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Zinc 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:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the Thermolysin in the Absence of Substrate Has An Open Conformation, PDB code: 1l3f:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1l3f

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn321

b:62.3
occ:1.00
OE2 E:GLU166 1.7 58.8 1.0
NE2 E:HIS146 1.9 68.9 1.0
NE2 E:HIS142 2.0 65.4 1.0
O E:HOH392 2.4 59.7 1.0
CD E:GLU166 2.7 57.3 1.0
CD2 E:HIS146 2.9 67.0 1.0
CE1 E:HIS142 2.9 64.0 1.0
ZN E:ZN322 2.9 64.4 0.5
OE1 E:GLU166 3.0 94.1 1.0
CE1 E:HIS146 3.0 68.5 1.0
OH E:TYR157 3.0 0.0 1.0
CD2 E:HIS142 3.0 66.7 1.0
OE2 E:GLU143 3.5 0.0 1.0
NE2 E:HIS231 4.0 76.9 1.0
CG E:GLU166 4.0 47.0 1.0
O E:HOH802 4.0 55.8 1.0
CG E:HIS146 4.1 66.4 1.0
ND1 E:HIS146 4.1 67.0 1.0
ND1 E:HIS142 4.1 53.2 1.0
CZ E:TYR157 4.1 0.0 1.0
CD E:GLU143 4.1 87.4 1.0
CG E:HIS142 4.2 54.3 1.0
OE1 E:GLU143 4.2 78.7 1.0
O E:HOH811 4.6 73.5 1.0
CE1 E:TYR157 4.6 0.0 1.0
O E:HOH814 4.6 67.6 1.0
OG E:SER169 4.7 58.2 1.0
CD2 E:HIS231 4.7 72.4 1.0
CB E:SER169 4.7 72.8 1.0
O E:HOH821 4.7 82.1 1.0
CA E:GLU166 4.8 55.5 1.0
CB E:GLU166 4.9 57.8 1.0
O E:HOH810 4.9 62.8 1.0
CE1 E:HIS231 5.0 81.3 1.0

Zinc binding site 2 out of 3 in 1l3f

Go back to Zinc Binding Sites List in 1l3f
Zinc binding site 2 out of 3 in the Thermolysin in the Absence of Substrate Has An Open Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn322

b:64.4
occ:0.50
NE2 E:HIS231 2.0 76.9 1.0
O E:HOH802 2.0 55.8 1.0
O E:HOH810 2.0 62.8 1.0
O E:HOH392 2.1 59.7 1.0
ZN E:ZN321 2.9 62.3 1.0
CE1 E:HIS231 3.0 81.3 1.0
O E:HOH811 3.0 73.5 1.0
CD2 E:HIS231 3.0 72.4 1.0
OH E:TYR157 3.3 0.0 1.0
OE1 E:GLU166 3.5 94.1 1.0
O E:HOH821 3.5 82.1 1.0
OE2 E:GLU166 3.6 58.8 1.0
OE2 E:GLU143 3.7 0.0 1.0
CD E:GLU166 3.8 57.3 1.0
O E:HOH814 3.9 67.6 1.0
NE2 E:HIS142 3.9 65.4 1.0
ND1 E:HIS231 4.1 71.1 1.0
CG E:HIS231 4.2 70.4 1.0
CE1 E:HIS142 4.5 64.0 1.0
CZ E:TYR157 4.7 0.0 1.0
NE2 E:HIS146 4.7 68.9 1.0
CD E:GLU143 4.8 87.4 1.0
CD2 E:HIS142 4.8 66.7 1.0
NH2 E:ARG203 4.8 69.9 1.0
CG E:GLU166 5.0 47.0 1.0

Zinc binding site 3 out of 3 in 1l3f

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn330

b:70.6
occ:1.00
ND1 E:HIS250 1.9 64.6 1.0
O E:HOH455 2.2 39.4 1.0
O E:HOH721 2.3 45.1 1.0
O E:HOH524 2.3 71.7 1.0
CE1 E:HIS250 2.6 61.0 1.0
CG E:HIS250 3.2 63.5 1.0
CE E:LYS239 3.5 0.0 1.0
CA E:HIS250 3.6 70.4 1.0
NZ E:LYS239 3.6 61.6 1.0
O E:THR249 3.7 94.4 1.0
CB E:HIS250 3.9 63.7 1.0
NE2 E:HIS250 3.9 54.6 1.0
CD2 E:HIS250 4.2 50.6 1.0
N E:TYR251 4.3 70.0 1.0
C E:THR249 4.5 76.7 1.0
C E:HIS250 4.5 70.4 1.0
N E:HIS250 4.5 68.7 1.0
CD E:LYS239 4.5 48.7 1.0
OD2 E:ASP215 4.5 79.2 1.0
O E:HOH714 4.7 68.2 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: Wed Dec 16 02:55:49 2020

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