Atomistry » Calcium » PDB 5fk0-5g38 » 5fss
Atomistry »
  Calcium »
    PDB 5fk0-5g38 »
      5fss »

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

Go back to Calcium Binding Sites List in 5fss
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy