Calcium in PDB 6sc1: Thermolysin in Complex with Fragment J96

Enzymatic activity of Thermolysin in Complex with Fragment J96

All present enzymatic activity of Thermolysin in Complex with Fragment J96:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with Fragment J96, PDB code: 6sc1 was solved by F.Magari, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.56
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.797, 92.797, 129.056, 90.00, 90.00, 120.00
R / Rfree (%) 15.1 / 17.5

Other elements in 6sc1:

The structure of Thermolysin in Complex with Fragment J96 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermolysin in Complex with Fragment J96 (pdb code 6sc1). 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 Complex with Fragment J96, PDB code: 6sc1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6sc1

Go back to Calcium Binding Sites List in 6sc1
Calcium binding site 1 out of 4 in the Thermolysin in Complex with Fragment J96


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermolysin in Complex with Fragment J96 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:15.2
occ:1.00
O E:GLN61 2.2 15.7 1.0
O E:HOH678 2.4 17.9 1.0
OD1 E:ASP57 2.4 15.4 1.0
O E:HOH591 2.4 16.9 1.0
OD1 E:ASP59 2.4 16.2 1.0
O E:HOH571 2.4 19.5 1.0
OD2 E:ASP57 2.6 14.2 1.0
CG E:ASP57 2.8 15.4 1.0
H E:GLN61 3.3 18.6 1.0
CG E:ASP59 3.4 19.6 1.0
C E:GLN61 3.4 14.1 1.0
H E:ASP59 3.5 20.4 1.0
HB2 E:GLN61 3.7 20.8 1.0
OD2 E:ASP59 3.8 21.3 1.0
O E:HOH629 4.0 22.5 1.0
N E:GLN61 4.0 15.5 1.0
HA E:PHE62 4.0 17.9 1.0
CA E:GLN61 4.2 14.0 1.0
H E:ALA58 4.3 19.1 1.0
CB E:ASP57 4.3 13.1 1.0
N E:ASP59 4.3 17.0 1.0
H E:ASN60 4.4 16.5 1.0
CB E:GLN61 4.4 17.3 1.0
O E:HOH711 4.4 35.8 1.0
N E:PHE62 4.5 12.6 1.0
O E:HOH615 4.5 17.2 1.0
OD2 E:ASP67 4.6 14.6 1.0
CB E:ASP59 4.6 17.4 1.0
O E:HOH531 4.7 14.4 1.0
N E:ASN60 4.7 13.8 1.0
HB2 E:ASP57 4.7 15.7 1.0
CA E:PHE62 4.7 14.9 1.0
N E:ALA58 4.7 15.9 1.0
HB3 E:ASP57 4.7 15.7 1.0
H E:PHE63 4.8 19.5 1.0
CA E:ASP59 4.8 14.4 1.0
O E:HOH703 4.8 32.2 1.0
HB3 E:GLN61 4.8 20.8 1.0
HA E:ASP57 4.9 18.6 1.0
C E:ASP59 4.9 14.6 1.0

Calcium binding site 2 out of 4 in 6sc1

Go back to Calcium Binding Sites List in 6sc1
Calcium binding site 2 out of 4 in the Thermolysin in Complex with Fragment J96


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermolysin in Complex with Fragment J96 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca403

b:16.9
occ:1.00
O E:ASN183 2.3 18.7 1.0
OE2 E:GLU190 2.3 17.1 1.0
O E:HOH552 2.3 17.7 1.0
OD2 E:ASP185 2.4 18.8 1.0
OE2 E:GLU177 2.4 14.8 1.0
O E:HOH540 2.4 20.4 1.0
CG E:ASP185 3.2 15.2 1.0
CD E:GLU177 3.3 13.4 1.0
CD E:GLU190 3.3 16.8 1.0
C E:ASN183 3.4 21.0 1.0
HG3 E:GLU190 3.5 20.6 1.0
HA E:PRO184 3.6 23.1 1.0
OD1 E:ASP185 3.6 15.9 1.0
HB2 E:ASN183 3.7 24.1 1.0
HG2 E:GLU190 3.7 20.6 1.0
HB3 E:ASN183 3.8 24.1 1.0
CG E:GLU190 3.8 17.2 1.0
OE1 E:GLU177 3.8 14.3 1.0
CA E:CA405 3.8 14.4 1.0
H E:ASP185 4.0 20.5 1.0
CB E:ASN183 4.1 20.1 1.0
OD2 E:ASP191 4.1 20.3 1.0
N E:ASP185 4.1 17.1 1.0
CA E:PRO184 4.1 19.2 1.0
HG2 E:GLU177 4.2 17.1 1.0
OD1 E:ASP191 4.2 20.3 1.0
C E:PRO184 4.2 18.6 1.0
CG E:GLU177 4.3 14.2 1.0
N E:PRO184 4.3 20.8 1.0
OE1 E:GLU190 4.3 15.5 1.0
O E:LYS182 4.3 20.0 1.0
HB3 E:ASP185 4.3 19.2 1.0
HG3 E:GLU177 4.4 17.1 1.0
CB E:ASP185 4.4 16.0 1.0
CA E:ASN183 4.4 19.4 1.0
O E:HOH537 4.4 31.3 1.0
CG E:ASP191 4.5 17.4 1.0
CA E:ASP185 4.9 17.3 1.0
O E:PRO184 4.9 20.5 1.0

Calcium binding site 3 out of 4 in 6sc1

Go back to Calcium Binding Sites List in 6sc1
Calcium binding site 3 out of 4 in the Thermolysin in Complex with Fragment J96


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermolysin in Complex with Fragment J96 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca404

b:18.2
occ:1.00
O E:ILE197 2.2 17.9 1.0
O E:TYR193 2.3 15.9 1.0
O E:HOH662 2.4 26.2 1.0
OD1 E:ASP200 2.4 19.5 1.0
O E:HOH562 2.4 18.9 1.0
OG1 E:THR194 2.4 20.1 1.0
O E:THR194 2.4 19.8 1.0
C E:THR194 3.2 21.4 1.0
C E:TYR193 3.4 17.0 1.0
CB E:THR194 3.4 19.5 1.0
C E:ILE197 3.4 22.1 1.0
CG E:ASP200 3.4 19.8 1.0
HB E:ILE197 3.5 39.9 1.0
H E:ILE197 3.6 30.5 1.0
HB E:THR194 3.6 23.4 1.0
CA E:THR194 3.7 18.0 1.0
OD2 E:ASP200 3.8 22.1 1.0
H E:ASP200 3.8 24.2 1.0
N E:THR194 3.9 17.2 1.0
HA E:SER198 4.1 28.8 1.0
HD2 E:TYR193 4.1 22.3 1.0
HB3 E:TYR193 4.1 22.5 1.0
CA E:ILE197 4.2 23.3 1.0
N E:ILE197 4.2 25.4 1.0
CB E:ILE197 4.3 33.3 1.0
N E:PRO195 4.3 18.9 1.0
HA E:PRO195 4.4 25.1 1.0
HG22 E:ILE197 4.4 31.2 1.0
N E:SER198 4.5 23.7 1.0
O E:ASP200 4.5 21.3 1.0
CA E:TYR193 4.6 18.8 1.0
HA E:THR194 4.6 21.6 1.0
N E:ASP200 4.6 20.2 1.0
H E:GLY199 4.6 27.9 1.0
CA E:SER198 4.6 24.0 1.0
CD2 E:TYR193 4.6 18.6 1.0
O E:GLU190 4.7 19.0 1.0
CA E:PRO195 4.7 20.9 1.0
CG2 E:THR194 4.7 19.2 1.0
CB E:TYR193 4.7 18.8 1.0
H E:THR194 4.7 20.6 1.0
CB E:ASP200 4.8 19.6 1.0
C E:ASP200 4.8 19.3 1.0
HG23 E:THR194 4.9 23.0 1.0
CG2 E:ILE197 4.9 26.0 1.0
N E:GLY199 4.9 23.2 1.0
C E:SER198 4.9 23.2 1.0
H E:TYR193 5.0 17.5 1.0
HG21 E:THR194 5.0 23.0 1.0
C E:PRO195 5.0 25.1 1.0
CA E:ASP200 5.0 18.5 1.0

Calcium binding site 4 out of 4 in 6sc1

Go back to Calcium Binding Sites List in 6sc1
Calcium binding site 4 out of 4 in the Thermolysin in Complex with Fragment J96


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermolysin in Complex with Fragment J96 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca405

b:14.4
occ:1.00
O E:GLU187 2.3 17.6 1.0
OD1 E:ASP138 2.4 13.8 1.0
OD1 E:ASP185 2.4 15.9 1.0
O E:HOH550 2.4 16.1 1.0
OE1 E:GLU177 2.5 14.3 1.0
OE2 E:GLU190 2.5 17.1 1.0
OE1 E:GLU190 2.5 15.5 1.0
OE2 E:GLU177 2.8 14.8 1.0
CD E:GLU190 2.9 16.8 1.0
CD E:GLU177 2.9 13.4 1.0
C E:GLU187 3.4 15.1 1.0
CG E:ASP138 3.4 17.7 1.0
CG E:ASP185 3.5 15.2 1.0
HB3 E:ASP138 3.6 16.8 1.0
HA E:ILE188 3.6 18.9 1.0
H E:GLU187 3.7 21.1 1.0
H E:GLY189 3.8 17.4 1.0
CA E:CA403 3.8 16.9 1.0
OD2 E:ASP185 3.8 18.8 1.0
CB E:ASP138 4.0 14.0 1.0
O E:HOH537 4.1 31.3 1.0
O E:ASP185 4.2 16.6 1.0
H E:ASP185 4.2 20.5 1.0
N E:GLU187 4.2 17.6 1.0
H E:GLU190 4.2 17.0 1.0
HB2 E:GLU187 4.2 23.3 1.0
HD13 E:ILE188 4.2 26.6 1.0
N E:ILE188 4.2 15.3 1.0
HB2 E:ASP138 4.2 16.8 1.0
OD2 E:ASP138 4.3 17.6 1.0
CA E:ILE188 4.3 15.8 1.0
CA E:GLU187 4.3 18.4 1.0
CG E:GLU190 4.3 17.2 1.0
CG E:GLU177 4.4 14.2 1.0
N E:GLY189 4.5 14.5 1.0
O E:HOH559 4.5 18.7 1.0
C E:ASP185 4.6 16.1 1.0
HG3 E:GLU190 4.6 20.6 1.0
HB2 E:GLU177 4.7 19.3 1.0
CB E:ASP185 4.8 16.0 1.0
N E:ASP185 4.8 17.1 1.0
CB E:GLU187 4.8 19.4 1.0
HG2 E:GLU190 4.8 20.6 1.0
C E:ILE188 4.8 15.7 1.0
HB3 E:GLU177 4.8 19.3 1.0
HG2 E:GLU177 4.9 17.1 1.0
HA E:THR174 4.9 15.8 1.0
HG3 E:GLU177 4.9 17.1 1.0
CB E:GLU177 4.9 16.1 1.0
HB3 E:GLU190 5.0 20.0 1.0
CA E:ASP185 5.0 17.3 1.0
H E:ILE188 5.0 18.3 1.0
N E:GLU190 5.0 14.2 1.0

Reference:

F.Magari, A.Heine, G.Klebe. Thermolysin in Complex with Fragment J96 To Be Published.
Page generated: Sat Dec 12 07:33:24 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy