Zinc in PDB 2wjv: Crystal Structure of the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2

The structure of Crystal Structure of the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2, PDB code: 2wjv was solved by M.Clerici, A.Mourao, I.Gutsche, N.H.Gehring, M.W.Hentze, A.Kulozik, J.Kadlec, M.Sattler, S.Cusack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.79 / 2.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	92.410, 97.290, 124.600, 90.00, 102.38, 90.00
R / Rfree (%)	20 / 24.8

The binding sites of Zinc atom in the Crystal Structure of the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2 (pdb code 2wjv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2, PDB code: 2wjv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2


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 the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:11.1 occ:1.00 ND1 A:HIS155 1.9 17.3 1.0 SG A:CYS145 2.2 15.1 1.0 SG A:CYS126 2.3 8.1 1.0 SG A:CYS123 2.3 8.0 1.0 CE1 A:HIS155 2.8 17.2 1.0 CG A:HIS155 3.0 17.4 1.0 CB A:CYS123 3.3 9.6 1.0 CB A:CYS126 3.3 8.6 1.0 CB A:CYS145 3.4 15.0 1.0 CB A:HIS155 3.5 17.3 1.0 N A:CYS126 3.9 8.8 1.0 N A:CYS145 3.9 14.5 1.0 NE2 A:HIS155 3.9 17.4 1.0 CD2 A:HIS155 4.1 17.6 1.0 CA A:CYS126 4.2 8.6 1.0 CA A:CYS145 4.2 14.7 1.0 CB A:TYR125 4.5 9.2 1.0 C A:CYS145 4.7 14.8 1.0 CA A:CYS123 4.7 9.7 1.0 O A:CYS145 4.8 14.8 1.0 C A:CYS126 4.8 8.6 1.0 O A:GLY147 4.8 15.0 1.0 N A:GLY127 4.8 8.7 1.0 CB A:ILE128 4.9 11.1 1.0 CA A:HIS155 4.9 17.2 1.0 C A:TYR125 5.0 9.0 1.0 CG1 A:ILE128 5.0 10.4 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2


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 the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:20.9 occ:0.50 SG A:CYS137 1.9 22.7 1.0 OG A:SER140 2.0 17.7 1.0 NE2 A:HIS159 2.2 19.3 1.0 SG A:CYS165 2.6 34.5 1.0 CB A:SER140 2.8 17.4 1.0 CD2 A:HIS159 3.0 19.5 1.0 CB A:CYS137 3.2 20.7 1.0 CE1 A:HIS159 3.3 19.7 1.0 CB A:CYS165 3.5 31.8 1.0 N A:SER140 3.6 17.9 1.0 CA A:SER140 3.8 17.4 1.0 CB A:ALA163 4.1 25.4 1.0 CG A:HIS159 4.1 19.0 1.0 ND1 A:HIS159 4.3 19.4 1.0 CA A:CYS137 4.5 20.5 1.0 CB A:THR139 4.7 18.9 1.0 C A:THR139 4.8 18.4 1.0 C A:CYS137 4.9 20.1 1.0 CA A:CYS165 4.9 31.7 1.0 CD2 A:LEU160 4.9 20.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2


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 the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:19.5 occ:1.00 SG A:CYS213 2.0 10.9 1.0 SG A:CYS183 2.1 12.3 1.0 SG A:CYS209 2.1 17.2 1.0 SG A:CYS186 2.4 11.3 1.0 CB A:CYS183 3.0 13.6 1.0 CB A:CYS213 3.1 13.0 1.0 CB A:CYS186 3.3 11.1 1.0 N A:CYS186 3.6 11.0 1.0 CB A:CYS209 3.7 16.0 1.0 N A:CYS209 3.8 15.6 1.0 CA A:CYS186 4.0 11.1 1.0 CA A:CYS209 4.3 15.9 1.0 CB A:ASN185 4.3 10.5 1.0 CA A:CYS213 4.4 13.0 1.0 CA A:CYS183 4.5 13.7 1.0 OD1 A:ASN185 4.6 7.0 1.0 C A:ASN185 4.6 10.9 1.0 CB A:CYS188 4.6 11.9 1.0 N A:CYS213 4.6 13.3 1.0 C A:CYS186 4.6 11.1 1.0 O A:CYS209 4.7 15.4 1.0 N A:GLY187 4.8 11.1 1.0 CA A:ASN185 4.8 10.8 1.0 N A:ASN185 4.8 11.2 1.0 C A:CYS183 4.9 13.0 1.0 C A:LEU208 4.9 15.6 1.0 O A:CYS183 4.9 12.9 1.0 NH1 D:ARG1128 4.9 43.0 1.0 CG A:ASN185 4.9 9.0 1.0 CA A:LEU208 5.0 15.6 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2


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 the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:10.6 occ:1.00 ND1 B:HIS155 2.0 15.3 1.0 SG B:CYS145 2.2 11.1 1.0 SG B:CYS126 2.3 13.0 1.0 SG B:CYS123 2.3 12.4 1.0 CE1 B:HIS155 2.9 15.2 1.0 CG B:HIS155 3.1 15.7 1.0 CB B:CYS123 3.2 12.5 1.0 CB B:CYS126 3.3 11.7 1.0 CB B:CYS145 3.4 12.1 1.0 CB B:HIS155 3.5 16.0 1.0 N B:CYS126 3.9 11.5 1.0 N B:CYS145 3.9 12.1 1.0 NE2 B:HIS155 4.0 14.8 1.0 CA B:CYS126 4.1 11.6 1.0 CD2 B:HIS155 4.1 15.4 1.0 CA B:CYS145 4.2 12.0 1.0 CB B:TYR125 4.5 11.2 1.0 CA B:CYS123 4.6 12.5 1.0 C B:CYS126 4.7 11.2 1.0 C B:CYS145 4.7 12.0 1.0 N B:GLY127 4.8 11.1 1.0 O B:CYS145 4.8 11.6 1.0 O B:GLY147 4.8 13.2 1.0 C B:TYR125 4.9 11.2 1.0 CB B:ILE128 4.9 12.0 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2


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 the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:24.2 occ:0.50 OG B:SER140 1.8 14.8 1.0 SG B:CYS137 2.0 20.8 1.0 NE2 B:HIS159 2.2 14.8 1.0 SG B:CYS165 2.5 32.9 1.0 CB B:SER140 2.8 14.6 1.0 CD2 B:HIS159 3.0 15.1 1.0 CE1 B:HIS159 3.3 15.3 1.0 CB B:CYS137 3.3 18.6 1.0 CB B:CYS165 3.5 31.4 1.0 N B:SER140 3.6 14.8 1.0 CA B:SER140 3.8 14.7 1.0 CB B:ALA163 3.9 25.4 1.0 CG B:HIS159 4.2 16.5 1.0 ND1 B:HIS159 4.3 15.2 1.0 CB B:THR139 4.6 15.0 1.0 CA B:CYS137 4.7 18.4 1.0 C B:THR139 4.7 14.9 1.0 CA B:CYS165 4.8 31.4 1.0 C B:CYS137 4.9 18.3 1.0 C B:SER140 5.0 14.5 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Complex Between Human Nonsense Mediated Decay Factors UPF1 and UPF2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3 b:13.9 occ:1.00 SG B:CYS209 2.0 16.8 1.0 SG B:CYS183 2.1 11.8 1.0 SG B:CYS213 2.2 17.7 1.0 SG B:CYS186 2.3 11.5 1.0 CB B:CYS183 3.2 12.8 1.0 CB B:CYS186 3.2 9.7 1.0 CB B:CYS213 3.4 19.2 1.0 N B:CYS186 3.5 9.9 1.0 CB B:CYS209 3.7 15.6 1.0 N B:CYS209 3.9 15.0 1.0 CA B:CYS186 3.9 9.8 1.0 CB B:ASN185 4.2 10.2 1.0 OD1 B:ASN185 4.3 7.7 1.0 CA B:CYS209 4.4 15.4 1.0 C B:ASN185 4.4 10.1 1.0 C B:CYS186 4.6 9.6 1.0 CA B:CYS183 4.6 12.9 1.0 CA B:ASN185 4.7 10.2 1.0 CG B:ASN185 4.7 9.5 1.0 CA B:CYS213 4.7 19.1 1.0 N B:ASN185 4.8 10.7 1.0 CB B:CYS188 4.8 10.9 1.0 N B:GLY187 4.8 9.9 1.0 N B:CYS213 4.8 18.4 1.0 NH2 E:ARG1128 4.9 38.1 1.0 C B:CYS183 4.9 12.3 1.0 C B:LEU208 4.9 14.5 1.0 O B:CYS183 5.0 12.0 1.0

M.Clerici, A.Mourao, I.Gutsche, N.H.Gehring, M.W.Hentze, A.Kulozik, J.Kadlec, M.Sattler, S.Cusack. Unusual Bipartite Mode of Interaction Between the Nonsense-Mediated Decay Factors, UPF1 and UPF2. Embo J. V. 28 2293 2009.
ISSN: ISSN 0261-4189
PubMed: 19556969
DOI: 10.1038/EMBOJ.2009.175