Zinc in PDB 5ife: Crystal Structure of the Human SF3B Core Complex

The structure of Crystal Structure of the Human SF3B Core Complex, PDB code: 5ife was solved by C.Cretu, O.Dybkov, E.De Laurentiis, C.L.Will, R.Luhrmann, V.Pena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.04 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.055, 154.436, 210.418, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 26

The structure of Crystal Structure of the Human SF3B Core Complex also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Human SF3B Core Complex (pdb code 5ife). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Human SF3B Core Complex, PDB code: 5ife:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Human SF3B Core Complex


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 Human SF3B Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:68.7 occ:1.00 SG D:CYS61 2.4 65.9 1.0 SG D:CYS23 2.5 61.9 1.0 SG D:CYS58 2.5 75.0 1.0 CB D:CYS26 2.7 71.2 1.0 SG D:CYS26 2.8 81.1 1.0 CB D:CYS61 3.6 62.2 1.0 CB D:CYS58 3.6 65.5 1.0 CB D:CYS23 3.6 62.8 1.0 N D:CYS61 3.7 66.9 1.0 CA D:CYS26 3.9 68.0 1.0 N D:CYS26 3.9 71.9 1.0 N D:CYS23 4.0 59.6 1.0 CA D:CYS61 4.2 67.5 1.0 CB D:ILE60 4.3 75.6 1.0 CA D:CYS23 4.3 66.7 1.0 C D:CYS26 4.7 66.2 1.0 N D:GLY62 4.7 68.7 1.0 O D:CYS26 4.7 78.3 1.0 C D:ILE60 4.7 70.2 1.0 CG2 D:ILE60 4.7 78.8 1.0 C D:CYS61 4.8 72.5 1.0 CA D:ILE60 4.9 70.1 1.0 N D:ILE60 4.9 68.8 1.0 C D:CYS23 4.9 69.6 1.0 N D:GLY63 4.9 76.3 1.0 O D:CYS23 5.0 73.9 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Human SF3B Core Complex


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 Human SF3B Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:52.9 occ:1.00 SG D:CYS85 2.3 66.0 1.0 SG D:CYS49 2.4 57.0 1.0 SG D:CYS46 2.4 46.5 1.0 SG D:CYS11 2.4 53.4 1.0 CB D:CYS11 3.0 47.7 1.0 CB D:CYS49 3.1 52.8 1.0 CB D:CYS46 3.7 53.1 1.0 CB D:CYS85 4.0 62.9 1.0 N D:CYS46 4.1 54.7 1.0 CA D:CYS49 4.3 59.9 1.0 N D:CYS49 4.4 62.1 1.0 CB D:LYS87 4.5 59.0 1.0 CA D:CYS46 4.5 57.6 1.0 CA D:CYS11 4.5 50.4 1.0 CB D:LYS13 4.8 63.7 1.0 O D:CYS85 4.8 60.7 1.0 O D:CYS46 5.0 60.2 1.0 C D:CYS11 5.0 52.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Human SF3B Core Complex


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 Human SF3B Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn203 b:59.6 occ:1.00 SG D:CYS30 2.3 62.6 1.0 SG D:CYS33 2.3 61.4 1.0 SG D:CYS72 2.3 63.7 1.0 SG D:CYS75 2.4 57.3 1.0 CB D:CYS30 2.7 47.9 1.0 CB D:CYS72 3.2 50.1 1.0 CB D:CYS75 3.5 50.4 1.0 N D:CYS72 3.6 56.4 1.0 CB D:CYS33 3.7 64.4 1.0 CA D:CYS72 3.9 52.9 1.0 N D:CYS33 4.0 61.1 1.0 CA D:CYS30 4.2 60.8 1.0 N D:CYS75 4.3 58.5 1.0 CA D:CYS33 4.4 64.4 1.0 CA D:CYS75 4.5 56.3 1.0 CB D:SER35 4.7 64.7 1.0 C D:CYS72 4.7 60.9 1.0 C D:TYR71 4.7 54.7 1.0 CB D:ILE32 4.8 53.2 1.0 C D:CYS30 4.8 68.2 1.0 O D:CYS72 4.9 60.6 1.0 C D:CYS33 4.9 62.1 1.0 N D:SER35 4.9 65.6 1.0 CA D:TYR71 5.0 49.8 1.0

C.Cretu, J.Schmitzova, A.Ponce-Salvatierra, O.Dybkov, E.I.De Laurentiis, K.Sharma, C.L.Will, H.Urlaub, R.Luhrmann, V.Pena. Molecular Architecture of SF3B and Structural Consequences of Its Cancer-Related Mutations. Mol.Cell V. 64 307 2016.
ISSN: ISSN 1097-2765
PubMed: 27720643
DOI: 10.1016/J.MOLCEL.2016.08.036