Calcium in PDB 1l3f: Thermolysin in the Absence of Substrate Has An Open Conformation

Enzymatic activity of Thermolysin in the Absence of Substrate Has An Open Conformation

All present enzymatic activity of Thermolysin in the Absence of Substrate Has An Open Conformation:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in the Absence of Substrate Has An Open Conformation, PDB code: 1l3f was solved by A.C.Hausrath, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 97.052, 97.052, 106.583, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 30.2

Other elements in 1l3f:

The structure of Thermolysin in the Absence of Substrate Has An Open Conformation also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin in the Absence of Substrate Has An Open Conformation (pdb code 1l3f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Thermolysin in the Absence of Substrate Has An Open Conformation, PDB code: 1l3f:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1l3f

Go back to Calcium Binding Sites List in 1l3f
Calcium binding site 1 out of 4 in the Thermolysin in the Absence of Substrate Has An Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin in the Absence of Substrate Has An Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca317

b:59.7
occ:1.00
O E:GLU187 2.1 58.2 1.0
OE1 E:GLU177 2.1 67.0 1.0
O E:HOH346 2.2 52.2 1.0
OE1 E:GLU190 2.3 50.1 1.0
OD1 E:ASP185 2.3 62.1 1.0
OD2 E:ASP138 2.4 70.8 1.0
OE2 E:GLU190 2.5 40.7 1.0
CD E:GLU190 2.7 60.2 1.0
CD E:GLU177 2.7 58.2 1.0
OE2 E:GLU177 2.9 60.4 1.0
C E:GLU187 3.2 76.5 1.0
CG E:ASP185 3.2 63.5 1.0
CG E:ASP138 3.2 61.5 1.0
CA E:CA318 3.5 53.0 1.0
OD2 E:ASP185 3.6 51.3 1.0
OD1 E:ASP138 3.9 69.3 1.0
CB E:ASP138 4.0 68.9 1.0
N E:GLU187 4.1 61.8 1.0
CG E:GLU190 4.1 51.4 1.0
CA E:GLU187 4.2 66.6 1.0
N E:ILE188 4.2 60.8 1.0
O E:ASP185 4.2 61.2 1.0
CG E:GLU177 4.2 64.0 1.0
O E:HOH353 4.2 49.5 1.0
CA E:ILE188 4.3 57.5 1.0
O E:HOH718 4.4 63.1 1.0
C E:ASP185 4.5 64.5 1.0
CB E:ASP185 4.5 52.2 1.0
CB E:GLU187 4.6 68.8 1.0
N E:GLY189 4.6 58.4 1.0
O E:HOH475 4.7 43.3 1.0
N E:ASP185 4.7 58.6 1.0
CB E:GLU177 4.8 66.2 1.0
CB E:GLU190 4.8 64.1 1.0
OG1 E:THR174 4.8 61.8 1.0
C E:ILE188 4.8 53.9 1.0
N E:GLU190 4.9 62.6 1.0
CA E:ASP185 4.9 54.2 1.0

Calcium binding site 2 out of 4 in 1l3f

Go back to Calcium Binding Sites List in 1l3f
Calcium binding site 2 out of 4 in the Thermolysin in the Absence of Substrate Has An Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin in the Absence of Substrate Has An Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:53.0
occ:1.00
O E:HOH475 1.6 43.3 1.0
OE2 E:GLU190 1.6 40.7 1.0
OD2 E:ASP185 1.7 51.3 1.0
O E:HOH353 1.8 49.5 1.0
O E:ASN183 1.9 61.0 1.0
OE2 E:GLU177 1.9 60.4 1.0
CG E:ASP185 2.7 63.5 1.0
CD E:GLU177 2.8 58.2 1.0
CD E:GLU190 2.8 60.2 1.0
C E:ASN183 3.1 65.3 1.0
OE1 E:GLU177 3.2 67.0 1.0
OD1 E:ASP185 3.2 62.1 1.0
CG E:GLU190 3.4 51.4 1.0
ND2 E:ASN183 3.4 97.7 1.0
CA E:CA317 3.5 59.7 1.0
OD1 E:ASP191 3.6 91.4 1.0
OE1 E:GLU190 3.8 50.1 1.0
C E:PRO184 3.8 66.3 1.0
CB E:ASP185 3.8 52.2 1.0
CG E:GLU177 3.8 64.0 1.0
CA E:PRO184 3.9 62.5 1.0
CG E:ASN183 3.9 0.0 1.0
N E:PRO184 3.9 59.6 1.0
OD2 E:ASP191 4.0 69.6 1.0
CB E:ASN183 4.1 83.9 1.0
N E:ASP185 4.1 58.6 1.0
CG E:ASP191 4.1 79.7 1.0
O E:PRO184 4.2 67.5 1.0
CA E:ASN183 4.2 60.5 1.0
CA E:ASP185 4.7 54.2 1.0
OD1 E:ASN183 4.7 0.0 1.0
CB E:GLU190 4.8 64.1 1.0
O E:HOH346 4.8 52.2 1.0
O E:LYS182 4.8 0.0 1.0
O E:HOH718 4.9 63.1 1.0

Calcium binding site 3 out of 4 in 1l3f

Go back to Calcium Binding Sites List in 1l3f
Calcium binding site 3 out of 4 in the Thermolysin in the Absence of Substrate Has An Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin in the Absence of Substrate Has An Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:81.9
occ:1.00
O E:HOH510 1.9 81.3 1.0
OD1 E:ASP59 2.1 87.1 1.0
O E:GLN61 2.2 83.0 1.0
OD1 E:ASP57 2.3 57.1 1.0
O E:HOH419 2.3 73.0 1.0
O E:HOH482 2.9 90.4 1.0
CG E:ASP57 2.9 55.8 1.0
CG E:ASP59 2.9 79.0 1.0
OD2 E:ASP57 3.0 57.8 1.0
C E:GLN61 3.3 78.6 1.0
OD2 E:ASP59 3.4 76.2 1.0
O E:HOH484 3.7 94.5 1.0
N E:ASP59 3.9 82.1 1.0
N E:GLN61 3.9 69.9 1.0
CA E:GLN61 4.0 69.4 1.0
O E:HOH628 4.1 0.0 1.0
O E:HOH356 4.1 89.1 1.0
CB E:ASP59 4.2 66.0 1.0
CB E:GLN61 4.2 70.9 1.0
O E:HOH508 4.3 75.3 1.0
CB E:ASP57 4.4 64.2 1.0
N E:PHE62 4.4 71.3 1.0
CA E:ASP59 4.5 69.0 1.0
OD2 E:ASP67 4.7 63.7 1.0
N E:ALA58 4.7 74.8 1.0
CA E:PHE62 4.7 64.8 1.0
C E:ASP59 4.7 72.0 1.0
N E:ASN60 4.8 74.3 1.0
C E:ALA58 4.9 91.3 1.0

Calcium binding site 4 out of 4 in 1l3f

Go back to Calcium Binding Sites List in 1l3f
Calcium binding site 4 out of 4 in the Thermolysin in the Absence of Substrate Has An Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin in the Absence of Substrate Has An Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:73.0
occ:1.00
OD1 E:ASP200 2.0 89.4 1.0
O E:HOH354 2.1 73.1 1.0
OG1 E:THR194 2.3 57.4 1.0
O E:TYR193 2.4 75.3 1.0
O E:ILE197 2.4 82.0 1.0
O E:THR194 2.5 76.9 1.0
CG E:ASP200 3.0 69.4 1.0
C E:THR194 3.2 78.4 1.0
OD2 E:ASP200 3.3 73.2 1.0
C E:TYR193 3.4 68.0 1.0
CB E:THR194 3.5 77.4 1.0
C E:ILE197 3.5 78.6 1.0
CA E:THR194 3.8 71.9 1.0
O E:HOH800 3.8 74.1 1.0
N E:THR194 4.0 70.6 1.0
CB E:ILE197 4.1 65.1 1.0
O E:GLU190 4.2 79.8 1.0
N E:PRO195 4.2 83.2 1.0
O E:ASP200 4.2 73.4 1.0
CA E:ILE197 4.3 65.5 1.0
CB E:ASP200 4.4 59.7 1.0
N E:ILE197 4.5 71.8 1.0
N E:SER198 4.5 81.8 1.0
CD2 E:TYR193 4.5 82.7 1.0
CB E:TYR193 4.5 62.2 1.0
C E:ASP200 4.5 76.1 1.0
CA E:TYR193 4.6 58.9 1.0
CG2 E:ILE197 4.6 58.4 1.0
N E:ASP200 4.6 71.6 1.0
CA E:SER198 4.7 88.0 1.0
CA E:PRO195 4.7 88.8 1.0
CG2 E:THR194 4.7 72.7 1.0
CA E:ASP200 4.7 68.1 1.0
CG E:TYR193 4.8 72.2 1.0
C E:PRO195 4.8 97.2 1.0
C E:SER198 5.0 75.1 1.0

Reference:

A.C.Hausrath, B.W.Matthews. Thermolysin in the Absence of Substrate Has An Open Conformation. Acta Crystallogr.,Sect.D V. 58 1002 2002.
ISSN: ISSN 0907-4449
PubMed: 12037302
DOI: 10.1107/S090744490200584X
Page generated: Sat Dec 12 03:04:41 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy