Calcium in PDB 3t2h: Tetragonal Thermolysin in the Presence of Tmao

Enzymatic activity of Tetragonal Thermolysin in the Presence of Tmao

All present enzymatic activity of Tetragonal Thermolysin in the Presence of Tmao:
3.4.24.27;

Protein crystallography data

The structure of Tetragonal Thermolysin in the Presence of Tmao, PDB code: 3t2h was solved by J.Cahn, N.S.Hti Lar Seng, D.Juers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.17 / 1.95
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.892, 96.892, 105.549, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 18.3

Other elements in 3t2h:

The structure of Tetragonal Thermolysin in the Presence of Tmao also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Chlorine (Cl) 8 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Tetragonal Thermolysin in the Presence of Tmao (pdb code 3t2h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Tetragonal Thermolysin in the Presence of Tmao, PDB code: 3t2h:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3t2h

Go back to Calcium Binding Sites List in 3t2h
Calcium binding site 1 out of 4 in the Tetragonal Thermolysin in the Presence of Tmao


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tetragonal Thermolysin in the Presence of Tmao within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca317

b:9.1
occ:1.00
 O E:GLU187 2.3 9.2 1.0
OD2 E:ASP138 2.4 7.6 1.0
O E:HOH361 2.4 8.6 1.0
OD1 E:ASP185 2.5 10.1 1.0
OE1 E:GLU190 2.5 9.1 1.0
OE1 E:GLU177 2.5 10.3 1.0
OE2 E:GLU190 2.5 6.6 1.0
OE2 E:GLU177 2.8 11.6 1.0
CD E:GLU190 2.8 9.7 1.0
CD E:GLU177 3.0 10.9 1.0
CG E:ASP138 3.3 10.3 1.0
C E:GLU187 3.4 9.6 1.0
CG E:ASP185 3.5 12.0 1.0
CA E:CA318 3.6 2.8 1.0
OD2 E:ASP185 3.8 13.4 1.0
CB E:ASP138 3.9 7.7 1.0
N E:ILE188 4.2 8.9 1.0
O E:ASP185 4.2 9.9 1.0
CA E:ILE188 4.2 9.0 1.0
OD1 E:ASP138 4.3 9.8 1.0
N E:GLU187 4.3 9.8 1.0
CG E:GLU190 4.4 9.3 1.0
CA E:GLU187 4.4 10.9 1.0
N E:GLY189 4.4 8.8 1.0
CG E:GLU177 4.4 7.8 1.0
O E:HOH365 4.5 12.5 1.0
O E:HOH368 4.5 13.9 1.0
C E:ASP185 4.7 11.1 1.0
C E:ILE188 4.8 8.4 1.0
CB E:ASP185 4.8 11.8 1.0
N E:ASP185 4.8 11.6 1.0
CB E:GLU187 4.9 12.5 1.0
CB E:GLU177 4.9 7.1 1.0
OG1 E:THR174 5.0 6.4 1.0
N E:GLU190 5.0 10.1 1.0

Calcium binding site 2 out of 4 in 3t2h

Go back to Calcium Binding Sites List in 3t2h
Calcium binding site 2 out of 4 in the Tetragonal Thermolysin in the Presence of Tmao


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tetragonal Thermolysin in the Presence of Tmao within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:2.8
occ:1.00
 OE2 E:GLU190 2.0 6.6 1.0
OD2 E:ASP185 2.0 13.4 1.0
O E:HOH368 2.1 13.9 1.0
O E:HOH413 2.1 9.6 1.0
OE2 E:GLU177 2.2 11.6 1.0
O E:ASN183 2.3 14.8 1.0
CG E:ASP185 3.0 12.0 1.0
CD E:GLU177 3.0 10.9 1.0
CD E:GLU190 3.0 9.7 1.0
OD1 E:ASP185 3.4 10.1 1.0
C E:ASN183 3.5 13.9 1.0
OE1 E:GLU177 3.5 10.3 1.0
CA E:CA317 3.6 9.1 1.0
CG E:GLU190 3.7 9.3 1.0
O E:HOH546 3.8 25.5 1.0
OE1 E:GLU190 4.0 9.1 1.0
CA E:PRO184 4.0 12.7 1.0
OD2 E:ASP191 4.0 12.4 1.0
OD1 E:ASP191 4.0 13.2 1.0
CG E:GLU177 4.0 7.8 1.0
C E:PRO184 4.1 12.6 1.0
N E:ASP185 4.1 11.6 1.0
N E:PRO184 4.2 13.4 1.0
CB E:ASP185 4.3 11.8 1.0
ND2 E:ASN183 4.3 5.0 0.5
CG E:ASP191 4.4 13.7 1.0
CG E:ASN183 4.4 12.7 0.5
CB E:ASN183 4.4 15.2 0.5
CB E:ASN183 4.6 13.4 0.5
CA E:ASN183 4.6 15.4 0.5
O E:PRO184 4.6 12.7 1.0
CA E:ASN183 4.6 14.6 0.5
CA E:ASP185 4.9 11.1 1.0
OD1 E:ASN183 4.9 11.0 0.5

Calcium binding site 3 out of 4 in 3t2h

Go back to Calcium Binding Sites List in 3t2h
Calcium binding site 3 out of 4 in the Tetragonal Thermolysin in the Presence of Tmao


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tetragonal Thermolysin in the Presence of Tmao within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:12.7
occ:1.00
 O E:GLN61 2.3 10.7 1.0
O E:HOH424 2.3 12.4 1.0
O E:HOH399 2.4 12.8 1.0
OD1 E:ASP57 2.4 11.7 1.0
OD1 E:ASP59 2.4 14.4 1.0
O E:HOH419 2.4 16.8 1.0
OD2 E:ASP57 2.5 10.4 1.0
CG E:ASP57 2.8 9.7 1.0
CG E:ASP59 3.4 15.0 1.0
C E:GLN61 3.5 12.1 1.0
OD2 E:ASP59 3.8 13.8 1.0
N E:GLN61 4.0 12.8 1.0
O E:HOH420 4.0 19.8 1.0
CA E:GLN61 4.2 13.2 1.0
N E:ASP59 4.3 12.1 1.0
CB E:ASP57 4.3 8.9 1.0
CB E:GLN61 4.4 14.8 1.0
O E:HOH426 4.4 12.4 1.0
O E:HOH481 4.5 26.9 1.0
N E:PHE62 4.5 11.4 1.0
OD2 E:ASP67 4.6 11.5 1.0
O E:HOH456 4.6 17.7 1.0
N E:ASN60 4.6 13.2 1.0
CB E:ASP59 4.6 13.1 1.0
O E:HOH469 4.7 22.2 1.0
O E:HOH371 4.7 10.1 1.0
N E:ALA58 4.7 11.2 1.0
CA E:PHE62 4.8 11.6 1.0
CA E:ASP59 4.8 13.7 1.0
C E:ASP59 4.9 13.5 1.0

Calcium binding site 4 out of 4 in 3t2h

Go back to Calcium Binding Sites List in 3t2h
Calcium binding site 4 out of 4 in the Tetragonal Thermolysin in the Presence of Tmao


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tetragonal Thermolysin in the Presence of Tmao within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:17.5
occ:1.00
 O E:HOH418 2.1 17.8 1.0
OG1 E:THR194 2.1 14.5 1.0
OD1 E:ASP200 2.4 16.4 1.0
O E:TYR193 2.4 13.1 1.0
O E:HOH369 2.4 14.6 1.0
O E:ILE197 2.4 25.5 1.0
O E:THR194 2.4 17.2 1.0
C E:THR194 3.2 17.3 1.0
CB E:THR194 3.3 16.6 1.0
C E:TYR193 3.4 13.1 1.0
CG E:ASP200 3.5 15.5 1.0
C E:ILE197 3.6 26.4 1.0
CA E:THR194 3.7 15.6 1.0
OD2 E:ASP200 3.9 16.9 1.0
N E:THR194 4.0 14.7 1.0
CB E:ILE197 4.2 26.5 1.0
CA E:ILE197 4.2 26.3 1.0
N E:ILE197 4.3 26.6 1.0
N E:PRO195 4.3 18.3 1.0
O E:HOH492 4.5 33.2 1.0
O E:GLU190 4.5 12.7 1.0
CG2 E:THR194 4.6 14.5 1.0
O E:HOH414 4.6 22.9 1.0
O E:ASP200 4.6 14.8 1.0
CA E:TYR193 4.6 13.2 1.0
N E:ASP200 4.6 19.4 1.0
CA E:PRO195 4.7 19.9 1.0
N E:SER198 4.7 25.9 1.0
CB E:TYR193 4.7 13.8 1.0
CB E:ASP200 4.8 16.3 1.0
CD2 E:TYR193 4.8 20.4 1.0
C E:ASP200 4.8 15.7 1.0
CA E:ASP200 4.9 16.9 1.0
CG2 E:ILE197 4.9 25.8 1.0
C E:PRO195 4.9 21.6 1.0
CA E:SER198 5.0 26.9 1.0

Reference:

H.Marshall, M.Venkat, N.S.Hti Lar Seng, J.Cahn, D.H.Juers. The Use of Trimethylamine N-Oxide As A Primary Precipitating Agent and Related Methylamine Osmolytes As Cryoprotective Agents For Macromolecular Crystallography. Acta Crystallogr.,Sect.D V. 68 69 2012.
ISSN: ISSN 0907-4449
PubMed: 22194335
DOI: 10.1107/S0907444911050360
Page generated: Sat Dec 12 04:30:56 2020

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