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Calcium in PDB 3p7v: Radiation Damage Study of Thermolysin - 160K Structure C (4.8 Mgy)

Enzymatic activity of Radiation Damage Study of Thermolysin - 160K Structure C (4.8 Mgy)

All present enzymatic activity of Radiation Damage Study of Thermolysin - 160K Structure C (4.8 Mgy):
3.4.24.27;

Protein crystallography data

The structure of Radiation Damage Study of Thermolysin - 160K Structure C (4.8 Mgy), PDB code: 3p7v 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) 31.67 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.850, 93.850, 128.740, 90.00, 90.00, 120.00
R / Rfree (%) 14.6 / 20.2

Other elements in 3p7v:

The structure of Radiation Damage Study of Thermolysin - 160K Structure C (4.8 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 C (4.8 Mgy) (pdb code 3p7v). 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 C (4.8 Mgy), PDB code: 3p7v:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3p7v

Go back to Calcium Binding Sites List in 3p7v
Calcium binding site 1 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure C (4.8 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 C (4.8 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca317

b:16.9
occ:1.00
 O E:GLU187 2.2 15.3 1.0
O E:HOH333 2.4 19.0 1.0
OD2 E:ASP138 2.4 20.2 1.0
OD1 E:ASP185 2.5 18.8 1.0
OE2 E:GLU190 2.5 17.7 1.0
OE1 E:GLU177 2.5 19.6 1.0
OE1 E:GLU190 2.6 19.1 1.0
OE2 E:GLU177 2.8 17.8 1.0
CD E:GLU190 2.9 20.2 1.0
CD E:GLU177 3.0 18.6 1.0
C E:GLU187 3.4 17.2 1.0
CG E:ASP185 3.5 21.1 1.0
CG E:ASP138 3.5 19.5 1.0
CA E:CA318 3.8 33.4 1.0
OD2 E:ASP185 3.8 23.3 1.0
CB E:ASP138 4.1 15.6 1.0
O E:ASP185 4.1 19.6 1.0
N E:ILE188 4.2 16.5 1.0
CA E:ILE188 4.3 18.6 1.0
N E:GLU187 4.3 17.4 1.0
CA E:GLU187 4.3 18.2 1.0
CG E:GLU190 4.4 19.3 1.0
N E:GLY189 4.4 19.9 1.0
CG E:GLU177 4.5 16.1 1.0
OD1 E:ASP138 4.5 21.2 1.0
O E:HOH337 4.6 22.9 1.0
C E:ASP185 4.6 20.1 1.0
CB E:GLU187 4.7 18.5 1.0
N E:ASP185 4.8 21.6 1.0
C E:ILE188 4.8 19.6 1.0
CB E:ASP185 4.8 20.3 1.0
CB E:GLU177 4.9 14.6 1.0
N E:GLU190 5.0 19.7 1.0

Calcium binding site 2 out of 4 in 3p7v

Go back to Calcium Binding Sites List in 3p7v
Calcium binding site 2 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure C (4.8 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 C (4.8 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:33.4
occ:1.00
 O E:HOH390 2.2 41.2 1.0
O E:HOH340 2.3 35.8 1.0
O E:ASN183 2.4 28.8 1.0
OE2 E:GLU190 2.4 17.7 1.0
OE2 E:GLU177 2.6 17.8 1.0
OD2 E:ASP185 2.7 23.3 1.0
CD E:GLU177 3.2 18.6 1.0
CG E:ASP185 3.4 21.1 1.0
CD E:GLU190 3.4 20.2 1.0
C E:ASN183 3.5 29.1 1.0
OE1 E:GLU177 3.6 19.6 1.0
OD1 E:ASP185 3.7 18.8 1.0
CA E:CA317 3.8 16.9 1.0
OD2 E:ASP191 3.9 32.9 1.0
CG E:GLU190 3.9 19.3 1.0
CA E:PRO184 4.1 24.4 1.0
O E:HOH482 4.1 33.8 1.0
CG E:GLU177 4.2 16.1 1.0
N E:ASP185 4.2 21.6 1.0
C E:PRO184 4.2 23.3 1.0
N E:PRO184 4.3 26.4 1.0
OD1 E:ASP191 4.3 32.3 1.0
O E:LYS182 4.3 33.4 1.0
CB E:ASN183 4.4 32.6 1.0
CG E:ASP191 4.4 27.9 1.0
OE1 E:GLU190 4.4 19.1 1.0
CB E:ASP185 4.5 20.3 1.0
CA E:ASN183 4.6 31.4 1.0
O E:PRO184 4.9 23.0 1.0

Calcium binding site 3 out of 4 in 3p7v

Go back to Calcium Binding Sites List in 3p7v
Calcium binding site 3 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure C (4.8 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 C (4.8 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:18.2
occ:1.00
 O E:GLN61 2.3 14.6 1.0
OD1 E:ASP57 2.3 13.3 1.0
O E:HOH396 2.4 20.7 1.0
O E:HOH406 2.4 19.4 1.0
O E:HOH374 2.5 17.8 1.0
OD1 E:ASP59 2.6 23.1 1.0
OD2 E:ASP57 2.6 11.6 1.0
CG E:ASP57 2.8 14.2 1.0
C E:GLN61 3.4 14.9 1.0
CG E:ASP59 3.5 20.8 1.0
OD2 E:ASP59 3.8 21.5 1.0
O E:HOH398 3.9 18.8 1.0
N E:GLN61 4.0 15.6 1.0
CA E:GLN61 4.1 17.7 1.0
O E:HOH447 4.2 32.7 1.0
CB E:ASP57 4.3 13.5 1.0
CB E:GLN61 4.3 17.1 1.0
N E:ASP59 4.4 16.5 1.0
O E:HOH343 4.5 13.6 1.0
O E:HOH410 4.5 18.5 1.0
N E:PHE62 4.5 14.2 1.0
O E:HOH462 4.5 37.9 1.0
OD2 E:ASP67 4.6 14.4 1.0
CB E:ASP59 4.7 17.1 1.0
CA E:PHE62 4.7 13.3 1.0
N E:ASN60 4.8 15.9 1.0
N E:ALA58 4.9 14.1 1.0
CA E:ASP59 4.9 16.9 1.0
C E:ASP59 5.0 16.3 1.0

Calcium binding site 4 out of 4 in 3p7v

Go back to Calcium Binding Sites List in 3p7v
Calcium binding site 4 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure C (4.8 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 C (4.8 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:27.1
occ:1.00
 O E:ILE197 2.4 38.9 1.0
OG1 E:THR194 2.4 29.9 1.0
OD1 E:ASP200 2.4 25.5 1.0
O E:HOH394 2.4 25.9 1.0
O E:TYR193 2.4 26.9 1.0
O E:HOH341 2.4 28.0 1.0
O E:THR194 2.5 34.1 1.0
C E:THR194 3.3 34.0 1.0
C E:TYR193 3.4 26.8 1.0
CG E:ASP200 3.5 27.3 1.0
C E:ILE197 3.5 39.6 1.0
CB E:THR194 3.5 31.4 1.0
CA E:THR194 3.7 31.9 1.0
OD2 E:ASP200 3.9 28.3 1.0
N E:THR194 4.0 29.6 1.0
N E:ILE197 4.1 41.2 1.0
CA E:ILE197 4.2 40.3 1.0
CB E:ILE197 4.3 40.9 1.0
N E:PRO195 4.4 36.3 1.0
O E:HOH497 4.4 53.0 1.0
O E:ASP200 4.5 27.8 1.0
O E:GLU190 4.5 20.3 1.0
N E:SER198 4.6 39.0 1.0
CA E:TYR193 4.6 25.7 1.0
O E:HOH478 4.6 39.1 1.0
N E:ASP200 4.6 30.6 1.0
CD2 E:TYR193 4.7 23.5 1.0
CG2 E:THR194 4.7 32.1 1.0
CB E:TYR193 4.8 25.7 1.0
CA E:PRO195 4.8 37.9 1.0
CB E:ASP200 4.8 28.3 1.0
O E:HOH391 4.8 42.1 1.0
CA E:SER198 4.9 39.1 1.0
C E:ASP200 4.9 28.3 1.0
C E:SER198 4.9 37.5 1.0
CG2 E:ILE197 5.0 39.9 1.0
CA E:ASP200 5.0 28.8 1.0

Reference:

D.H.Juers, M.Weik. Radiation Damage Study of Thermolysin - 160K Structure C (4.8 Mgy) To Be Published.
Page generated: Sat Jul 13 16:37:52 2024

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