Zinc in PDB 6j2l: Crystal Structure of Bi-Functional Enzyme

All present enzymatic activity of Crystal Structure of Bi-Functional Enzyme:
3.5.4.19; 3.6.1.31;

The structure of Crystal Structure of Bi-Functional Enzyme, PDB code: 6j2l was solved by H.Zhang, G.Shang, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.75 / 2.17
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.050, 45.230, 65.259, 90.00, 112.53, 90.00
R / Rfree (%)	20.4 / 24.9

The structure of Crystal Structure of Bi-Functional Enzyme also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Bi-Functional Enzyme (pdb code 6j2l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Bi-Functional Enzyme, PDB code: 6j2l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Bi-Functional Enzyme


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 Bi-Functional Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:54.2 occ:1.00 OD1 A:ASP84 1.9 58.0 1.0 OD2 A:ASP80 2.0 71.2 1.0 O B:HOH413 2.1 55.7 1.0 OD1 A:ASP82 2.2 84.6 1.0 O A:HOH421 2.2 56.8 1.0 CG A:ASP84 2.9 53.5 1.0 CG A:ASP80 3.0 55.9 1.0 CG A:ASP82 3.1 71.3 1.0 OD2 A:ASP84 3.2 56.8 1.0 OD1 A:ASP80 3.3 54.8 1.0 OD2 A:ASP82 3.3 75.8 1.0 O A:HOH407 3.5 45.7 1.0 OG1 A:THR85 3.9 47.5 1.0 O A:HOH451 4.2 55.2 1.0 CB A:ASP84 4.3 49.2 1.0 CB A:ASP80 4.3 51.6 1.0 N A:ASP84 4.3 50.2 1.0 CB A:THR85 4.4 51.2 1.0 O B:LEU34 4.5 52.6 1.0 C A:ASP84 4.5 50.7 1.0 CB A:ASP82 4.5 52.1 1.0 CA A:ASP84 4.6 58.2 1.0 N A:THR85 4.6 46.0 1.0 N A:ASP82 4.7 46.5 1.0 O A:ASP84 4.7 46.8 1.0 C A:ASP82 4.8 50.9 1.0 CA A:ASP82 4.9 52.6 1.0 N A:ASN83 4.9 51.4 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Bi-Functional Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Bi-Functional Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:61.7 occ:1.00 SG B:CYS81 2.4 63.6 1.0 SG A:CYS104 2.4 63.6 1.0 SG A:CYS97 2.5 65.6 1.0 O A:HOH442 2.7 56.8 1.0 CB A:CYS97 3.2 74.0 1.0 CB A:CYS104 3.3 56.9 1.0 CB B:CYS81 3.5 60.9 1.0 CA A:CYS97 3.5 79.7 1.0 ZN A:ZN304 3.7 30.6 0.0 CA A:CYS104 3.7 57.0 1.0 CD2 A:HIS98 3.8 73.9 1.0 N A:HIS98 4.0 0.8 1.0 C A:CYS97 4.3 80.1 1.0 NE2 A:HIS98 4.4 68.5 1.0 N A:CYS97 4.6 75.0 1.0 N A:CYS104 4.6 49.5 1.0 CA B:CYS81 4.8 54.2 1.0 O A:CYS104 4.8 43.9 1.0 CG A:HIS98 4.8 81.9 1.0 C A:CYS104 4.8 42.4 1.0 N B:CYS81 4.8 43.4 1.0 O A:THR96 4.9 74.2 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Bi-Functional Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Bi-Functional Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:72.1 occ:1.00 OE1 A:GLU172 2.0 63.8 1.0 OE1 A:GLU153 2.2 60.7 1.0 OD2 A:ASP175 2.3 64.9 1.0 CD A:GLU153 2.9 57.4 1.0 CD A:GLU172 2.9 65.5 1.0 OE2 A:GLU153 3.0 62.4 1.0 CG A:ASP175 3.3 60.7 1.0 OE2 A:GLU172 3.3 74.8 1.0 CB A:ASP175 3.5 45.4 1.0 OE1 A:GLU156 3.7 82.7 1.0 CD A:GLU156 3.9 74.7 1.0 OE2 A:GLU156 4.1 78.0 1.0 CG A:GLU172 4.3 57.1 1.0 CG A:GLU153 4.4 48.3 1.0 OD1 A:ASP175 4.4 68.2 1.0 CA A:GLU172 4.5 54.4 1.0 CG A:GLU156 4.6 63.3 1.0 CB A:GLU172 4.6 58.3 1.0 CB A:GLU156 4.7 51.7 1.0 CB A:GLU153 4.9 40.7 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Bi-Functional Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Bi-Functional Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:30.6 occ:0.00 NE2 A:HIS98 2.4 68.5 1.0 SG B:CYS81 2.5 63.6 1.0 CD2 A:HIS98 2.7 73.9 1.0 CB B:CYS81 3.6 60.9 1.0 CE1 A:HIS98 3.7 74.8 1.0 ZN A:ZN302 3.7 61.7 1.0 CG A:HIS98 4.0 81.9 1.0 O A:HOH442 4.0 56.8 1.0 N B:ASP82 4.1 40.4 1.0 C B:CYS81 4.2 51.1 1.0 CB B:ASP82 4.3 47.4 1.0 ND1 A:HIS98 4.4 81.3 1.0 CG B:ASP82 4.5 63.2 1.0 CA B:CYS81 4.5 54.2 1.0 O B:CYS81 4.6 56.1 1.0 CA B:ASP82 4.7 54.4 1.0 OD1 B:ASP82 4.8 64.6 1.0 OD2 B:ASP82 4.8 84.0 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Bi-Functional Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Bi-Functional Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:52.6 occ:1.00 OD1 B:ASP84 1.9 59.1 1.0 OD2 B:ASP80 2.0 52.8 1.0 O B:HOH415 2.3 56.8 1.0 OD1 B:ASP82 2.4 64.6 1.0 O A:HOH423 2.4 60.9 1.0 CG B:ASP84 2.8 55.8 1.0 CG B:ASP80 2.9 49.8 1.0 OD2 B:ASP84 3.1 50.0 1.0 CG B:ASP82 3.2 63.2 1.0 OD1 B:ASP80 3.3 45.6 1.0 OD2 B:ASP82 3.4 84.0 1.0 O B:HOH407 3.5 47.0 1.0 OG1 B:THR85 4.1 48.6 1.0 CB B:ASP84 4.2 55.3 1.0 CB B:ASP80 4.3 41.9 1.0 N B:ASP84 4.3 48.0 1.0 C B:ASP84 4.4 48.3 1.0 N B:THR85 4.4 56.8 1.0 CA B:ASP84 4.5 52.2 1.0 CB B:THR85 4.5 49.4 1.0 CB B:ASP82 4.6 47.4 1.0 O A:LEU34 4.6 48.9 1.0 N B:ASP82 4.7 40.4 1.0 O B:ASP84 4.8 49.4 1.0 C B:ASP82 4.8 51.4 1.0 CA B:ASP82 4.9 54.4 1.0

Y.Wang, F.Zhang, Y.Nie, G.Shang, H.Zhang. Structural Analysis of Shigella Flexneri Bi-Functional Enzyme Hisie in Histidine Biosynthesis. Biochem.Biophys.Res.Commun. V. 516 540 2019.
ISSN: ESSN 1090-2104
PubMed: 31235255
DOI: 10.1016/J.BBRC.2019.06.099