Calcium in PDB 5a3y: Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection

Enzymatic activity of Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection

All present enzymatic activity of Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection:
3.4.24.27;

Protein crystallography data

The structure of Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection, PDB code: 5a3y was solved by U.Zander, G.Bourenkov, A.N.Popov, D.De Sanctis, A.A.Mccarthy, O.Svensson, E.S.Round, V.I.Gordeliy, C.Mueller-Dieckmann, G.A.Leonard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.27
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.874, 92.874, 129.167, 90.00, 90.00, 120.00
R / Rfree (%) 14.3 / 16.6

Other elements in 5a3y:

The structure of Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection (pdb code 5a3y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection, PDB code: 5a3y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5a3y

Go back to Calcium Binding Sites List in 5a3y
Calcium binding site 1 out of 4 in the Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1318

b:13.7
occ:1.00
 O A:GLU187 2.3 13.4 1.0
OD2 A:ASP138 2.4 13.0 1.0
OD1 A:ASP185 2.4 14.9 1.0
O A:HOH2188 2.4 14.8 1.0
OE1 A:GLU177 2.5 13.8 1.0
OE2 A:GLU190 2.5 13.8 1.0
OE1 A:GLU190 2.5 13.5 1.0
OE2 A:GLU177 2.7 14.5 1.0
CD A:GLU190 2.8 13.4 1.0
CD A:GLU177 2.9 13.7 1.0
CG A:ASP138 3.4 12.8 1.0
C A:GLU187 3.4 13.7 1.0
CG A:ASP185 3.4 15.3 1.0
OD2 A:ASP185 3.8 16.0 1.0
CA A:CA1319 3.8 16.4 1.0
CB A:ASP138 4.0 12.2 1.0
O A:ASP185 4.1 14.6 1.0
N A:GLU187 4.2 14.7 1.0
N A:ILE188 4.3 12.7 1.0
CA A:GLU187 4.3 14.2 1.0
OD1 A:ASP138 4.3 16.2 1.0
CG A:GLU190 4.3 14.1 1.0
O A:HOH2186 4.3 27.9 1.0
CA A:ILE188 4.3 13.2 1.0
CG A:GLU177 4.4 13.9 1.0
O A:HOH2187 4.4 20.7 1.0
N A:GLY189 4.4 12.9 1.0
CB A:GLU187 4.6 16.1 1.0
C A:ASP185 4.6 14.0 1.0
CB A:ASP185 4.7 14.7 1.0
N A:ASP185 4.7 14.6 1.0
C A:ILE188 4.8 12.7 1.0
CB A:GLU177 4.9 13.2 1.0
O A:HOH2211 4.9 20.0 1.0
CA A:ASP185 5.0 14.2 1.0
N A:GLU190 5.0 13.2 1.0

Calcium binding site 2 out of 4 in 5a3y

Go back to Calcium Binding Sites List in 5a3y
Calcium binding site 2 out of 4 in the Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1319

b:16.4
occ:1.00
 O A:ASN183 2.2 17.6 1.0
O A:HOH2214 2.3 20.2 1.0
OD2 A:ASP185 2.3 16.0 1.0
OE2 A:GLU190 2.3 13.8 1.0
O A:HOH2211 2.3 20.0 1.0
OE2 A:GLU177 2.4 14.5 1.0
CG A:ASP185 3.2 15.3 1.0
CD A:GLU177 3.2 13.7 1.0
CD A:GLU190 3.3 13.4 1.0
C A:ASN183 3.4 17.7 1.0
OD1 A:ASP185 3.6 14.9 1.0
OE1 A:GLU177 3.7 13.8 1.0
CG A:GLU190 3.8 14.1 1.0
CA A:CA1318 3.8 13.7 1.0
CB A:ASN183 4.1 21.8 1.0
CA A:PRO184 4.1 14.9 1.0
N A:ASP185 4.2 14.6 1.0
OD2 A:ASP191 4.2 20.5 1.0
OD1 A:ASP191 4.2 19.5 1.0
C A:PRO184 4.2 16.1 1.0
CG A:GLU177 4.2 13.9 1.0
N A:PRO184 4.3 15.7 1.0
OE1 A:GLU190 4.3 13.5 1.0
CB A:ASP185 4.4 14.7 1.0
O A:LYS182 4.4 22.5 1.0
CA A:ASN183 4.4 19.7 1.0
CG A:ASP191 4.5 17.3 1.0
O A:HOH2186 4.5 27.9 1.0
O A:HOH2099 4.6 30.5 1.0
CA A:ASP185 4.9 14.2 1.0
O A:PRO184 4.9 18.0 1.0

Calcium binding site 3 out of 4 in 5a3y

Go back to Calcium Binding Sites List in 5a3y
Calcium binding site 3 out of 4 in the Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1320

b:15.3
occ:1.00
 O A:GLN61 2.3 14.1 1.0
O A:HOH2095 2.4 16.6 1.0
O A:HOH2096 2.4 18.3 1.0
OD1 A:ASP59 2.4 16.4 1.0
OD1 A:ASP57 2.4 15.2 1.0
OD2 A:ASP57 2.6 14.8 1.0
CG A:ASP57 2.8 14.0 1.0
CG A:ASP59 3.4 16.2 1.0
C A:GLN61 3.5 13.1 1.0
OD2 A:ASP59 3.8 19.4 1.0
O A:HOH2098 3.9 20.9 1.0
N A:GLN61 4.0 13.7 1.0
CA A:GLN61 4.2 14.0 1.0
N A:ASP59 4.3 16.1 1.0
CB A:GLN61 4.4 17.0 1.0
CB A:ASP57 4.4 14.7 1.0
O A:HOH2042 4.5 19.8 1.0
N A:PHE62 4.5 11.8 1.0
OD2 A:ASP67 4.6 14.8 1.0
CB A:ASP59 4.6 16.1 1.0
O A:HOH2043 4.7 27.7 1.0
O A:HOH2091 4.7 15.5 1.0
N A:ASN60 4.7 15.2 1.0
N A:ALA58 4.7 15.4 1.0
CA A:PHE62 4.8 12.2 1.0
CA A:ASP59 4.8 15.5 1.0
C A:ASP59 4.9 15.8 1.0

Calcium binding site 4 out of 4 in 5a3y

Go back to Calcium Binding Sites List in 5a3y
Calcium binding site 4 out of 4 in the Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Sad Structure of Thermolysin Obtained By Multi Crystal Data Collection within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1321

b:18.6
occ:1.00
 O A:ILE197 2.3 22.0 1.0
O A:TYR193 2.3 16.2 1.0
OD1 A:ASP200 2.4 18.5 1.0
O A:HOH2222 2.4 26.6 1.0
O A:HOH2220 2.4 18.1 1.0
O A:THR194 2.4 18.9 1.0
OG1 A:THR194 2.4 18.6 1.0
C A:THR194 3.2 18.1 1.0
C A:TYR193 3.4 15.6 1.0
CG A:ASP200 3.4 18.6 1.0
CB A:THR194 3.5 18.6 1.0
C A:ILE197 3.5 23.9 1.0
CA A:THR194 3.7 17.1 1.0
OD2 A:ASP200 3.8 19.6 1.0
N A:THR194 3.9 16.1 1.0
CA A:ILE197 4.2 25.8 1.0
CB A:ILE197 4.2 27.2 1.0
N A:ILE197 4.3 25.1 1.0
N A:PRO195 4.3 19.8 1.0
O A:HOH2225 4.4 36.4 1.0
O A:ASP200 4.4 16.9 1.0
N A:SER198 4.5 22.2 1.0
CA A:TYR193 4.6 15.5 1.0
O A:GLU190 4.6 15.2 1.0
N A:ASP200 4.6 19.4 1.0
CA A:PRO195 4.7 21.1 1.0
CB A:TYR193 4.7 16.8 1.0
CD2 A:TYR193 4.7 18.5 1.0
CB A:ASP200 4.7 17.9 1.0
CA A:SER198 4.7 24.8 1.0
CG2 A:THR194 4.8 20.0 1.0
CG2 A:ILE197 4.8 27.1 1.0
O A:HOH2221 4.8 30.4 1.0
C A:ASP200 4.8 16.8 1.0
CA A:ASP200 5.0 18.2 1.0
C A:PRO195 5.0 23.3 1.0

Reference:

U.Zander, G.Bourenkov, A.N.Popov, D.De Sanctis, O.Svensson, A.A.Mccarthy, E.Round, V.Gordeliy, C.Mueller-Dieckmann, G.A.Leonard. Meshandcollect: An Automated Multi-Crystal Data-Collection Workflow For Synchrotron Macromolecular Crystallography Beamlines. Acta Crystallogr.,Sect.D V. 71 2328 2015.
ISSN: ISSN 0907-4449
PubMed: 26527148
DOI: 10.1107/S1399004715017927
Page generated: Sun Jul 14 16:18:55 2024

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