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Calcium in PDB 5fss: Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure

Enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure

All present enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure:
3.4.24.27;

Protein crystallography data

The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure, PDB code: 5fss was solved by B.Lafumat, C.Mueller-Dieckmann, N.Colloc'h, T.Prange, A.Royant, P.Van Derlinden, P.Carpentier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.38 / 1.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.749, 92.749, 128.995, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 18

Other elements in 5fss:

The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure also contains other interesting chemical elements:

Krypton (Kr) 2 atoms
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure (pdb code 5fss). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure, PDB code: 5fss:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5fss

Go back to Calcium Binding Sites List in 5fss
Calcium binding site 1 out of 4 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:12.5
occ:1.00
 O A:GLU187 2.3 12.8 1.0
OD1 A:ASP185 2.4 14.2 1.0
OD2 A:ASP138 2.4 12.2 1.0
OE2 A:GLU190 2.5 15.1 1.0
OE1 A:GLU177 2.5 13.3 1.0
O A:HOH2217 2.5 13.9 1.0
OE1 A:GLU190 2.6 13.1 1.0
OE2 A:GLU177 2.7 14.2 1.0
CD A:GLU190 2.8 13.0 1.0
CD A:GLU177 2.9 14.0 1.0
C A:GLU187 3.4 10.7 1.0
CG A:ASP138 3.4 11.3 1.0
CG A:ASP185 3.4 16.5 1.0
CA A:CA402 3.8 16.0 0.5
OD2 A:ASP185 3.8 19.0 1.0
CB A:ASP138 4.0 9.2 1.0
O A:ASP185 4.0 14.0 1.0
N A:GLU187 4.1 14.2 1.0
CA A:GLU187 4.3 13.2 1.0
N A:ILE188 4.3 11.2 1.0
O A:HOH2194 4.3 14.5 1.0
OD1 A:ASP138 4.3 13.4 1.0
CG A:GLU190 4.3 13.8 1.0
CA A:ILE188 4.3 11.9 1.0
CG A:GLU177 4.4 12.4 1.0
N A:GLY189 4.4 10.7 1.0
C A:ASP185 4.5 14.7 1.0
CB A:GLU187 4.6 15.3 1.0
O A:HOH2220 4.6 25.3 1.0
N A:ASP185 4.7 14.9 1.0
CB A:ASP185 4.7 13.8 1.0
C A:ILE188 4.8 11.9 1.0
CA A:ASP185 4.9 12.6 1.0
CB A:GLU177 4.9 11.5 1.0
N A:GLU190 5.0 12.8 1.0

Calcium binding site 2 out of 4 in 5fss

Go back to Calcium Binding Sites List in 5fss
Calcium binding site 2 out of 4 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:16.0
occ:0.50
 OE2 A:GLU190 2.3 15.1 1.0
O A:HOH2220 2.4 25.3 1.0
O A:HOH2223 2.4 32.9 1.0
O A:ASN183 2.5 23.0 1.0
OD2 A:ASP185 2.7 19.0 1.0
OE2 A:GLU177 2.7 14.2 1.0
CD A:GLU190 3.3 13.0 1.0
CD A:GLU177 3.3 14.0 1.0
CG A:ASP185 3.4 16.5 1.0
C A:ASN183 3.7 18.1 1.0
OD1 A:ASP185 3.7 14.2 1.0
OE1 A:GLU177 3.7 13.3 1.0
CG A:GLU190 3.7 13.8 1.0
CA A:CA401 3.8 12.5 1.0
O A:HOH2222 4.0 32.2 1.0
CA A:PRO184 4.1 15.7 1.0
N A:ASP185 4.2 14.9 1.0
OD2 A:ASP191 4.2 18.1 1.0
OD1 A:ASP191 4.2 18.0 1.0
OE1 A:GLU190 4.3 13.1 1.0
C A:PRO184 4.3 18.0 1.0
CG A:GLU177 4.3 12.4 1.0
CB A:ASN183 4.4 31.1 1.0
CB A:ASP185 4.4 13.8 1.0
N A:PRO184 4.4 17.3 1.0
O A:LYS182 4.5 29.3 1.0
CG A:ASP191 4.5 17.2 1.0
CA A:ASN183 4.7 25.5 1.0
O A:HOH2194 4.8 14.5 1.0
O A:HOH2224 4.9 34.4 1.0
CA A:ASP185 4.9 12.6 1.0

Calcium binding site 3 out of 4 in 5fss

Go back to Calcium Binding Sites List in 5fss
Calcium binding site 3 out of 4 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:12.6
occ:1.00
 O A:GLN61 2.3 12.4 1.0
OD1 A:ASP59 2.4 12.5 1.0
OD2 A:ASP57 2.4 12.9 1.0
O A:HOH2109 2.4 15.5 1.0
O A:HOH2112 2.4 14.8 1.0
O A:HOH2110 2.5 13.9 1.0
OD1 A:ASP57 2.6 12.2 1.0
CG A:ASP57 2.8 13.7 1.0
CG A:ASP59 3.4 13.9 1.0
C A:GLN61 3.5 10.4 1.0
OD2 A:ASP59 3.8 16.6 1.0
N A:GLN61 3.9 12.1 1.0
O A:HOH2116 4.0 16.2 1.0
CA A:GLN61 4.1 11.1 1.0
N A:ASP59 4.3 12.3 1.0
CB A:GLN61 4.3 13.3 1.0
CB A:ASP57 4.3 11.7 1.0
O A:HOH2043 4.4 21.8 1.0
O A:HOH2111 4.5 16.2 1.0
N A:PHE62 4.6 10.7 1.0
O A:HOH2042 4.6 29.4 1.0
CB A:ASP59 4.6 11.6 1.0
OD2 A:ASP67 4.6 11.8 1.0
N A:ASN60 4.6 12.2 1.0
O A:HOH2105 4.6 11.9 1.0
O A:HOH2044 4.7 32.7 1.0
N A:ALA58 4.7 11.9 1.0
CA A:ASP59 4.8 11.8 1.0
CA A:PHE62 4.8 10.4 1.0
C A:ASP59 4.9 13.5 1.0

Calcium binding site 4 out of 4 in 5fss

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Calcium binding site 4 out of 4 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 40 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:15.5
occ:1.00
 O A:ILE197 2.3 20.2 1.0
O A:TYR193 2.3 15.8 1.0
O A:THR194 2.4 17.8 1.0
OD1 A:ASP200 2.4 16.5 1.0
OG1 A:THR194 2.4 18.6 1.0
O A:HOH2228 2.4 15.9 1.0
O A:HOH2231 2.5 22.2 1.0
C A:THR194 3.2 17.1 1.0
C A:TYR193 3.3 15.8 1.0
C A:ILE197 3.4 25.5 1.0
CG A:ASP200 3.5 13.4 1.0
CB A:THR194 3.5 16.1 1.0
CA A:THR194 3.7 16.1 1.0
OD2 A:ASP200 3.8 17.6 1.0
N A:THR194 3.9 15.2 1.0
CA A:ILE197 4.2 24.1 1.0
CB A:ILE197 4.2 22.1 1.0
N A:ILE197 4.3 26.5 1.0
N A:PRO195 4.3 16.4 1.0
O A:HOH2234 4.4 30.0 1.0
O A:ASP200 4.5 16.2 1.0
N A:SER198 4.5 27.4 1.0
CA A:TYR193 4.5 14.9 1.0
O A:GLU190 4.6 15.2 1.0
O A:HOH2229 4.6 23.9 1.0
N A:ASP200 4.6 18.3 1.0
CA A:SER198 4.6 25.9 1.0
CA A:PRO195 4.7 18.2 1.0
CD2 A:TYR193 4.7 16.4 1.0
CB A:TYR193 4.7 14.5 1.0
CG2 A:THR194 4.7 19.1 1.0
CB A:ASP200 4.8 17.5 1.0
C A:ASP200 4.8 13.1 1.0
CG2 A:ILE197 4.8 23.1 1.0
N A:GLY199 4.9 23.9 1.0
C A:SER198 4.9 23.5 1.0
CA A:ASP200 5.0 17.7 1.0
C A:PRO195 5.0 23.0 1.0

Reference:

B.Lafumat, C.Mueller-Dieckmann, N.Colloc'h, T.Prange, A.Royant, P.Van Der Linden, P.Carpentier. Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using A Novel `Soak-and-Freeze' Methodology. J.Appl.Crystallogr. V. 49 1478 2016.
ISSN: ISSN 0021-8898
DOI: 10.1107/S1600576716010992
Page generated: Sun Jul 14 19:20:39 2024

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