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Calcium in PDB 3p7r: Radiation Damage Study of Thermolysin - 100K Structure C (4.9 Mgy)

Enzymatic activity of Radiation Damage Study of Thermolysin - 100K Structure C (4.9 Mgy)

All present enzymatic activity of Radiation Damage Study of Thermolysin - 100K Structure C (4.9 Mgy):
3.4.24.27;

Protein crystallography data

The structure of Radiation Damage Study of Thermolysin - 100K Structure C (4.9 Mgy), PDB code: 3p7r 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 (°) 93.310, 93.310, 128.730, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 20.2

Other elements in 3p7r:

The structure of Radiation Damage Study of Thermolysin - 100K Structure C (4.9 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 C (4.9 Mgy) (pdb code 3p7r). 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 C (4.9 Mgy), PDB code: 3p7r:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3p7r

Go back to Calcium Binding Sites List in 3p7r
Calcium binding site 1 out of 4 in the Radiation Damage Study of Thermolysin - 100K Structure C (4.9 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 C (4.9 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca317

b:11.3
occ:1.00
 O E:GLU187 2.2 9.9 1.0
OD2 E:ASP138 2.4 15.5 1.0
OD1 E:ASP185 2.4 12.7 1.0
O E:HOH334 2.4 9.8 1.0
OE2 E:GLU190 2.5 12.4 1.0
OE1 E:GLU177 2.6 12.5 1.0
OE1 E:GLU190 2.6 10.1 1.0
OE2 E:GLU177 2.8 12.0 1.0
CD E:GLU190 2.9 12.7 1.0
CD E:GLU177 3.0 12.3 1.0
C E:GLU187 3.4 11.9 1.0
CG E:ASP185 3.4 13.9 1.0
CG E:ASP138 3.5 12.8 1.0
OD2 E:ASP185 3.8 17.4 1.0
CA E:CA318 3.9 17.0 1.0
CB E:ASP138 4.1 9.2 1.0
O E:ASP185 4.1 12.0 1.0
N E:ILE188 4.2 11.0 1.0
N E:GLU187 4.2 12.4 1.0
CA E:ILE188 4.3 11.5 1.0
CA E:GLU187 4.3 13.3 1.0
O E:HOH338 4.4 18.4 1.0
CG E:GLU190 4.4 10.8 1.0
N E:GLY189 4.4 10.6 1.0
OD1 E:ASP138 4.4 15.5 1.0
C E:ASP185 4.5 12.6 1.0
CG E:GLU177 4.5 9.4 1.0
N E:ASP185 4.7 13.1 1.0
CB E:ASP185 4.7 12.3 1.0
CB E:GLU187 4.7 13.5 1.0
C E:ILE188 4.8 11.7 1.0
CA E:ASP185 4.9 12.7 1.0
CB E:GLU177 5.0 9.3 1.0
N E:GLU190 5.0 11.3 1.0

Calcium binding site 2 out of 4 in 3p7r

Go back to Calcium Binding Sites List in 3p7r
Calcium binding site 2 out of 4 in the Radiation Damage Study of Thermolysin - 100K Structure C (4.9 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 C (4.9 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:17.0
occ:1.00
 O E:HOH393 2.1 19.9 1.0
O E:HOH341 2.3 19.1 1.0
O E:ASN183 2.3 17.5 1.0
OE2 E:GLU190 2.4 12.4 1.0
OE2 E:GLU177 2.5 12.0 1.0
OD2 E:ASP185 2.6 17.4 1.0
CD E:GLU177 3.2 12.3 1.0
CG E:ASP185 3.4 13.9 1.0
CD E:GLU190 3.4 12.7 1.0
C E:ASN183 3.5 17.9 1.0
OE1 E:GLU177 3.7 12.5 1.0
OD1 E:ASP185 3.8 12.7 1.0
CA E:CA317 3.9 11.3 1.0
CG E:GLU190 3.9 10.8 1.0
OD2 E:ASP191 3.9 20.9 1.0
CA E:PRO184 4.1 14.4 1.0
CG E:GLU177 4.2 9.4 1.0
OD1 E:ASP191 4.2 20.2 1.0
O E:LYS182 4.2 22.6 1.0
O E:HOH487 4.2 22.9 1.0
CB E:ASN183 4.2 21.0 1.0
C E:PRO184 4.2 13.7 1.0
N E:ASP185 4.3 13.1 1.0
N E:PRO184 4.3 16.1 1.0
CG E:ASP191 4.4 16.9 1.0
OE1 E:GLU190 4.5 10.1 1.0
CA E:ASN183 4.5 20.1 1.0
CB E:ASP185 4.5 12.3 1.0
O E:PRO184 4.9 14.1 1.0
O E:HOH504 4.9 29.9 1.0

Calcium binding site 3 out of 4 in 3p7r

Go back to Calcium Binding Sites List in 3p7r
Calcium binding site 3 out of 4 in the Radiation Damage Study of Thermolysin - 100K Structure C (4.9 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 C (4.9 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:10.9
occ:1.00
 O E:GLN61 2.3 8.6 1.0
O E:HOH410 2.3 8.9 1.0
OD1 E:ASP57 2.4 10.5 1.0
O E:HOH376 2.4 8.2 1.0
OD1 E:ASP59 2.5 17.1 1.0
O E:HOH400 2.5 13.7 1.0
OD2 E:ASP57 2.6 8.5 1.0
CG E:ASP57 2.8 9.1 1.0
C E:GLN61 3.4 9.6 1.0
CG E:ASP59 3.5 13.8 1.0
OD2 E:ASP59 3.8 15.7 1.0
O E:HOH402 3.9 14.1 1.0
N E:GLN61 4.0 9.8 1.0
CA E:GLN61 4.1 11.8 1.0
O E:HOH452 4.3 21.7 1.0
CB E:ASP57 4.3 8.9 1.0
CB E:GLN61 4.4 11.6 1.0
O E:HOH414 4.4 13.8 1.0
N E:ASP59 4.4 8.9 1.0
N E:PHE62 4.5 8.5 1.0
O E:HOH344 4.5 9.9 1.0
OD2 E:ASP67 4.5 9.6 1.0
O E:HOH467 4.6 34.5 1.0
CB E:ASP59 4.7 10.1 1.0
CA E:PHE62 4.8 8.9 1.0
N E:ASN60 4.8 9.2 1.0
N E:ALA58 4.8 8.7 1.0
CA E:ASP59 4.9 9.6 1.0

Calcium binding site 4 out of 4 in 3p7r

Go back to Calcium Binding Sites List in 3p7r
Calcium binding site 4 out of 4 in the Radiation Damage Study of Thermolysin - 100K Structure C (4.9 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 C (4.9 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:14.6
occ:1.00
 O E:HOH398 2.3 18.0 1.0
O E:ILE197 2.3 23.0 1.0
O E:HOH342 2.3 14.3 1.0
OG1 E:THR194 2.4 13.9 1.0
O E:TYR193 2.4 14.6 1.0
OD1 E:ASP200 2.4 14.3 1.0
O E:THR194 2.4 17.3 1.0
C E:THR194 3.3 17.4 1.0
C E:TYR193 3.4 14.4 1.0
C E:ILE197 3.5 23.5 1.0
CG E:ASP200 3.5 16.7 1.0
CB E:THR194 3.5 15.0 1.0
CA E:THR194 3.7 15.9 1.0
OD2 E:ASP200 3.9 15.8 1.0
N E:THR194 4.0 14.9 1.0
CA E:ILE197 4.1 23.8 1.0
N E:ILE197 4.2 24.8 1.0
CB E:ILE197 4.3 23.9 1.0
O E:ASP200 4.3 16.7 1.0
N E:PRO195 4.4 19.2 1.0
O E:HOH503 4.5 27.6 1.0
O E:HOH627 4.5 35.1 1.0
O E:GLU190 4.5 11.9 1.0
N E:SER198 4.6 22.7 1.0
O E:HOH483 4.6 26.1 1.0
CA E:TYR193 4.6 13.8 1.0
CD2 E:TYR193 4.6 11.4 1.0
N E:ASP200 4.6 18.4 1.0
CB E:TYR193 4.7 14.6 1.0
CA E:PRO195 4.7 20.9 1.0
CG2 E:THR194 4.8 14.9 1.0
O E:HOH394 4.8 31.2 1.0
CB E:ASP200 4.8 16.9 1.0
CA E:SER198 4.8 22.9 1.0
C E:ASP200 4.9 17.2 1.0
C E:SER198 4.9 21.7 1.0
N E:GLY199 4.9 21.6 1.0
C E:PRO195 4.9 22.5 1.0

Reference:

D.H.Juers, M.Weik. Radiation Damage Study of Thermolysin - 100K Structure C (4.9 Mgy) To Be Published.
Page generated: Sat Jul 13 16:35:57 2024

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