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Calcium in PDB 5fsj: Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure

Enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure

All present enzymatic activity of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure:
3.4.24.27;

Protein crystallography data

The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure, PDB code: 5fsj 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) 46.46 / 1.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.922, 92.922, 130.252, 90.00, 90.00, 120.00
R / Rfree (%) 10.4 / 12.2

Other elements in 5fsj:

The structure of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure also contains other interesting chemical elements:

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 45 Bar of Oxygen Pressure (pdb code 5fsj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure, PDB code: 5fsj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5fsj

Go back to Calcium Binding Sites List in 5fsj
Calcium binding site 1 out of 5 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen 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 45 Bar of Oxygen Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:15.3
occ:1.00
 O A:ILE197 2.3 26.5 1.0
O A:TYR193 2.4 14.3 1.0
OD1 A:ASP200 2.4 16.4 1.0
O A:THR194 2.4 16.9 1.0
O A:HOH2371 2.4 16.5 1.0
OG1 A:THR194 2.4 15.9 1.0
O A:HOH2375 2.4 21.6 1.0
HG1 A:THR194 2.8 19.1 0.0
C A:THR194 3.2 16.5 1.0
C A:TYR193 3.4 13.8 1.0
CG A:ASP200 3.4 17.1 1.0
HB A:ILE197 3.5 41.3 1.0
C A:ILE197 3.5 27.6 1.0
CB A:THR194 3.5 16.8 1.0
H A:ILE197 3.6 34.7 1.0
CA A:THR194 3.7 15.9 1.0
HB A:THR194 3.7 20.1 1.0
OD2 A:ASP200 3.8 19.1 1.0
H A:ASP200 3.9 23.5 1.0
N A:THR194 3.9 13.8 1.0
HA A:SER198 4.1 38.8 1.0
HD2 A:TYR193 4.1 19.2 1.0
HB3 A:TYR193 4.1 16.9 1.0
CA A:ILE197 4.2 31.2 1.0
CB A:ILE197 4.2 34.4 1.0
N A:ILE197 4.3 28.9 1.0
N A:PRO195 4.3 18.6 1.0
HA A:PRO195 4.3 24.4 1.0
HG23 A:ILE197 4.4 36.0 1.0
O A:HOH2382 4.4 42.7 1.0
O A:ASP200 4.5 16.4 1.0
N A:SER198 4.5 29.0 1.0
O A:HOH2378 4.5 42.0 1.0
CA A:TYR193 4.6 12.1 1.0
HA A:THR194 4.6 19.0 1.0
O A:GLU190 4.6 12.9 1.0
N A:ASP200 4.6 19.6 1.0
O A:HOH2373 4.6 27.8 1.0
CA A:SER198 4.7 32.3 1.0
O A:HOH2370 4.7 39.2 1.0
CA A:PRO195 4.7 20.4 1.0
CD2 A:TYR193 4.7 16.0 1.0
CB A:TYR193 4.7 14.1 1.0
H A:THR194 4.7 16.6 1.0
CB A:ASP200 4.7 17.2 1.0
H A:GLY199 4.7 29.3 1.0
CG2 A:THR194 4.8 17.3 1.0
C A:ASP200 4.8 16.2 1.0
CG2 A:ILE197 4.9 29.9 1.0
HG21 A:THR194 4.9 20.7 1.0
H A:TYR193 4.9 14.1 1.0
C A:PRO195 4.9 27.0 1.0
CA A:ASP200 5.0 18.0 1.0
C A:SER198 5.0 27.9 1.0

Calcium binding site 2 out of 5 in 5fsj

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Calcium binding site 2 out of 5 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen 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 45 Bar of Oxygen Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:12.2
occ:0.69
 OE2 A:GLU190 2.3 11.5 1.0
O A:ASN183 2.3 15.7 1.0
O A:HOH2353 2.3 23.0 1.0
O A:HOH2361 2.4 18.1 1.0
OD2 A:ASP185 2.4 14.2 1.0
OE2 A:GLU177 2.6 12.4 1.0
CG A:ASP185 3.2 12.3 1.0
CD A:GLU190 3.3 10.7 1.0
CD A:GLU177 3.3 10.4 1.0
HG3 A:GLU190 3.5 14.7 1.0
C A:ASN183 3.5 15.5 1.0
HA A:PRO184 3.5 15.7 1.0
OD1 A:ASP185 3.6 11.7 1.0
HB2 A:ASN183 3.7 25.7 1.0
OE1 A:GLU177 3.7 11.4 1.0
HG2 A:GLU190 3.7 14.7 1.0
CG A:GLU190 3.8 12.2 1.0
CA A:CA1009 3.8 10.6 1.0
O A:HOH2365 3.9 46.5 1.0
H A:ASP185 4.0 14.1 1.0
CA A:PRO184 4.1 13.1 1.0
HB3 A:ASN183 4.1 25.7 1.0
N A:ASP185 4.1 11.8 1.0
OD1 A:ASP191 4.2 16.1 1.0
O A:HOH2360 4.2 26.4 1.0
C A:PRO184 4.2 13.0 1.0
CB A:ASN183 4.3 21.4 1.0
OD2 A:ASP191 4.3 15.1 1.0
OE1 A:GLU190 4.3 11.5 1.0
N A:PRO184 4.3 13.8 1.0
CG A:GLU177 4.3 10.9 1.0
HB3 A:ASP185 4.3 14.4 1.0
HG2 A:GLU177 4.3 13.1 1.0
CB A:ASP185 4.4 12.0 1.0
H A:ASN183 4.4 27.5 1.0
HG3 A:GLU177 4.4 13.1 1.0
O A:HOH2316 4.5 26.4 1.0
O A:HOH2178 4.5 52.5 1.0
CA A:ASN183 4.5 18.7 1.0
CG A:ASP191 4.5 13.8 1.0
O A:LYS182 4.7 24.2 0.6
CA A:ASP185 4.9 12.4 1.0
O A:HOH2364 4.9 40.2 1.0
O A:PRO184 4.9 15.9 1.0
O A:HOH2317 5.0 17.8 1.0

Calcium binding site 3 out of 5 in 5fsj

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Calcium binding site 3 out of 5 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen 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 45 Bar of Oxygen Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:22.4
occ:0.69
 CA A:CA1010 2.4 10.8 1.0
O A:HOH2545 2.7 27.8 1.0
OD2 A:ASP59 2.8 15.9 1.0
OD1 A:ASP59 3.0 11.5 1.0
O A:HOH2179 3.0 17.2 1.0
O A:HOH2172 3.1 11.7 1.0
O A:HOH2171 3.2 13.8 1.0
CG A:ASP59 3.2 11.8 1.0
HB2 A:GLN61 3.2 14.9 1.0
O A:GLN61 3.5 10.8 1.0
O A:HOH2176 3.5 30.1 0.3
O A:HOH2546 3.6 24.4 1.0
O A:HOH2077 4.1 33.4 1.0
CB A:GLN61 4.2 12.4 1.0
C A:GLN61 4.3 9.8 1.0
H A:GLN61 4.4 12.2 1.0
O A:HOH2078 4.4 16.3 1.0
HB3 A:GLN61 4.5 14.9 1.0
OD2 A:ASP57 4.7 10.8 1.0
CB A:ASP59 4.7 11.9 1.0
O A:HOH2183 4.7 24.0 1.0
O A:HOH2086 4.7 30.0 1.0
H A:PHE63 4.7 12.7 1.0
OD1 A:ASP57 4.7 10.6 1.0
CA A:GLN61 4.8 10.7 1.0
HB3 A:ASP59 4.9 14.2 1.0
H A:ASP59 4.9 13.0 1.0

Calcium binding site 4 out of 5 in 5fsj

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Calcium binding site 4 out of 5 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen 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 45 Bar of Oxygen Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1009

b:10.6
occ:1.00
 O A:GLU187 2.3 11.1 1.0
OD2 A:ASP138 2.4 10.9 1.0
O A:HOH2318 2.4 11.8 1.0
OD1 A:ASP185 2.5 11.7 1.0
OE2 A:GLU190 2.5 11.5 1.0
OE1 A:GLU177 2.5 11.4 1.0
OE1 A:GLU190 2.5 11.5 1.0
OE2 A:GLU177 2.7 12.4 1.0
CD A:GLU190 2.8 10.7 1.0
CD A:GLU177 2.9 10.4 1.0
CG A:ASP138 3.4 10.5 1.0
C A:GLU187 3.4 11.5 1.0
CG A:ASP185 3.5 12.3 1.0
HB3 A:ASP138 3.6 11.5 1.0
HA A:ILE188 3.7 12.1 1.0
H A:GLU187 3.7 14.1 1.0
CA A:CA1004 3.8 12.2 0.7
H A:GLY189 3.8 12.3 1.0
OD2 A:ASP185 3.8 14.2 1.0
HB2 A:GLU187 3.8 17.6 1.0
CB A:ASP138 4.0 9.6 1.0
O A:ASP185 4.1 11.8 1.0
H A:ASP185 4.1 14.1 1.0
H A:GLU190 4.2 12.8 1.0
N A:GLU187 4.2 11.7 1.0
N A:ILE188 4.2 11.0 1.0
O A:HOH2316 4.2 26.4 1.0
OD1 A:ASP138 4.3 12.4 1.0
HB2 A:ASP138 4.3 11.5 1.0
CA A:GLU187 4.3 12.4 1.0
HD11 A:ILE188 4.3 16.7 1.0
CG A:GLU190 4.3 12.2 1.0
CA A:ILE188 4.3 10.1 1.0
O A:HOH2317 4.4 17.8 1.0
CG A:GLU177 4.4 10.9 1.0
N A:GLY189 4.4 10.2 1.0
CB A:GLU187 4.5 14.7 1.0
C A:ASP185 4.5 11.3 1.0
HG3 A:GLU190 4.6 14.7 1.0
HB2 A:GLU177 4.7 12.6 1.0
N A:ASP185 4.7 11.8 1.0
O A:HOH2353 4.8 23.0 1.0
CB A:ASP185 4.8 12.0 1.0
HB3 A:GLU177 4.8 12.6 1.0
HG2 A:GLU190 4.8 14.7 1.0
HG2 A:GLU177 4.8 13.1 1.0
C A:ILE188 4.8 10.4 1.0
HA A:THR174 4.9 10.9 1.0
HG3 A:GLU177 4.9 13.1 1.0
CB A:GLU177 4.9 10.4 1.0
CA A:ASP185 4.9 12.4 1.0
HB3 A:GLU187 5.0 17.6 1.0
HB3 A:GLU190 5.0 14.4 1.0
N A:GLU190 5.0 10.6 1.0

Calcium binding site 5 out of 5 in 5fsj

Go back to Calcium Binding Sites List in 5fsj
Calcium binding site 5 out of 5 in the Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Thermolysin Prepared By the 'Soak-and-Freeze' Method Under 45 Bar of Oxygen Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1010

b:10.8
occ:1.00
 O A:GLN61 2.3 10.8 1.0
O A:HOH2171 2.3 13.8 1.0
OD2 A:ASP57 2.4 10.8 1.0
CA A:CA1005 2.4 22.4 0.7
OD1 A:ASP59 2.4 11.5 1.0
O A:HOH2172 2.4 11.7 1.0
OD1 A:ASP57 2.6 10.6 1.0
CG A:ASP57 2.8 10.4 1.0
H A:GLN61 3.3 12.2 1.0
CG A:ASP59 3.4 11.8 1.0
C A:GLN61 3.4 9.8 1.0
H A:ASP59 3.5 13.0 1.0
HB2 A:GLN61 3.6 14.9 1.0
OD2 A:ASP59 3.8 15.9 1.0
N A:GLN61 4.0 10.2 1.0
O A:HOH2179 4.0 17.2 1.0
HA A:PHE62 4.0 11.0 1.0
CA A:GLN61 4.1 10.7 1.0
H A:ALA58 4.3 12.5 1.0
CB A:ASP57 4.3 10.6 1.0
N A:ASP59 4.3 10.8 1.0
CB A:GLN61 4.3 12.4 1.0
H A:ASN60 4.4 12.3 1.0
O A:HOH2174 4.5 14.5 1.0
N A:PHE62 4.5 9.3 1.0
O A:HOH2078 4.5 16.3 1.0
CB A:ASP59 4.6 11.9 1.0
OD2 A:ASP67 4.6 10.5 1.0
N A:ASN60 4.7 10.2 1.0
O A:HOH2167 4.7 10.5 1.0
O A:HOH2077 4.7 33.4 1.0
HB2 A:ASP57 4.7 12.7 1.0
O A:HOH2545 4.7 27.8 1.0
N A:ALA58 4.7 10.4 1.0
CA A:PHE62 4.8 9.2 1.0
HB3 A:ASP57 4.8 12.7 1.0
CA A:ASP59 4.8 11.4 1.0
H A:PHE63 4.8 12.7 1.0
HA A:ASP57 4.9 11.8 1.0
C A:ASP59 4.9 10.9 1.0
HB3 A:GLN61 4.9 14.9 1.0
HB3 A:ASP59 5.0 14.2 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 19:19:25 2024

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