Zinc in PDB 7rdn: Crystal Structure of S. Cerevisiae Pre-Mrna Leakage Protein 39 (PML39)

The structure of Crystal Structure of S. Cerevisiae Pre-Mrna Leakage Protein 39 (PML39), PDB code: 7rdn was solved by H.Hashimoto, D.H.Ramirez, N.Pawlak, G.Blobel, B.Palancade, E.W.Debler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.34 / 2.49
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	53.01, 53.01, 171.27, 90, 90, 120
R / Rfree (%)	23.3 / 26.3

The binding sites of Zinc atom in the Crystal Structure of S. Cerevisiae Pre-Mrna Leakage Protein 39 (PML39) (pdb code 7rdn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of S. Cerevisiae Pre-Mrna Leakage Protein 39 (PML39), PDB code: 7rdn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of S. Cerevisiae Pre-Mrna Leakage Protein 39 (PML39)


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 S. Cerevisiae Pre-Mrna Leakage Protein 39 (PML39) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:75.5 occ:1.00 ND1 A:HIS288 2.1 70.2 1.0 SG A:CYS292 2.3 64.0 1.0 SG A:CYS271 2.3 68.9 1.0 SG A:CYS268 2.5 67.7 1.0 HB3 A:CYS271 2.8 71.0 1.0 CE1 A:HIS288 3.0 79.2 1.0 H A:CYS271 3.0 71.8 1.0 CB A:CYS271 3.1 59.2 1.0 HB2 A:CYS292 3.1 98.3 1.0 HE1 A:HIS288 3.1 95.1 1.0 HB3 A:HIS288 3.1 91.8 1.0 CG A:HIS288 3.2 94.0 1.0 CB A:CYS292 3.3 81.9 1.0 HB3 A:CYS268 3.3 86.4 1.0 CB A:CYS268 3.3 72.0 1.0 HB2 A:CYS268 3.3 86.4 1.0 HA A:HIS288 3.4 93.1 1.0 HB3 A:CYS292 3.5 98.3 1.0 CB A:HIS288 3.5 76.5 1.0 HD2 A:TYR294 3.6 69.2 1.0 N A:CYS271 3.6 59.9 1.0 CA A:CYS271 3.9 68.1 1.0 HB2 A:TYR294 3.9 74.1 1.0 HB2 A:CYS271 3.9 71.0 1.0 CA A:HIS288 4.0 77.6 1.0 H A:ALA289 4.0 87.6 1.0 HB3 A:ALA270 4.1 66.8 1.0 NE2 A:HIS288 4.2 74.5 1.0 H A:PHE272 4.2 76.9 1.0 H A:ALA270 4.2 68.9 1.0 CD2 A:HIS288 4.3 85.7 1.0 H A:TYR294 4.3 76.6 1.0 H A:HIS273 4.4 81.3 1.0 HB2 A:HIS288 4.5 91.8 1.0 HB2 A:HIS273 4.5 106.3 1.0 CD2 A:TYR294 4.5 57.7 1.0 C A:CYS271 4.6 69.0 1.0 C A:ALA270 4.6 61.5 1.0 N A:ALA289 4.6 73.0 1.0 N A:PHE272 4.6 64.1 1.0 CA A:CYS292 4.7 74.7 1.0 HA A:CYS271 4.7 81.7 1.0 CA A:CYS268 4.8 68.8 1.0 HA A:CYS292 4.8 89.6 1.0 CB A:TYR294 4.8 61.8 1.0 C A:HIS288 4.9 79.3 1.0 HE2 A:HIS288 4.9 89.5 1.0 N A:ALA270 4.9 57.4 1.0 CB A:ALA270 5.0 55.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of S. Cerevisiae Pre-Mrna Leakage Protein 39 (PML39)


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 S. Cerevisiae Pre-Mrna Leakage Protein 39 (PML39) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:91.1 occ:1.00 ND1 A:HIS172 2.2 77.3 1.0 HB2 A:CYS137 2.3 123.1 1.0 SG A:CYS134 2.4 84.7 1.0 SG A:CYS137 2.4 104.1 1.0 SG A:CYS176 2.6 84.8 1.0 H A:CYS137 2.7 141.3 1.0 CB A:CYS137 2.7 102.6 1.0 CE1 A:HIS172 3.0 80.7 1.0 HE1 A:HIS172 3.0 96.9 1.0 HB3 A:CYS134 3.1 101.9 1.0 CB A:CYS134 3.2 84.9 1.0 HB2 A:CYS134 3.2 101.9 1.0 CG A:HIS172 3.3 79.3 1.0 HA A:HIS172 3.4 109.0 1.0 N A:CYS137 3.4 117.8 1.0 HB3 A:HIS172 3.4 108.9 1.0 HB2 A:CYS176 3.4 115.9 1.0 HB2 A:TRP178 3.4 109.4 1.0 CB A:CYS176 3.5 96.6 1.0 HB3 A:CYS176 3.5 115.9 1.0 HB3 A:CYS137 3.5 123.1 1.0 CA A:CYS137 3.6 108.4 1.0 CB A:HIS172 3.7 90.7 1.0 H A:LEU173 3.8 129.8 1.0 HD1 A:TRP178 3.8 116.1 1.0 HB2 A:CYS136 3.9 125.8 1.0 CA A:HIS172 4.0 90.9 1.0 HA A:CYS137 4.0 130.1 1.0 NE2 A:HIS172 4.2 79.7 1.0 H A:CYS136 4.2 119.7 1.0 CD2 A:HIS172 4.3 85.5 1.0 CB A:TRP178 4.4 91.2 1.0 N A:LEU173 4.4 108.1 1.0 HB3 A:ALA139 4.5 105.7 1.0 H A:TRP178 4.5 118.4 1.0 C A:CYS136 4.5 114.4 1.0 CD1 A:TRP178 4.6 96.7 1.0 CA A:CYS134 4.6 82.1 1.0 H A:ALA139 4.6 105.5 1.0 HB2 A:HIS172 4.7 108.9 1.0 H A:HIS138 4.7 120.0 1.0 CB A:CYS136 4.7 104.8 1.0 HB3 A:TRP178 4.7 109.4 1.0 C A:HIS172 4.8 100.6 1.0 C A:CYS137 4.9 107.9 1.0 CG A:TRP178 4.9 93.5 1.0 HE2 A:HIS172 4.9 95.6 1.0 N A:CYS136 4.9 99.8 1.0 CA A:CYS176 4.9 103.2 1.0 HB2 A:LEU173 5.0 146.5 1.0 CA A:CYS136 5.0 108.9 1.0 HA A:CYS134 5.0 98.5 1.0

H.Hashimoto, D.H.Ramirez, N.Pawlak, G.Blobel, B.Palancade, E.W.Debler. Crystal Structure of the Two Tandem Bir-Like Modules of Pre-Mrna Leakage Protein 39 (PML39) From Saccharomyces Cerevisiae To Be Published.