Zinc in PDB 4a4k: Crystal Structure of the S. Cerevisiae SKI2 Insertion Domain

All present enzymatic activity of Crystal Structure of the S. Cerevisiae SKI2 Insertion Domain:
3.6.4.13;

The structure of Crystal Structure of the S. Cerevisiae SKI2 Insertion Domain, PDB code: 4a4k was solved by F.Halbach, M.Rode, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.16 / 3.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	230.463, 123.139, 153.201, 90.00, 131.05, 90.00
R / Rfree (%)	23.6 / 25.7

The binding sites of Zinc atom in the Crystal Structure of the S. Cerevisiae SKI2 Insertion Domain (pdb code 4a4k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the S. Cerevisiae SKI2 Insertion Domain, PDB code: 4a4k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the S. Cerevisiae SKI2 Insertion Domain


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 S. Cerevisiae SKI2 Insertion Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2083 b:0.4 occ:1.00 ND1 A:HIS1060 2.4 97.4 1.0 SG A:CYS1054 2.5 0.6 1.0 SG A:CYS861 2.6 0.1 1.0 SG A:CYS864 2.8 0.8 1.0 CE1 A:HIS1060 2.8 0.6 1.0 CB A:CYS861 3.4 0.3 1.0 CG A:HIS1060 3.5 0.9 1.0 CB A:CYS1054 3.6 0.1 1.0 CB A:CYS864 3.8 0.1 1.0 NE2 A:HIS1060 3.9 0.4 1.0 CB A:HIS1060 4.3 0.4 1.0 CD2 A:HIS1060 4.3 0.2 1.0 C A:ASN1056 4.5 1.0 1.0 N A:LEU1057 4.5 0.1 1.0 O A:ASN1056 4.5 0.1 1.0 N A:CYS864 4.6 0.3 1.0 CA A:LEU1057 4.7 0.8 1.0 C A:ILE863 4.7 0.7 1.0 CB A:ILE863 4.7 64.5 1.0 CA A:CYS864 4.8 0.1 1.0 CA A:CYS861 4.9 0.3 1.0 CA A:CYS1054 4.9 0.6 1.0 N A:ASN1056 4.9 0.8 1.0 O A:ILE863 4.9 0.7 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the S. Cerevisiae SKI2 Insertion Domain


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 S. Cerevisiae SKI2 Insertion Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2083 b:0.2 occ:1.00 ND1 C:HIS1060 2.4 90.4 1.0 SG C:CYS1054 2.6 76.6 1.0 SG C:CYS861 2.6 0.4 1.0 SG C:CYS864 2.7 0.9 1.0 CE1 C:HIS1060 2.9 0.8 1.0 CB C:CYS1054 3.4 0.7 1.0 CG C:HIS1060 3.6 0.3 1.0 CB C:CYS861 3.7 0.0 1.0 CB C:CYS864 3.7 0.2 1.0 NE2 C:HIS1060 4.0 96.7 1.0 CB C:HIS1060 4.2 0.0 1.0 CD2 C:HIS1060 4.4 98.9 1.0 N C:CYS864 4.4 0.5 1.0 C C:ILE863 4.4 0.5 1.0 CB C:ILE863 4.5 51.5 1.0 O C:ILE863 4.6 0.7 1.0 CA C:CYS864 4.6 0.5 1.0 N C:LEU1057 4.7 0.7 1.0 C C:ASN1056 4.8 75.3 1.0 CA C:CYS1054 4.8 0.1 1.0 CA C:LEU1057 4.9 0.8 1.0 CA C:ILE863 4.9 0.7 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the S. Cerevisiae SKI2 Insertion Domain


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 S. Cerevisiae SKI2 Insertion Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn2083 b:1.0 occ:1.00 ND1 E:HIS1060 2.4 0.5 1.0 SG E:CYS1054 2.6 0.2 1.0 SG E:CYS861 2.6 1.0 1.0 SG E:CYS864 2.7 0.3 1.0 CE1 E:HIS1060 2.9 0.1 1.0 CB E:CYS1054 3.5 0.6 1.0 CB E:CYS861 3.5 0.0 1.0 CB E:CYS864 3.6 0.6 1.0 CG E:HIS1060 3.6 0.3 1.0 NE2 E:HIS1060 4.1 0.9 1.0 CB E:HIS1060 4.3 0.8 1.0 C E:ILE863 4.4 0.0 1.0 N E:CYS864 4.4 0.1 1.0 CD2 E:HIS1060 4.5 0.0 1.0 O E:ILE863 4.5 0.2 1.0 O E:ASN1056 4.6 0.5 1.0 C E:ASN1056 4.6 0.7 1.0 CB E:ILE863 4.6 0.8 1.0 CA E:CYS864 4.6 0.8 1.0 N E:LEU1057 4.6 1.0 1.0 CA E:LEU1057 4.7 0.2 1.0 CA E:CYS1054 4.9 0.9 1.0 CA E:ILE863 4.9 0.6 1.0 CA E:CYS861 5.0 0.8 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the S. Cerevisiae SKI2 Insertion Domain


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 S. Cerevisiae SKI2 Insertion Domain within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn2083 b:0.3 occ:1.00 ND1 G:HIS1060 2.4 0.7 1.0 SG G:CYS1054 2.6 0.5 1.0 SG G:CYS861 2.7 0.9 1.0 SG G:CYS864 2.7 0.2 1.0 CE1 G:HIS1060 2.8 0.1 1.0 CG G:HIS1060 3.5 0.3 1.0 CB G:CYS861 3.6 0.9 1.0 CB G:CYS864 3.6 0.1 1.0 CB G:CYS1054 3.6 0.3 1.0 NE2 G:HIS1060 4.0 99.5 1.0 CB G:HIS1060 4.2 0.9 1.0 CD2 G:HIS1060 4.3 0.1 1.0 N G:CYS864 4.4 0.1 1.0 C G:ILE863 4.6 0.1 1.0 CA G:CYS864 4.6 0.6 1.0 CB G:ILE863 4.6 92.4 1.0 C G:ASN1056 4.7 0.5 1.0 O G:ASN1056 4.8 0.1 1.0 N G:LEU1057 4.8 0.8 1.0 CA G:LEU1057 4.9 0.5 1.0 O G:ILE863 4.9 0.2 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the S. Cerevisiae SKI2 Insertion Domain


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 S. Cerevisiae SKI2 Insertion Domain within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn2083 b:1.0 occ:1.00 ND1 I:HIS1060 2.4 82.6 1.0 SG I:CYS1054 2.6 84.5 1.0 SG I:CYS861 2.6 0.4 1.0 SG I:CYS864 2.7 0.8 1.0 CE1 I:HIS1060 2.9 94.0 1.0 CG I:HIS1060 3.5 95.5 1.0 CB I:CYS861 3.5 0.8 1.0 CB I:CYS1054 3.6 0.9 1.0 CB I:CYS864 3.7 0.5 1.0 NE2 I:HIS1060 4.1 89.7 1.0 CB I:HIS1060 4.1 99.6 1.0 CD2 I:HIS1060 4.4 96.2 1.0 N I:CYS864 4.5 0.8 1.0 N I:LEU1057 4.6 0.7 1.0 C I:ILE863 4.6 0.1 1.0 C I:ASN1056 4.6 84.5 1.0 CB I:ILE863 4.7 58.7 1.0 CA I:CYS864 4.7 0.8 1.0 CA I:LEU1057 4.8 95.9 1.0 O I:ASN1056 4.8 82.0 1.0 O I:ILE863 4.8 0.3 1.0 CB I:ASN1056 4.9 0.0 1.0 CA I:CYS1054 5.0 0.7 1.0 CA I:CYS861 5.0 0.7 1.0

F.Halbach, M.Rode, E.Conti. The Crystal Structure of S. Cerevisiae SKI2, A Dexh Helicase Associated with the Cytoplasmic Functions of the Exosome. Rna V. 18 124 2012.
ISSN: ISSN 1355-8382
PubMed: 22114319
DOI: 10.1261/RNA.029553.111