Zinc in PDB 4hvl: Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System

The structure of Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System, PDB code: 4hvl was solved by K.V.Korotkov, T.J.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.92 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.950, 73.080, 75.420, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.6

The structure of Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System (pdb code 4hvl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System, PDB code: 4hvl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:20.3 occ:0.85 OE1 A:GLU203 2.0 23.2 1.0 OG1 A:THR156 2.1 21.6 1.0 ND1 A:HIS155 2.1 19.3 1.0 CL A:CL513 2.4 20.0 0.8 CE1 A:HIS155 3.0 19.5 1.0 CD A:GLU203 3.0 22.1 1.0 CB A:THR156 3.2 19.5 1.0 CG A:HIS155 3.3 17.8 1.0 CB A:GLU203 3.4 19.1 1.0 CG A:GLU203 3.5 20.3 1.0 CB A:HIS155 3.7 16.4 1.0 N A:THR156 3.7 17.0 1.0 C A:HIS155 3.7 17.2 1.0 O A:HOH654 3.8 31.1 1.0 CA A:THR156 3.9 18.4 1.0 O A:HIS155 4.0 18.2 1.0 CA A:GLU203 4.1 18.2 1.0 OE2 A:GLU203 4.1 24.4 1.0 NE2 A:HIS155 4.1 19.6 1.0 CD2 A:HIS155 4.3 18.6 1.0 CG2 A:THR156 4.3 20.6 1.0 CA A:HIS155 4.3 16.1 1.0 O A:HOH784 4.5 45.7 1.0 O A:HOH809 4.6 45.6 1.0 N A:GLU203 4.7 17.1 1.0 O A:HOH785 4.8 38.5 1.0 OG A:SER180 4.9 22.4 1.0

Zinc binding site 2 out of 7 in the Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:21.2 occ:1.00 OD1 A:ASP37 2.0 29.1 1.0 ND1 A:HIS190 2.1 19.8 1.0 N3 A:IMD508 2.2 20.7 1.0 N3 A:IMD509 2.2 24.1 1.0 OD2 A:ASP37 2.6 31.6 1.0 CG A:ASP37 2.6 28.8 1.0 CE1 A:HIS190 3.0 19.1 1.0 C4 A:IMD508 3.1 21.0 1.0 C2 A:IMD509 3.1 26.6 1.0 C4 A:IMD509 3.2 27.4 1.0 C2 A:IMD508 3.2 21.5 1.0 CG A:HIS190 3.2 17.8 1.0 CB A:HIS190 3.7 17.4 1.0 CA A:HIS190 3.9 16.7 1.0 CB A:ASP37 4.1 27.7 1.0 NE2 A:HIS190 4.2 18.6 1.0 C5 A:IMD508 4.3 19.5 1.0 N1 A:IMD509 4.3 26.6 1.0 C5 A:IMD509 4.3 28.2 1.0 CD2 A:HIS190 4.3 18.1 1.0 N1 A:IMD508 4.3 21.0 1.0 O A:ASP37 4.4 25.8 1.0 C A:ASP37 4.5 25.7 1.0 ND2 A:ASN193 4.6 18.9 1.0 O A:HIS190 4.7 15.7 1.0 CB A:ASN193 4.7 18.0 1.0 CA A:ASP37 4.7 26.0 1.0 C A:HIS190 4.8 16.6 1.0 N A:HIS190 5.0 16.8 1.0

Zinc binding site 3 out of 7 in the Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:17.7 occ:0.32 OE2 A:GLU38 2.0 33.1 1.0 N1 A:IMD509 2.2 26.6 1.0 CD A:GLU38 2.8 32.4 1.0 OE1 A:GLU38 2.9 35.9 1.0 C5 A:IMD509 3.1 28.2 1.0 C2 A:IMD509 3.3 26.6 1.0 CG A:GLU38 4.2 29.7 1.0 C4 A:IMD509 4.3 27.4 1.0 N3 A:IMD509 4.4 24.1 1.0 CA A:GLU38 4.5 25.5 1.0 O A:ASP37 4.6 25.8 1.0 N A:THR39 4.6 22.8 1.0 CB A:GLU38 4.8 27.6 1.0 OG1 A:THR39 5.0 22.8 1.0

Zinc binding site 4 out of 7 in the Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:23.4 occ:1.00 NE2 A:HIS227 2.1 21.4 1.0 N1 A:IMD510 2.1 22.3 1.0 O A:HOH806 2.2 27.8 1.0 O A:HOH805 2.3 24.0 1.0 C5 A:IMD510 2.7 23.3 1.0 CE1 A:HIS227 3.0 20.2 1.0 CD2 A:HIS227 3.1 20.4 1.0 C2 A:IMD510 3.4 22.6 1.0 C4 A:IMD510 4.0 23.1 1.0 ND1 A:HIS227 4.2 20.1 1.0 CG A:HIS227 4.3 20.0 1.0 N3 A:IMD510 4.3 22.6 1.0 O A:HOH630 4.3 27.2 1.0 CG1 A:VAL226 4.5 19.9 1.0 CD2 A:LEU276 4.7 26.1 1.0 CB A:ALA357 4.7 21.1 1.0

Zinc binding site 5 out of 7 in the Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:18.7 occ:0.85 O A:HOH807 1.8 23.6 0.8 O A:HOH808 2.0 14.6 0.8 O A:MET23 2.0 34.7 1.0 N A:MET23 2.1 38.9 1.0 C A:MET23 2.7 34.6 1.0 CA A:MET23 2.9 37.6 1.0 CB A:MET23 3.8 40.0 1.0 N A:ILE24 4.0 32.7 1.0 CA A:ILE24 4.8 30.9 1.0 CG A:MET23 4.9 43.3 1.0 CG A:GLU25 4.9 40.9 1.0

Zinc binding site 6 out of 7 in the Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:17.0 occ:0.56 OXT A:ACT512 2.1 13.1 0.6 O A:HOH720 2.1 11.6 0.6 NE2 A:HIS123 2.1 19.5 1.0 O A:ACT512 2.1 16.1 0.6 OG A:SER334 2.2 18.9 1.0 C A:ACT512 2.4 14.6 0.6 CE1 A:HIS123 3.0 19.1 1.0 CD2 A:HIS123 3.2 18.9 1.0 CB A:SER334 3.4 17.3 1.0 CH3 A:ACT512 3.9 14.3 0.6 O A:HOH697 4.1 28.1 1.0 ND1 A:HIS123 4.2 18.4 1.0 O A:ALA331 4.2 15.8 1.0 CG A:HIS123 4.3 17.9 1.0 N A:SER334 4.4 16.4 1.0 ND2 A:ASN239 4.4 21.2 1.0 O A:HOH619 4.4 25.1 1.0 CA A:SER334 4.5 16.5 1.0 CA A:GLY332 4.5 16.1 1.0 CE2 A:PHE335 4.7 18.0 1.0 CD2 A:PHE335 4.9 17.2 1.0 C A:GLY332 4.9 15.8 1.0

Zinc binding site 7 out of 7 in the Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A Serine Protease MYCP1, An Essential Component of the Type VII (Esx-1) Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:40.8 occ:0.70 OE2 A:GLU25 2.0 51.6 1.0 CD A:GLU25 2.7 44.5 1.0 OE1 A:GLU25 2.7 48.4 1.0 CG A:GLU25 4.2 40.9 1.0 O A:HOH807 4.9 23.6 0.8

J.M.Wagner, T.J.Evans, J.Chen, H.Zhu, E.N.Houben, W.Bitter, K.V.Korotkov. Understanding Specificity of the Mycosin Proteases in Esx/Type VII Secretion By Structural and Functional Analysis. J.Struct.Biol. V. 184 115 2013.
ISSN: ISSN 1047-8477
PubMed: 24113528
DOI: 10.1016/J.JSB.2013.09.022