Zinc in PDB 5udx: Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc

The structure of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc, PDB code: 5udx was solved by M.Fellner, B.Desguin, R.P.Hausinger, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.11 / 2.78
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	107.828, 107.828, 319.784, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 25.9

The binding sites of Zinc atom in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc (pdb code 5udx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc, PDB code: 5udx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:43.2 occ:1.00 OD2 A:ASP231 2.0 76.0 1.0 OD1 A:ASP231 2.0 69.8 1.0 OD1 C:ASP231 2.0 68.3 1.0 OD2 C:ASP231 2.0 62.0 1.0 OD1 B:ASP231 2.0 68.7 1.0 OD2 B:ASP231 2.0 82.7 1.0 O A:HOH402 2.1 24.0 1.0 CG A:ASP231 2.3 55.8 1.0 CG C:ASP231 2.3 55.3 1.0 CG B:ASP231 2.3 63.9 1.0 CB A:ASP231 3.8 38.7 1.0 CB C:ASP231 3.8 48.4 1.0 CB B:ASP231 3.9 52.4 1.0 O B:ALA227 4.6 51.8 1.0 CA A:ASP231 4.7 32.4 1.0 CA C:ASP231 4.7 50.7 1.0 CA B:ASP231 4.7 52.7 1.0 O C:ALA227 4.8 53.5 1.0 N A:ASP231 4.8 38.2 1.0 N B:ASP231 4.8 61.0 1.0 N C:ASP231 4.8 55.3 1.0 O A:ALA227 5.0 51.8 1.0

Zinc binding site 2 out of 6 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:77.9 occ:1.00 NE2 A:HIS190 2.0 90.4 1.0 O A:HOH410 2.5 60.8 1.0 O A:HOH413 2.6 59.8 1.0 CE1 A:HIS190 3.0 80.8 1.0 CD2 A:HIS190 3.0 75.1 1.0 O2 A:SO4305 3.7 0.6 1.0 O4 A:SO4305 4.1 0.0 1.0 ND1 A:HIS190 4.1 73.0 1.0 CG A:HIS190 4.2 66.1 1.0 S A:SO4305 4.6 0.6 1.0 OD1 A:ASP82 4.7 73.0 1.0 OD2 A:ASP82 4.9 84.0 1.0

Zinc binding site 3 out of 6 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:85.9 occ:0.65 OD1 B:ASP218 2.0 0.4 1.0 NE2 D:HIS216 2.0 0.4 1.0 CE1 D:HIS216 2.9 85.7 1.0 CG B:ASP218 3.0 83.7 1.0 CD2 D:HIS216 3.1 83.8 1.0 OD2 B:ASP218 3.5 93.9 1.0 ND1 D:HIS216 4.0 87.5 1.0 CG D:HIS216 4.2 77.3 1.0 CB B:ASP218 4.3 65.3 1.0 CE1 B:TYR250 4.3 47.4 1.0 CD1 B:TYR250 4.7 40.6 1.0

Zinc binding site 4 out of 6 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:73.5 occ:1.00 OD1 D:ASP231 2.0 73.2 1.0 OD2 F:ASP231 2.0 74.8 1.0 OD1 E:ASP231 2.0 71.9 1.0 OD2 E:ASP231 2.0 75.7 1.0 OD1 F:ASP231 2.0 77.0 1.0 OD2 D:ASP231 2.1 77.7 1.0 O F:HOH401 2.1 30.6 1.0 CG D:ASP231 2.3 63.3 1.0 CG E:ASP231 2.3 57.2 1.0 CG F:ASP231 2.3 56.4 1.0 CB E:ASP231 3.8 40.1 1.0 CB D:ASP231 3.9 51.9 1.0 CB F:ASP231 3.9 38.5 1.0 O D:ALA227 4.7 54.2 1.0 CA E:ASP231 4.7 48.2 1.0 CA F:ASP231 4.7 50.4 1.0 O E:ALA227 4.7 62.4 1.0 CA D:ASP231 4.8 47.2 1.0 N F:ASP231 4.8 53.2 1.0 N E:ASP231 4.8 58.0 1.0 N D:ASP231 4.8 50.8 1.0 O F:ALA227 4.9 50.8 1.0

Zinc binding site 5 out of 6 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:0.2 occ:1.00 OD2 D:ASP63 2.0 0.8 1.0 OD2 D:ASP59 2.0 0.7 1.0 CG D:ASP63 2.8 87.3 1.0 OD1 D:ASP63 3.0 93.2 1.0 CG D:ASP59 3.2 0.0 1.0 OD1 D:ASP59 3.9 0.5 1.0 CB D:ASP63 4.3 66.4 1.0 CB D:ASP59 4.3 80.9 1.0 O D:ASP59 4.6 51.5 1.0

Zinc binding site 6 out of 6 in the Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Lare, A Sulfur Transferase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:99.6 occ:0.72 OD1 F:ASP82 2.0 0.3 1.0 OE2 F:GLU55 2.0 0.8 1.0 OE1 F:GLU55 2.0 0.8 1.0 NE2 F:HIS190 2.1 0.1 1.0 OD2 F:ASP82 2.1 0.1 1.0 CD F:GLU55 2.3 0.1 1.0 CG F:ASP82 2.3 0.1 1.0 CE1 F:HIS190 2.7 0.6 1.0 CD2 F:HIS190 3.3 0.1 1.0 CG F:GLU55 3.8 87.1 1.0 CB F:ASP82 3.8 88.6 1.0 ND1 F:HIS190 3.9 0.9 1.0 CG F:HIS190 4.2 97.2 1.0 CB F:LEU84 4.3 44.2 1.0 CD1 F:LEU84 4.5 57.1 1.0 CA F:ASP82 4.6 69.2 1.0 CB F:GLU55 4.7 75.6 1.0 CG F:LEU84 4.8 53.0 1.0

M.Fellner, B.Desguin, R.P.Hausinger, J.Hu. Structural Insights Into the Catalytic Mechanism of A Sacrificial Sulfur Insertase of the N-Type Atp Pyrophosphatase Family, Lare. Proc. Natl. Acad. Sci. V. 114 9074 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28784764
DOI: 10.1073/PNAS.1704967114