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Calcium in PDB 3p7w: Radiation Damage Study of Thermolysin - 160K Structure D (7.1 Mgy)

Enzymatic activity of Radiation Damage Study of Thermolysin - 160K Structure D (7.1 Mgy)

All present enzymatic activity of Radiation Damage Study of Thermolysin - 160K Structure D (7.1 Mgy):
3.4.24.27;

Protein crystallography data

The structure of Radiation Damage Study of Thermolysin - 160K Structure D (7.1 Mgy), PDB code: 3p7w 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 (°) 93.940, 93.940, 128.680, 90.00, 90.00, 120.00
R / Rfree (%) 15.3 / 21

Other elements in 3p7w:

The structure of Radiation Damage Study of Thermolysin - 160K Structure D (7.1 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 - 160K Structure D (7.1 Mgy) (pdb code 3p7w). 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 D (7.1 Mgy), PDB code: 3p7w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3p7w

Go back to Calcium Binding Sites List in 3p7w
Calcium binding site 1 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure D (7.1 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 - 160K Structure D (7.1 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca317

b:22.9
occ:1.00
 O E:GLU187 2.3 20.9 1.0
O E:HOH333 2.3 22.9 1.0
OD2 E:ASP138 2.4 26.3 1.0
OD1 E:ASP185 2.5 23.6 1.0
OE1 E:GLU177 2.5 25.0 1.0
OE2 E:GLU190 2.6 23.3 1.0
OE1 E:GLU190 2.6 25.1 1.0
OE2 E:GLU177 2.9 20.8 1.0
CD E:GLU190 2.9 25.3 1.0
CD E:GLU177 3.0 22.4 1.0
C E:GLU187 3.4 22.6 1.0
CG E:ASP138 3.5 25.0 1.0
CG E:ASP185 3.5 26.4 1.0
CA E:CA318 3.9 39.3 1.0
OD2 E:ASP185 3.9 29.0 1.0
O E:ASP185 4.1 25.2 1.0
CB E:ASP138 4.1 20.0 1.0
N E:ILE188 4.3 21.6 1.0
N E:GLU187 4.3 22.4 1.0
CA E:ILE188 4.3 23.5 1.0
CA E:GLU187 4.4 23.4 1.0
N E:GLY189 4.4 25.1 1.0
OD1 E:ASP138 4.4 28.8 1.0
CG E:GLU190 4.5 24.5 1.0
CG E:GLU177 4.5 18.9 1.0
C E:ASP185 4.5 25.3 1.0
O E:HOH337 4.6 28.2 1.0
CB E:GLU187 4.8 23.6 1.0
N E:ASP185 4.8 26.9 1.0
CB E:ASP185 4.8 25.5 1.0
C E:ILE188 4.8 24.3 1.0
CB E:GLU177 4.9 18.0 1.0
N E:GLU190 5.0 24.8 1.0
CA E:ASP185 5.0 25.9 1.0

Calcium binding site 2 out of 4 in 3p7w

Go back to Calcium Binding Sites List in 3p7w
Calcium binding site 2 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure D (7.1 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 - 160K Structure D (7.1 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:39.3
occ:1.00
 O E:HOH389 2.3 51.0 1.0
O E:ASN183 2.4 34.8 1.0
OE2 E:GLU190 2.4 23.3 1.0
O E:HOH340 2.5 45.7 1.0
OE2 E:GLU177 2.7 20.8 1.0
OD2 E:ASP185 2.7 29.0 1.0
CD E:GLU177 3.3 22.4 1.0
CD E:GLU190 3.4 25.3 1.0
CG E:ASP185 3.5 26.4 1.0
C E:ASN183 3.5 35.6 1.0
OE1 E:GLU177 3.6 25.0 1.0
OD1 E:ASP185 3.8 23.6 1.0
OD2 E:ASP191 3.8 39.1 1.0
CA E:CA317 3.9 22.9 1.0
CG E:GLU190 3.9 24.5 1.0
CA E:PRO184 4.1 30.8 1.0
O E:HOH476 4.1 37.0 1.0
CG E:GLU177 4.3 18.9 1.0
N E:PRO184 4.3 32.6 1.0
C E:PRO184 4.3 29.1 1.0
O E:LYS182 4.3 40.5 1.0
OD1 E:ASP191 4.3 39.7 1.0
N E:ASP185 4.3 26.9 1.0
OE1 E:GLU190 4.4 25.1 1.0
CG E:ASP191 4.4 34.2 1.0
CB E:ASN183 4.4 39.3 1.0
CA E:ASN183 4.6 38.0 1.0
CB E:ASP185 4.6 25.5 1.0
O E:PRO184 5.0 28.8 1.0
O E:HOH488 5.0 44.7 1.0

Calcium binding site 3 out of 4 in 3p7w

Go back to Calcium Binding Sites List in 3p7w
Calcium binding site 3 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure D (7.1 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 - 160K Structure D (7.1 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:23.9
occ:1.00
 O E:GLN61 2.3 18.1 1.0
O E:HOH405 2.4 24.6 1.0
OD1 E:ASP57 2.4 17.8 1.0
O E:HOH395 2.4 24.6 1.0
OD1 E:ASP59 2.5 26.4 1.0
O E:HOH374 2.6 20.4 1.0
OD2 E:ASP57 2.6 15.8 1.0
CG E:ASP57 2.9 17.2 1.0
CG E:ASP59 3.4 25.3 1.0
C E:GLN61 3.5 18.7 1.0
O E:HOH397 3.8 22.6 1.0
OD2 E:ASP59 3.8 26.9 1.0
N E:GLN61 4.0 19.3 1.0
CA E:GLN61 4.1 20.6 1.0
O E:HOH445 4.2 37.9 1.0
CB E:GLN61 4.3 21.0 1.0
N E:ASP59 4.4 20.0 1.0
CB E:ASP57 4.4 16.5 1.0
O E:HOH343 4.5 18.9 1.0
O E:HOH456 4.5 46.9 1.0
O E:HOH409 4.5 23.0 1.0
N E:PHE62 4.5 18.1 1.0
OD2 E:ASP67 4.6 19.3 1.0
CB E:ASP59 4.7 21.4 1.0
CA E:PHE62 4.7 16.9 1.0
N E:ASN60 4.8 19.9 1.0
N E:ALA58 4.9 17.9 1.0
CA E:ASP59 4.9 20.5 1.0
C E:ASP59 5.0 20.3 1.0

Calcium binding site 4 out of 4 in 3p7w

Go back to Calcium Binding Sites List in 3p7w
Calcium binding site 4 out of 4 in the Radiation Damage Study of Thermolysin - 160K Structure D (7.1 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 - 160K Structure D (7.1 Mgy) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:33.8
occ:1.00
 O E:ILE197 2.3 44.9 1.0
O E:THR194 2.4 40.2 1.0
OD1 E:ASP200 2.4 30.4 1.0
O E:HOH341 2.4 31.5 1.0
OG1 E:THR194 2.4 35.6 1.0
O E:TYR193 2.4 33.6 1.0
O E:HOH393 2.5 27.8 1.0
C E:THR194 3.2 40.2 1.0
C E:TYR193 3.4 33.6 1.0
CG E:ASP200 3.5 32.5 1.0
C E:ILE197 3.5 45.7 1.0
CB E:THR194 3.5 37.7 1.0
CA E:THR194 3.7 37.5 1.0
OD2 E:ASP200 3.8 32.2 1.0
N E:THR194 3.9 36.1 1.0
N E:ILE197 4.1 47.4 1.0
CA E:ILE197 4.1 46.6 1.0
N E:PRO195 4.3 42.5 1.0
CB E:ILE197 4.3 47.1 1.0
O E:ASP200 4.5 34.0 1.0
O E:GLU190 4.5 25.6 1.0
N E:SER198 4.6 45.1 1.0
CD2 E:TYR193 4.6 30.4 1.0
CA E:TYR193 4.7 33.3 1.0
O E:HOH390 4.7 45.7 1.0
N E:ASP200 4.7 36.3 1.0
O E:HOH472 4.7 45.4 1.0
CA E:PRO195 4.7 44.0 1.0
CG2 E:THR194 4.8 38.2 1.0
CB E:ASP200 4.8 33.8 1.0
CB E:TYR193 4.8 32.6 1.0
CA E:SER198 4.9 44.6 1.0
C E:PRO195 5.0 45.1 1.0
C E:ASP200 5.0 34.1 1.0
C E:SER198 5.0 43.1 1.0

Reference:

D.H.Juers, M.Weik. Radiation Damage Study of Thermolysin - 160K Structure D (7.1 Mgy) To Be Published.
Page generated: Sat Jul 13 16:38:10 2024

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