (7.2 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca317

b:13.2
occ:1.00
 O E:GLU187 2.2 13.1 1.0
O E:HOH334 2.4 14.0 1.0
OD1 E:ASP185 2.4 15.5 1.0
OD2 E:ASP138 2.4 19.1 1.0
OE2 E:GLU190 2.5 15.3 1.0
OE1 E:GLU177 2.6 15.9 1.0
OE1 E:GLU190 2.6 12.8 1.0
OE2 E:GLU177 2.8 14.5 1.0
CD E:GLU190 2.9 14.6 1.0
CD E:GLU177 3.0 14.8 1.0
C E:GLU187 3.4 15.0 1.0
CG E:ASP185 3.4 17.2 1.0
CG E:ASP138 3.5 16.3 1.0
OD2 E:ASP185 3.8 20.8 1.0
CA E:CA318 3.9 19.5 1.0
O E:ASP185 4.0 14.8 1.0
CB E:ASP138 4.0 12.3 1.0
N E:ILE188 4.2 14.0 1.0
N E:GLU187 4.2 15.1 1.0
CA E:ILE188 4.3 14.6 1.0
CA E:GLU187 4.3 16.4 1.0
CG E:GLU190 4.4 12.8 1.0
N E:GLY189 4.4 14.2 1.0
O E:HOH338 4.4 20.1 1.0
OD1 E:ASP138 4.5 19.8 1.0
C E:ASP185 4.5 15.3 1.0
CG E:GLU177 4.5 12.4 1.0
N E:ASP185 4.7 15.6 1.0
CB E:ASP185 4.7 15.3 1.0
CB E:GLU187 4.7 16.7 1.0
C E:ILE188 4.8 15.0 1.0
CA E:ASP185 4.9 15.5 1.0
CB E:GLU177 5.0 11.5 1.0
N E:GLU190 5.0 14.2 1.0

Calcium binding site 2 out of 4 in 3p7s

Go back to Calcium Binding Sites List in 3p7s
Calcium binding site 2 out of 4 in the Radiation Damage Study of Thermolysin - 100K Structure D (7.2 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 D (7.2 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:19.5
occ:1.00
 O E:HOH393 2.2 24.7 1.0
O E:HOH341 2.3 24.1 1.0
O E:ASN183 2.3 19.6 1.0
OE2 E:GLU190 2.5 15.3 1.0
OE2 E:GLU177 2.5 14.5 1.0
OD2 E:ASP185 2.6 20.8 1.0
CD E:GLU177 3.2 14.8 1.0
CG E:ASP185 3.4 17.2 1.0
CD E:GLU190 3.4 14.6 1.0
C E:ASN183 3.5 20.2 1.0
OE1 E:GLU177 3.7 15.9 1.0
OD1 E:ASP185 3.8 15.5 1.0
CG E:GLU190 3.9 12.8 1.0
CA E:CA317 3.9 13.2 1.0
OD2 E:ASP191 3.9 25.0 1.0
CA E:PRO184 4.1 17.0 1.0
OD1 E:ASP191 4.2 24.3 1.0
CG E:GLU177 4.2 12.4 1.0
O E:LYS182 4.2 25.8 1.0
CB E:ASN183 4.2 23.4 1.0
O E:HOH488 4.2 28.9 1.0
N E:ASP185 4.3 15.6 1.0
C E:PRO184 4.3 16.1 1.0
N E:PRO184 4.3 18.5 1.0
CG E:ASP191 4.4 20.5 1.0
OE1 E:GLU190 4.5 12.8 1.0
CA E:ASN183 4.5 22.6 1.0
CB E:ASP185 4.5 15.3 1.0
O E:PRO184 4.9 16.7 1.0
O E:HOH505 4.9 34.0 1.0

Calcium binding site 3 out of 4 in 3p7s

Go back to Calcium Binding Sites List in 3p7s
Calcium binding site 3 out of 4 in the Radiation Damage Study of Thermolysin - 100K Structure D (7.2 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 D (7.2 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:13.8
occ:1.00
 O E:GLN61 2.3 10.8 1.0
O E:HOH410 2.3 13.8 1.0
OD1 E:ASP57 2.4 12.9 1.0
O E:HOH376 2.4 14.0 1.0
O E:HOH400 2.4 14.2 1.0
OD1 E:ASP59 2.5 19.2 1.0
OD2 E:ASP57 2.6 11.3 1.0
CG E:ASP57 2.8 11.5 1.0
C E:GLN61 3.4 11.7 1.0
CG E:ASP59 3.5 16.2 1.0
OD2 E:ASP59 3.8 19.1 1.0
O E:HOH402 3.9 16.5 1.0
N E:GLN61 4.0 11.8 1.0
CA E:GLN61 4.1 14.0 1.0
CB E:GLN61 4.3 14.1 1.0
CB E:ASP57 4.4 11.5 1.0
O E:HOH453 4.4 28.3 1.0
N E:ASP59 4.4 10.6 1.0
O E:HOH414 4.4 16.7 1.0
O E:HOH344 4.5 10.4 1.0
O E:HOH468 4.5 33.9 1.0
N E:PHE62 4.5 10.6 1.0
OD2 E:ASP67 4.5 11.9 1.0
CB E:ASP59 4.7 12.1 1.0
CA E:PHE62 4.8 10.7 1.0
N E:ASN60 4.8 11.1 1.0
N E:ALA58 4.8 10.3 1.0
CA E:ASP59 4.9 11.5 1.0

Calcium binding site 4 out of 4 in 3p7s

Go back to Calcium Binding Sites List in 3p7s
Calcium binding site 4 out of 4 in the Radiation Damage Study of Thermolysin - 100K Structure D (7.2 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 D (7.2 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:17.6
occ:1.00
 O E:HOH398 2.2 18.2 1.0
O E:ILE197 2.3 25.5 1.0
O E:HOH342 2.3 17.2 1.0
OG1 E:THR194 2.4 17.1 1.0
OD1 E:ASP200 2.4 16.0 1.0
O E:TYR193 2.4 17.0 1.0
O E:THR194 2.5 19.8 1.0
C E:THR194 3.3 20.2 1.0
C E:TYR193 3.4 16.9 1.0
C E:ILE197 3.5 26.4 1.0
CG E:ASP200 3.5 19.7 1.0
CB E:THR194 3.5 17.8 1.0
CA E:THR194 3.7 18.7 1.0
OD2 E:ASP200 3.9 19.2 1.0
N E:THR194 4.0 17.6 1.0
CA E:ILE197 4.1 26.9 1.0
N E:ILE197 4.2 27.9 1.0
CB E:ILE197 4.2 27.2 1.0
O E:ASP200 4.3 20.0 1.0
N E:PRO195 4.4 22.4 1.0
O E:HOH504 4.5 31.3 1.0
O E:GLU190 4.5 14.7 1.0
N E:SER198 4.5 25.8 1.0
CA E:TYR193 4.6 16.3 1.0
CD2 E:TYR193 4.6 14.2 1.0
N E:ASP200 4.6 21.7 1.0
CB E:TYR193 4.6 16.7 1.0
O E:HOH484 4.7 30.3 1.0
CA E:PRO195 4.7 24.2 1.0
O E:HOH394 4.7 29.9 1.0
CG2 E:THR194 4.8 18.4 1.0
CB E:ASP200 4.8 20.1 1.0
CA E:SER198 4.8 26.2 1.0
C E:ASP200 4.9 20.3 1.0
C E:PRO195 4.9 25.8 1.0
C E:SER198 4.9 25.0 1.0
N E:GLY199 5.0 24.8 1.0
CG2 E:ILE197 5.0 26.5 1.0

Reference:

D.H.Juers, M.Weik. Radiation Damage Study of Thermolysin - 100K Structure D (7.2 Mgy) To Be Published.
Page generated: Sat Jul 13 16:37:16 2024

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