Zinc in PDB 2xzl: UPF1-Rna Complex

All present enzymatic activity of UPF1-Rna Complex:
3.6.4.13;

The structure of UPF1-Rna Complex, PDB code: 2xzl was solved by S.Chakrabarti, U.Jayachandran, F.Bonneau, F.Fiorini, C.Basquin, S.Domcke, H.Le Hir, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.882 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.135, 114.117, 65.730, 90.00, 110.24, 90.00
R / Rfree (%)	19.74 / 24.31

The structure of UPF1-Rna Complex also contains other interesting chemical elements:

Aluminium	(Al)	1 atom
Magnesium	(Mg)	1 atom
Fluorine	(F)	4 atoms

The binding sites of Zinc atom in the UPF1-Rna Complex (pdb code 2xzl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the UPF1-Rna Complex, PDB code: 2xzl:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the UPF1-Rna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of UPF1-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1851 b:13.3 occ:1.00 ND1 A:HIS94 2.2 18.1 1.0 SG A:CYS62 2.5 13.3 1.0 SG A:CYS84 2.6 13.3 1.0 SG A:CYS65 2.6 9.4 1.0 CE1 A:HIS94 3.1 19.8 1.0 CB A:CYS62 3.3 13.9 1.0 CG A:HIS94 3.3 11.7 1.0 CB A:CYS84 3.6 12.0 1.0 CB A:CYS65 3.6 10.0 1.0 CB A:HIS94 3.7 14.3 1.0 N A:CYS65 3.8 15.3 1.0 O A:HOH2002 4.0 24.6 1.0 N A:CYS84 4.0 12.4 1.0 CB A:TYR64 4.2 21.1 1.0 NE2 A:HIS94 4.2 21.0 1.0 CA A:CYS65 4.3 19.4 1.0 CA A:CYS84 4.3 18.3 1.0 CD2 A:HIS94 4.4 14.1 1.0 CA A:CYS62 4.7 14.6 1.0 N A:GLY66 4.7 13.6 1.0 CB A:ILE67 4.8 19.3 1.0 C A:CYS84 4.8 15.9 1.0 C A:TYR64 4.8 18.2 1.0 CD1 A:ILE67 4.9 14.2 1.0 O A:CYS84 4.9 12.8 1.0 CA A:TYR64 4.9 17.7 1.0 C A:CYS65 4.9 14.3 1.0 N A:ILE67 5.0 18.3 1.0 N A:TYR64 5.0 18.6 1.0

Zinc binding site 2 out of 3 in the UPF1-Rna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of UPF1-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1852 b:19.1 occ:1.00 NE2 A:HIS98 2.2 10.0 1.0 ND1 A:HIS104 2.3 23.6 1.0 SG A:CYS76 2.5 18.1 1.0 SG A:CYS79 2.7 30.3 1.0 CD2 A:HIS98 3.1 13.4 1.0 CE1 A:HIS104 3.1 22.6 1.0 CE1 A:HIS98 3.2 15.8 1.0 CG A:HIS104 3.3 16.9 1.0 CB A:CYS76 3.5 26.7 1.0 CB A:CYS79 3.6 30.7 1.0 CB A:HIS104 3.7 17.2 1.0 N A:CYS79 3.9 28.0 1.0 OG A:SER102 3.9 20.7 1.0 CG A:HIS98 4.3 12.2 1.0 ND1 A:HIS98 4.3 10.7 1.0 NE2 A:HIS104 4.3 16.6 1.0 CB A:SER78 4.3 20.9 1.0 CA A:CYS79 4.4 27.4 1.0 CD2 A:HIS104 4.4 18.0 1.0 CB A:SER102 4.6 18.8 1.0 CA A:CYS76 4.8 24.7 1.0 C A:SER78 4.9 32.6 1.0 CA A:SER78 5.0 23.0 1.0 CE2 A:PHE83 5.0 15.9 1.0 O A:CYS76 5.0 25.6 1.0

Zinc binding site 3 out of 3 in the UPF1-Rna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of UPF1-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1853 b:43.3 occ:1.00 SG A:CYS152 2.6 40.8 1.0 SG A:CYS125 2.6 47.9 1.0 SG A:CYS148 2.7 51.3 1.0 SG A:CYS122 2.7 34.0 1.0 CB A:CYS122 3.1 28.5 1.0 CB A:CYS148 3.2 28.3 1.0 CB A:CYS125 3.4 51.1 1.0 CB A:CYS152 3.7 31.4 1.0 N A:CYS125 3.7 30.4 1.0 N A:CYS148 3.8 24.3 1.0 CA A:CYS148 4.1 23.3 1.0 CA A:CYS125 4.1 34.5 1.0 CD A:ARG127 4.2 35.9 1.0 N A:GLY126 4.3 36.3 1.0 N A:ARG127 4.6 40.3 1.0 CB A:ASN124 4.6 41.6 1.0 C A:CYS125 4.6 33.6 1.0 CA A:CYS122 4.6 29.6 1.0 CB A:ARG127 4.6 41.8 1.0 NH1 A:ARG127 4.7 32.7 1.0 CG A:ARG127 4.8 50.5 1.0 C A:ASN124 4.9 41.0 1.0 CA A:CYS152 5.0 33.9 1.0 C A:LEU147 5.0 26.0 1.0

S.Chakrabarti, U.Jayachandran, F.Bonneau, F.Fiorini, C.Basquin, S.Domcke, H.Le Hir, E.Conti. Molecular Mechanisms For the Rna-Dependent Atpase Activity of UPF1 and Its Regulation By UPF2. Mol.Cell V. 41 693 2011.
ISSN: ISSN 1097-2765
PubMed: 21419344
DOI: 10.1016/J.MOLCEL.2011.02.010