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Calcium in PDB 3for: Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide)

Enzymatic activity of Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide)

All present enzymatic activity of Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide):
3.4.24.27;

Protein crystallography data

The structure of Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide), PDB code: 3for was solved by S.-F.Wang, J.-Y.Jin, G.-R.Tian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.48 / 1.93
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.094, 93.094, 129.280, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 21.3

Other elements in 3for:

The structure of Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide) (pdb code 3for). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide), PDB code: 3for:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3for

Go back to Calcium Binding Sites List in 3for
Calcium binding site 1 out of 4 in the Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:18.0
occ:1.00
 O A:GLU187 2.6 16.7 1.0
OD1 A:ASP185 2.6 14.6 1.0
OE1 A:GLU177 2.7 15.0 1.0
OD2 A:ASP138 2.7 19.8 1.0
O A:HOH365 2.7 15.8 1.0
OE1 A:GLU190 2.7 15.1 1.0
OE2 A:GLU190 2.7 16.9 1.0
OE2 A:GLU177 2.9 13.1 1.0
CD A:GLU190 3.0 17.0 1.0
CD A:GLU177 3.1 17.5 1.0
CG A:ASP138 3.5 18.9 1.0
C A:GLU187 3.5 17.9 1.0
CG A:ASP185 3.6 19.6 1.0
OD2 A:ASP185 3.9 18.4 1.0
CA A:CA802 3.9 20.4 1.0
CB A:ASP138 4.0 15.4 1.0
O A:ASP185 4.1 16.5 1.0
N A:GLU187 4.2 18.9 1.0
N A:ILE188 4.3 16.2 1.0
CA A:ILE188 4.3 17.4 1.0
CA A:GLU187 4.3 18.7 1.0
N A:GLY189 4.4 16.5 1.0
OD1 A:ASP138 4.4 17.8 1.0
CG A:GLU190 4.4 17.6 1.0
O A:HOH411 4.5 25.0 1.0
CG A:GLU177 4.5 15.4 1.0
CB A:GLU187 4.6 21.3 1.0
C A:ASP185 4.6 18.8 1.0
C A:ILE188 4.8 17.3 1.0
N A:ASP185 4.8 20.3 1.0
CB A:ASP185 4.9 18.7 1.0
N A:GLU190 4.9 18.1 1.0

Calcium binding site 2 out of 4 in 3for

Go back to Calcium Binding Sites List in 3for
Calcium binding site 2 out of 4 in the Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:20.4
occ:1.00
 O A:ASN183 2.5 26.4 1.0
OE2 A:GLU190 2.6 16.9 1.0
OD2 A:ASP185 2.6 18.4 1.0
OE2 A:GLU177 2.6 13.1 1.0
O A:HOH505 2.7 23.5 1.0
CD A:GLU177 3.4 17.5 1.0
CG A:ASP185 3.4 19.6 1.0
CD A:GLU190 3.5 17.0 1.0
C A:ASN183 3.6 26.5 1.0
OD1 A:ASP185 3.8 14.6 1.0
OE1 A:GLU177 3.8 15.0 1.0
CA A:CA801 3.9 18.0 1.0
CG A:GLU190 4.0 17.6 1.0
OD2 A:ASP191 4.0 22.4 1.0
OD1 A:ASP191 4.2 22.6 1.0
CB A:ASN183 4.2 28.4 1.0
CA A:PRO184 4.3 23.8 1.0
N A:ASP185 4.3 20.3 1.0
C A:PRO184 4.3 23.6 1.0
O A:HOH453 4.4 33.6 1.0
CG A:ASP191 4.4 22.3 1.0
N A:PRO184 4.4 25.4 1.0
CG A:GLU177 4.4 15.4 1.0
O A:LYS182 4.4 30.9 1.0
OE1 A:GLU190 4.4 15.1 1.0
CB A:ASP185 4.5 18.7 1.0
CA A:ASN183 4.6 28.5 1.0
O A:PRO184 4.9 22.7 1.0

Calcium binding site 3 out of 4 in 3for

Go back to Calcium Binding Sites List in 3for
Calcium binding site 3 out of 4 in the Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:18.2
occ:1.00
 O A:GLN61 2.4 14.7 1.0
OD1 A:ASP57 2.6 16.6 1.0
OD1 A:ASP59 2.6 16.4 1.0
O A:HOH392 2.7 16.9 1.0
O A:HOH353 2.7 22.0 1.0
OD2 A:ASP57 2.7 14.8 1.0
CG A:ASP57 3.0 17.1 1.0
CG A:ASP59 3.6 18.6 1.0
C A:GLN61 3.6 17.3 1.0
OD2 A:ASP59 3.9 18.0 1.0
O A:HOH379 3.9 20.4 1.0
N A:GLN61 4.0 16.9 1.0
CA A:GLN61 4.2 18.6 1.0
CB A:GLN61 4.3 22.4 1.0
N A:ASP59 4.4 16.9 1.0
CB A:ASP57 4.5 15.1 1.0
O A:HOH490 4.5 25.5 1.0
O A:HOH324 4.6 13.1 1.0
N A:PHE62 4.6 16.0 1.0
OD2 A:ASP67 4.6 15.9 1.0
N A:ASN60 4.7 16.5 1.0
CA A:PHE62 4.8 16.3 1.0
CB A:ASP59 4.8 17.8 1.0
N A:ALA58 4.9 17.4 1.0
CA A:ASP59 4.9 16.4 1.0
C A:ASP59 5.0 17.2 1.0

Calcium binding site 4 out of 4 in 3for

Go back to Calcium Binding Sites List in 3for
Calcium binding site 4 out of 4 in the Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin Complexed with Bnpa (2-Benzyl-3-Nitro Propanoic Acid Amide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca804

b:22.2
occ:1.00
 O A:ILE197 2.5 31.3 1.0
O A:TYR193 2.5 19.7 1.0
O A:THR194 2.5 23.2 1.0
OD1 A:ASP200 2.6 23.5 1.0
O A:HOH332 2.6 18.1 1.0
OG1 A:THR194 2.7 22.8 1.0
O A:HOH497 2.8 25.3 1.0
C A:THR194 3.3 22.4 1.0
C A:TYR193 3.5 19.3 1.0
CG A:ASP200 3.6 21.6 1.0
C A:ILE197 3.6 33.0 1.0
CB A:THR194 3.8 22.1 1.0
CA A:THR194 3.8 22.1 1.0
OD2 A:ASP200 4.0 23.4 1.0
N A:THR194 4.0 19.2 1.0
N A:ILE197 4.3 32.3 1.0
N A:PRO195 4.3 23.1 1.0
CA A:ILE197 4.3 32.9 1.0
O A:ASP200 4.4 19.7 1.0
CB A:ILE197 4.4 34.0 1.0
O A:GLU190 4.5 18.1 1.0
CA A:TYR193 4.6 19.4 1.0
CD2 A:TYR193 4.6 22.0 1.0
N A:SER198 4.7 33.5 1.0
N A:ASP200 4.7 24.7 1.0
CA A:PRO195 4.7 24.8 1.0
CB A:TYR193 4.7 18.3 1.0
O A:HOH483 4.8 35.4 1.0
CA A:SER198 4.8 33.2 1.0
C A:ASP200 4.9 21.7 1.0
O A:HOH429 4.9 35.7 1.0
CB A:ASP200 4.9 22.3 1.0
C A:PRO195 4.9 26.5 1.0

Reference:

S.-F.Wang, J.-Y.Jin, G.-R.Tian. Nitro As Zbg in the Inhibition of Thermolysin To Be Published.
Page generated: Tue Jul 8 12:27:15 2025

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