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Zinc in PDB 3n21: Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol

Enzymatic activity of Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol

All present enzymatic activity of Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol:
3.4.24.27;

Protein crystallography data

The structure of Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol, PDB code: 3n21 was solved by J.Behnen, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.87
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.138, 93.138, 128.620, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 23.2

Other elements in 3n21:

The structure of Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol (pdb code 3n21). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol, PDB code: 3n21:

Zinc binding site 1 out of 1 in 3n21

Go back to Zinc Binding Sites List in 3n21
Zinc binding site 1 out of 1 in the Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Thermolysin in Complex with S-1,2-Propandiol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:19.1
occ:1.00
 O A:HOH1180 2.0 32.4 1.0
OE1 A:GLU166 2.0 17.7 1.0
NE2 A:HIS146 2.0 15.7 1.0
NE2 A:HIS142 2.1 15.7 1.0
O A:HOH1052 2.4 33.1 1.0
CD A:GLU166 2.8 19.4 1.0
CE1 A:HIS146 2.9 18.0 1.0
CD2 A:HIS142 3.0 16.2 1.0
OE2 A:GLU166 3.0 22.6 1.0
CD2 A:HIS146 3.1 14.8 1.0
CE1 A:HIS142 3.1 18.8 1.0
OE2 A:GLU143 3.7 25.2 1.0
OH A:TYR157 3.9 23.9 1.0
ND1 A:HIS146 4.0 21.7 1.0
CG A:HIS142 4.1 17.1 1.0
NE2 A:HIS231 4.2 19.4 1.0
ND1 A:HIS142 4.2 18.3 1.0
CG A:HIS146 4.2 20.3 1.0
CG A:GLU166 4.2 19.9 1.0
O1 A:PGO601 4.4 28.1 0.5
CD A:GLU143 4.4 20.1 1.0
OE1 A:GLU143 4.5 22.3 1.0
CB A:SER169 4.6 16.3 1.0
OG A:SER169 4.7 19.4 1.0
CD2 A:HIS231 4.8 22.1 1.0
CZ A:TYR157 4.8 29.6 1.0
O A:HOH1183 4.9 30.5 1.0
CA A:GLU166 4.9 16.8 1.0
CE2 A:TYR157 5.0 28.3 1.0

Reference:

J.Behnen, H.Koster, G.Neudert, T.Craan, A.Heine, G.Klebe. Experimental and Computational Active Site Mapping As A Starting Point to Fragment-Based Lead Discovery. Chemmedchem V. 7 248 2012.
ISSN: ISSN 1860-7179
PubMed: 22213702
DOI: 10.1002/CMDC.201100490
Page generated: Wed Aug 20 12:03:38 2025

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