Zinc in PDB 5syb: Crystal Structure of Human PHF5A

The structure of Crystal Structure of Human PHF5A, PDB code: 5syb was solved by J.H.C.Tsai, T.Teng, P.Zhu, P.Fekkes, N.A.Larsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.06 / 1.82
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	82.116, 82.116, 82.116, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.3

The binding sites of Zinc atom in the Crystal Structure of Human PHF5A (pdb code 5syb). 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 Human PHF5A, PDB code: 5syb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Human PHF5A


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 Human PHF5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:22.8 occ:1.00 SG A:CYS11 2.3 22.2 1.0 SG A:CYS49 2.3 25.6 1.0 SG A:CYS85 2.3 20.2 1.0 SG A:CYS46 2.4 21.3 1.0 CB A:CYS85 3.1 19.6 1.0 CB A:CYS11 3.1 22.2 1.0 CB A:CYS49 3.2 23.0 1.0 CB A:CYS46 3.5 21.8 1.0 N A:CYS46 3.9 19.4 1.0 N A:CYS49 4.1 20.4 1.0 CA A:CYS49 4.3 23.8 1.0 CA A:CYS46 4.3 18.6 1.0 CA A:CYS85 4.5 19.7 1.0 CE A:LYS13 4.5 43.5 1.0 CA A:CYS11 4.6 23.3 1.0 CB A:LYS13 4.7 23.2 1.0 CB A:LYS87 4.7 28.2 1.0 O A:CYS46 4.8 19.5 1.0 C A:CYS46 4.9 18.0 1.0 C A:CYS85 4.9 19.0 1.0 NZ A:LYS13 4.9 53.9 1.0 N A:LYS13 4.9 19.1 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Human PHF5A


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 Human PHF5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:23.1 occ:1.00 SG A:CYS75 2.3 26.1 1.0 SG A:CYS30 2.3 20.2 1.0 SG A:CYS72 2.3 22.4 1.0 SG A:CYS33 2.4 23.2 1.0 CB A:CYS30 3.2 21.0 1.0 CB A:CYS75 3.2 22.0 1.0 CB A:CYS33 3.4 24.1 1.0 CB A:CYS72 3.4 21.5 1.0 N A:CYS33 3.8 24.2 1.0 N A:CYS72 4.0 17.7 1.0 N A:CYS75 4.0 20.5 1.0 CA A:CYS33 4.2 26.3 1.0 CA A:CYS75 4.2 21.4 1.0 CA A:CYS72 4.2 19.5 1.0 OG A:SER35 4.4 31.0 1.0 CB A:ILE32 4.6 24.1 1.0 CA A:CYS30 4.6 22.5 1.0 O A:CYS72 4.7 17.2 1.0 C A:CYS72 4.7 18.3 1.0 C A:ILE32 4.8 26.3 1.0 C A:CYS33 4.9 30.4 1.0 N A:ILE32 5.0 22.8 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Human PHF5A


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 Human PHF5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:29.3 occ:1.00 SG A:CYS23 2.3 29.8 1.0 SG A:CYS61 2.3 30.4 1.0 SG A:CYS26 2.3 31.3 1.0 SG A:CYS58 2.4 25.0 1.0 CB A:CYS26 3.2 29.0 1.0 CB A:CYS58 3.2 25.0 1.0 CB A:CYS61 3.4 31.1 1.0 CB A:CYS23 3.5 27.9 1.0 N A:CYS61 3.7 28.8 1.0 N A:CYS23 4.0 23.7 1.0 N A:CYS26 4.1 31.0 1.0 CA A:CYS61 4.1 31.6 1.0 CA A:CYS26 4.3 31.7 1.0 CA A:CYS23 4.3 26.0 1.0 CB A:ILE60 4.5 32.2 1.0 CA A:CYS58 4.6 22.6 1.0 N A:GLY63 4.7 28.8 1.0 C A:ILE60 4.7 30.2 1.0 C A:CYS61 4.8 39.5 1.0 N A:GLY62 4.8 30.9 1.0 C A:CYS23 4.9 30.8 1.0 CA A:ILE60 5.0 27.1 1.0 CG2 A:ILE60 5.0 31.4 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Human PHF5A


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 Human PHF5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:22.5 occ:1.00 SG B:CYS46 2.3 21.2 1.0 SG B:CYS49 2.4 23.2 1.0 SG B:CYS11 2.4 22.5 1.0 SG B:CYS85 2.4 21.0 1.0 CB B:CYS85 3.1 19.6 1.0 CB B:CYS11 3.2 24.4 1.0 CB B:CYS49 3.3 22.7 1.0 CB B:CYS46 3.5 18.9 1.0 N B:CYS46 4.0 18.0 1.0 N B:CYS49 4.2 21.3 1.0 CA B:CYS46 4.3 17.4 1.0 CA B:CYS49 4.3 23.7 1.0 CA B:CYS85 4.6 21.8 1.0 CB B:LYS87 4.6 26.9 1.0 CA B:CYS11 4.6 24.1 1.0 CB B:LYS13 4.7 23.8 1.0 CE B:LYS13 4.8 45.1 1.0 C B:CYS46 4.8 20.4 1.0 O B:CYS46 4.9 19.7 1.0 N B:LYS13 4.9 21.1 1.0 C B:CYS85 5.0 22.0 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Human PHF5A


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 Human PHF5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:29.1 occ:1.00 SG B:CYS72 2.3 25.4 1.0 SG B:CYS30 2.3 26.6 1.0 SG B:CYS75 2.3 29.8 1.0 SG B:CYS33 2.4 30.4 1.0 CB B:CYS30 3.1 28.6 1.0 CB B:CYS75 3.3 24.5 1.0 CB B:CYS33 3.3 31.2 1.0 CB B:CYS72 3.3 22.6 1.0 N B:CYS33 3.8 31.7 1.0 N B:CYS72 4.0 23.4 1.0 N B:CYS75 4.0 22.1 1.0 CA B:CYS72 4.2 22.0 1.0 CA B:CYS33 4.2 35.0 1.0 CA B:CYS75 4.3 23.4 1.0 OG B:SER35 4.3 47.5 1.0 CB B:ILE32 4.6 27.1 1.0 CA B:CYS30 4.6 25.3 1.0 O B:CYS72 4.7 21.6 1.0 C B:CYS72 4.7 22.4 1.0 C B:ILE32 4.8 33.8 1.0 C B:CYS33 4.9 35.9 1.0 N B:ILE32 5.0 25.1 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Human PHF5A


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 Human PHF5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:26.9 occ:1.00 SG B:CYS23 2.3 28.4 1.0 SG B:CYS26 2.3 30.7 1.0 SG B:CYS61 2.4 25.5 1.0 SG B:CYS58 2.4 22.6 1.0 CB B:CYS26 3.1 29.9 1.0 CB B:CYS58 3.2 18.5 1.0 CB B:CYS61 3.4 23.3 1.0 CB B:CYS23 3.5 24.1 1.0 N B:CYS61 3.8 23.1 1.0 N B:CYS23 3.9 25.5 1.0 N B:CYS26 4.1 32.0 1.0 CA B:CYS61 4.2 25.4 1.0 CA B:CYS26 4.2 30.4 1.0 CA B:CYS23 4.3 28.6 1.0 CB B:ILE60 4.3 26.5 1.0 CA B:CYS58 4.7 20.2 1.0 C B:ILE60 4.8 28.1 1.0 N B:GLY63 4.8 21.6 1.0 C B:CYS61 4.8 24.8 1.0 CG2 B:ILE60 4.9 33.6 1.0 N B:GLY62 4.9 22.5 1.0 C B:CYS23 4.9 29.6 1.0 CA B:ILE60 5.0 26.1 1.0

T.Teng, J.H.Tsai, X.Puyang, M.Seiler, S.Peng, S.Prajapati, D.Aird, S.Buonamici, B.Caleb, B.Chan, L.Corson, J.Feala, P.Fekkes, B.Gerard, C.Karr, M.Korpal, X.Liu, J.T Lowe, Y.Mizui, J.Palacino, E.Park, P.G.Smith, V.Subramanian, Z.J.Wu, J.Zou, L.Yu, A.Chicas, M.Warmuth, N.Larsen, P.Zhu. Splicing Modulators Act at the Branch Point Adenosine Binding Pocket Defined By the PHF5A-SF3B Complex. Nat Commun V. 8 15522 2017.
ISSN: ESSN 2041-1723
PubMed: 28541300
DOI: 10.1038/NCOMMS15522