Zinc in PDB 4gbm: Sulfotransferase Domain From the Curacin Biosynthetic Pathway

The structure of Sulfotransferase Domain From the Curacin Biosynthetic Pathway, PDB code: 4gbm was solved by J.G.Mccarthy, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.34 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.856, 67.299, 118.016, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 18.2

The structure of Sulfotransferase Domain From the Curacin Biosynthetic Pathway also contains other interesting chemical elements:

Chlorine

(Cl)

9 atoms

The binding sites of Zinc atom in the Sulfotransferase Domain From the Curacin Biosynthetic Pathway (pdb code 4gbm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Sulfotransferase Domain From the Curacin Biosynthetic Pathway, PDB code: 4gbm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Sulfotransferase Domain From the Curacin Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sulfotransferase Domain From the Curacin Biosynthetic Pathway within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:12.6 occ:0.50 O A:HOH710 2.0 28.4 1.0 OE1 A:GLU83 2.0 30.1 1.0 CL A:CL414 2.2 28.2 1.0 OE2 A:GLU83 2.7 27.5 1.0 CD A:GLU83 2.7 27.9 1.0 O A:HOH776 3.5 48.1 1.0 OE1 A:GLN86 3.9 34.4 1.0 O A:HOH684 4.1 40.1 1.0 CG A:GLU83 4.1 23.0 1.0 CD1 A:LEU81 4.4 25.9 1.0 CB A:ALA260 4.7 19.4 1.0 CD A:GLN86 4.8 30.1 1.0

Zinc binding site 2 out of 5 in the Sulfotransferase Domain From the Curacin Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sulfotransferase Domain From the Curacin Biosynthetic Pathway within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:11.0 occ:1.00 OD1 A:ASP266 2.0 10.5 1.0 NE2 A:HIS258 2.1 13.0 1.0 CL A:CL407 2.2 12.3 1.0 CL A:CL411 2.2 11.7 1.0 CG A:ASP266 2.8 10.8 1.0 OD2 A:ASP266 2.9 11.6 1.0 CE1 A:HIS258 3.1 14.4 1.0 CD2 A:HIS258 3.1 13.4 1.0 N A:ASN268 3.8 9.3 1.0 CA A:ASN268 4.0 9.5 1.0 ND1 A:HIS258 4.2 15.3 1.0 CG A:HIS258 4.2 13.6 1.0 CB A:ASP266 4.2 10.6 1.0 CD1 A:LEU262 4.3 19.6 1.0 N A:PHE269 4.3 9.3 1.0 N A:LEU270 4.4 10.3 1.0 NZ A:LYS271 4.4 18.0 1.0 CD A:PRO267 4.5 11.0 1.0 C A:ASN268 4.5 9.4 1.0 CD2 A:LEU262 4.5 17.5 1.0 CB A:LEU270 4.7 11.8 1.0 N A:PRO267 4.7 9.2 1.0 CA A:ASP266 4.7 10.1 1.0 OD1 A:ASN268 4.8 10.5 1.0 C A:ASP266 4.9 9.4 1.0 CG A:PRO267 4.9 13.4 1.0 CG A:LEU262 4.9 18.1 1.0 C A:PRO267 5.0 9.7 1.0

Zinc binding site 3 out of 5 in the Sulfotransferase Domain From the Curacin Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sulfotransferase Domain From the Curacin Biosynthetic Pathway within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:10.0 occ:1.00 OD2 A:ASP276 2.0 14.1 1.0 ND1 A:HIS272 2.1 9.9 1.0 CL A:CL413 2.2 10.0 1.0 CE1 A:HIS272 3.0 12.9 1.0 CG A:ASP276 3.0 13.3 1.0 CG A:HIS272 3.2 9.7 1.0 CB A:ASP276 3.4 9.6 1.0 CB A:HIS272 3.6 9.8 1.0 CA A:HIS272 4.1 10.4 1.0 OD1 A:ASP276 4.1 13.5 1.0 NE2 A:HIS272 4.1 9.8 1.0 CD2 A:HIS272 4.3 9.4 1.0 O A:LYS271 4.6 11.7 1.0 CA A:ASP276 4.8 10.4 1.0 N A:ASN273 5.0 10.8 1.0

Zinc binding site 4 out of 5 in the Sulfotransferase Domain From the Curacin Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sulfotransferase Domain From the Curacin Biosynthetic Pathway within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:9.0 occ:1.00 O5P A:A3P406 2.0 9.9 1.0 CL A:CL408 2.2 13.5 1.0 CL A:CL409 2.2 11.8 1.0 CL A:CL410 2.2 14.9 1.0 P2 A:A3P406 3.2 7.3 1.0 O6P A:A3P406 3.7 6.2 1.0 NH2 A:ARG39 3.7 10.7 1.0 O4P A:A3P406 3.8 7.1 1.0 N A:ARG39 4.4 8.0 1.0 O5' A:A3P406 4.4 7.2 1.0 O A:HOH561 4.4 19.4 1.0 CG A:PRO135 4.5 14.9 1.0 CB A:PRO267 4.5 10.0 1.0 CD A:ARG39 4.6 9.1 1.0 OG1 A:THR43 4.6 7.9 1.0 CZ A:ARG39 4.6 10.3 1.0 CA A:PRO267 4.6 9.3 1.0 O A:HOH696 4.7 33.1 1.0 OG A:SER42 4.8 8.2 1.0 C5' A:A3P406 4.8 8.2 1.0 O A:HOH541 4.9 16.1 1.0 N A:PRO267 4.9 9.2 1.0 CD1 A:ILE264 4.9 18.8 1.0 NE A:ARG39 5.0 8.0 1.0 CG1 A:ILE264 5.0 18.9 1.0

Zinc binding site 5 out of 5 in the Sulfotransferase Domain From the Curacin Biosynthetic Pathway


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sulfotransferase Domain From the Curacin Biosynthetic Pathway within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:15.1 occ:1.00 ND1 A:HIS62 2.1 14.4 1.0 O A:HOH656 2.1 12.4 1.0 CL A:CL412 2.2 17.2 1.0 CL A:CL415 2.2 20.3 1.0 CE1 A:HIS62 3.0 11.8 1.0 CG A:HIS62 3.2 11.8 1.0 CB A:HIS62 3.6 12.1 1.0 CA A:HIS62 3.9 11.6 1.0 O A:HOH599 4.0 23.6 1.0 OG1 A:THR136 4.0 17.9 1.0 NE2 A:HIS62 4.2 13.1 1.0 CD2 A:HIS62 4.3 12.5 1.0 O A:HOH531 4.3 12.4 1.0 CD1 A:LEU76 4.4 23.8 1.0 CD2 A:LEU78 4.6 23.6 1.0 OG A:SER134 4.7 13.9 1.0 CG A:PRO65 4.7 15.6 1.0 N A:HIS62 4.7 11.0 1.0 CB A:THR136 5.0 15.5 1.0 CG2 A:THR136 5.0 16.5 1.0

J.G.Mccarthy, E.B.Eisman, S.Kulkarni, L.Gerwick, W.H.Gerwick, P.Wipf, D.H.Sherman, J.L.Smith. Structural Basis of Functional Group Activation By Sulfotransferases in Complex Metabolic Pathways. Acs Chem.Biol. V. 7 1994 2012.
ISSN: ISSN 1554-8929
PubMed: 22991895
DOI: 10.1021/CB300385M