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Calcium in PDB 5fsp: Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure

Enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure

All present enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 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 100 Bar of Krypton Pressure, PDB code: 5fsp 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) 46.50 / 1.70
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.007, 93.007, 129.120, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 17.8

Other elements in 5fsp:

The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure also contains other interesting chemical elements:

Krypton (Kr) 8 atoms
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 Bar of Krypton Pressure (pdb code 5fsp). 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 100 Bar of Krypton Pressure, PDB code: 5fsp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5fsp

Go back to Calcium Binding Sites List in 5fsp
Calcium binding site 1 out of 4 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 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 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1326

b:13.9
occ:1.00
 O A:ILE197 2.3 19.1 1.0
O A:TYR193 2.3 12.5 1.0
O A:HOH2199 2.4 17.1 1.0
O A:THR194 2.4 19.5 1.0
OD1 A:ASP200 2.4 15.2 1.0
O A:HOH2201 2.4 19.3 1.0
OG1 A:THR194 2.4 15.6 1.0
C A:THR194 3.2 13.7 1.0
C A:TYR193 3.4 14.6 1.0
CG A:ASP200 3.4 13.5 1.0
CB A:THR194 3.5 11.8 1.0
C A:ILE197 3.5 25.1 1.0
CA A:THR194 3.7 15.3 1.0
OD2 A:ASP200 3.8 17.4 1.0
N A:THR194 3.9 14.0 1.0
CA A:ILE197 4.2 20.3 1.0
CB A:ILE197 4.2 19.9 1.0
N A:ILE197 4.3 28.2 1.0
N A:PRO195 4.3 14.4 1.0
O A:ASP200 4.4 12.2 1.0
N A:SER198 4.5 21.0 1.0
N A:ASP200 4.6 13.8 1.0
CA A:TYR193 4.6 9.7 1.0
O A:GLU190 4.6 13.5 1.0
CA A:PRO195 4.7 19.8 1.0
CD2 A:TYR193 4.7 15.5 1.0
KR A:KR1320 4.7 20.6 0.3
CG2 A:ILE197 4.7 21.6 1.0
CB A:ASP200 4.7 14.1 1.0
CG2 A:THR194 4.8 17.5 1.0
CB A:TYR193 4.8 10.5 1.0
CA A:SER198 4.8 19.4 1.0
C A:ASP200 4.8 9.4 1.0
C A:SER198 4.9 20.8 1.0
N A:GLY199 4.9 21.3 1.0
CA A:ASP200 4.9 13.6 1.0
C A:PRO195 5.0 22.1 1.0

Calcium binding site 2 out of 4 in 5fsp

Go back to Calcium Binding Sites List in 5fsp
Calcium binding site 2 out of 4 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 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 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1327

b:11.1
occ:1.00
 O A:GLN61 2.3 9.4 1.0
O A:HOH2087 2.4 14.3 1.0
OD1 A:ASP59 2.4 12.4 1.0
OD2 A:ASP57 2.4 11.9 1.0
O A:HOH2090 2.5 12.7 1.0
O A:HOH2088 2.5 11.4 1.0
OD1 A:ASP57 2.6 10.7 1.0
CG A:ASP57 2.8 11.1 1.0
CG A:ASP59 3.4 15.2 1.0
C A:GLN61 3.4 7.0 1.0
OD2 A:ASP59 3.8 15.8 1.0
O A:HOH2092 3.9 15.8 1.0
N A:GLN61 4.0 8.2 1.0
CA A:GLN61 4.1 8.3 1.0
CB A:GLN61 4.3 13.3 1.0
CB A:ASP57 4.3 10.1 1.0
N A:ASP59 4.3 9.7 1.0
O A:HOH2034 4.4 26.7 1.0
N A:PHE62 4.5 8.9 1.0
O A:HOH2089 4.5 13.9 1.0
O A:HOH2085 4.6 9.7 1.0
OD2 A:ASP67 4.6 10.5 1.0
CB A:ASP59 4.6 10.5 1.0
N A:ASN60 4.7 11.1 1.0
O A:HOH2033 4.7 32.0 1.0
CA A:PHE62 4.7 9.5 1.0
N A:ALA58 4.7 8.9 1.0
CA A:ASP59 4.8 11.4 1.0
C A:ASP59 4.9 11.3 1.0

Calcium binding site 3 out of 4 in 5fsp

Go back to Calcium Binding Sites List in 5fsp
Calcium binding site 3 out of 4 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 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 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1328

b:10.0
occ:1.00
 O A:GLU187 2.3 12.8 1.0
OD1 A:ASP185 2.4 11.9 1.0
OD2 A:ASP138 2.4 10.5 1.0
OE2 A:GLU190 2.5 15.9 1.0
O A:HOH2189 2.5 11.0 1.0
OE1 A:GLU177 2.5 11.7 1.0
OE1 A:GLU190 2.6 13.1 1.0
OE2 A:GLU177 2.6 14.3 1.0
CD A:GLU190 2.9 13.0 1.0
CD A:GLU177 2.9 14.7 1.0
C A:GLU187 3.4 9.2 1.0
CG A:ASP138 3.4 17.4 1.0
CG A:ASP185 3.5 20.0 1.0
OD2 A:ASP185 3.9 22.1 1.0
O A:ASP185 4.0 12.9 1.0
CB A:ASP138 4.0 7.8 1.0
N A:GLU187 4.2 10.7 1.0
CA A:CA1329 4.2 52.5 1.0
CA A:GLU187 4.3 11.6 1.0
N A:ILE188 4.3 10.0 1.0
O A:HOH2163 4.3 13.8 1.0
OD1 A:ASP138 4.4 12.1 1.0
CA A:ILE188 4.4 9.0 1.0
CG A:GLU190 4.4 12.1 1.0
CG A:GLU177 4.4 12.5 1.0
N A:GLY189 4.4 8.0 1.0
C A:ASP185 4.5 13.9 1.0
CB A:GLU187 4.6 13.2 1.0
O A:HOH2192 4.6 32.5 1.0
N A:ASP185 4.6 11.5 1.0
CB A:ASP185 4.7 12.9 1.0
C A:ILE188 4.8 11.4 1.0
CA A:ASP185 4.9 13.4 1.0
CB A:GLU177 4.9 9.6 1.0
N A:GLU190 5.0 11.9 1.0

Calcium binding site 4 out of 4 in 5fsp

Go back to Calcium Binding Sites List in 5fsp
Calcium binding site 4 out of 4 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 100 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 100 Bar of Krypton Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1329

b:52.5
occ:1.00
 O A:HOH2192 2.6 32.5 1.0
OE2 A:GLU190 2.6 15.9 1.0
O A:ASN183 2.7 17.2 1.0
OE2 A:GLU177 3.1 14.3 1.0
OD2 A:ASP185 3.3 22.1 1.0
CD A:GLU177 3.6 14.7 1.0
CD A:GLU190 3.6 13.0 1.0
O A:HOH2194 3.8 30.6 1.0
C A:ASN183 3.8 13.9 1.0
CG A:ASP185 3.8 20.0 1.0
OE1 A:GLU177 3.9 11.7 1.0
CG A:GLU190 4.0 12.1 1.0
OD2 A:ASP191 4.1 20.1 1.0
CA A:PRO184 4.1 12.1 1.0
O A:LYS182 4.1 21.1 1.0
OD1 A:ASP185 4.2 11.9 1.0
OD1 A:ASP191 4.2 18.7 1.0
CA A:CA1328 4.2 10.0 1.0
N A:ASP185 4.4 11.5 1.0
C A:PRO184 4.4 16.3 1.0
CG A:ASP191 4.4 21.6 1.0
N A:PRO184 4.4 14.8 1.0
CG A:GLU177 4.5 12.5 1.0
CB A:ASN183 4.6 32.5 1.0
O A:HOH2200 4.6 33.6 1.0
OE1 A:GLU190 4.7 13.1 1.0
CB A:ASP185 4.7 12.9 1.0
CA A:ASN183 4.8 22.2 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 19:19:34 2024

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