Zinc in PDB 5vdc: Crystal Structure of the Human DPF2 Tandem Phd Finger Domain

The structure of Crystal Structure of the Human DPF2 Tandem Phd Finger Domain, PDB code: 5vdc was solved by F.M.Huber, A.M.Davenport, A.Hoelz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.75 / 1.60
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	107.500, 107.500, 53.300, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 19.1

The binding sites of Zinc atom in the Crystal Structure of the Human DPF2 Tandem Phd Finger Domain (pdb code 5vdc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Human DPF2 Tandem Phd Finger Domain, PDB code: 5vdc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Human DPF2 Tandem Phd Finger 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 Human DPF2 Tandem Phd Finger Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:27.8 occ:1.00 ND1 A:HIS34 2.0 29.4 1.0 SG A:CYS37 2.3 31.0 1.0 SG A:CYS7 2.3 27.9 1.0 SG A:CYS4 2.3 28.1 1.0 CE1 A:HIS34 2.9 30.7 1.0 HB2 A:HIS34 3.0 33.0 1.0 HE1 A:HIS34 3.1 36.9 1.0 HB3 A:CYS7 3.1 32.6 1.0 HB3 A:CYS4 3.1 32.7 1.0 CG A:HIS34 3.1 27.6 1.0 CB A:CYS4 3.2 27.2 1.0 HB2 A:CYS37 3.2 35.6 1.0 H A:CYS7 3.2 34.5 1.0 HB2 A:CYS4 3.2 32.7 1.0 H A:HIS34 3.3 34.4 1.0 CB A:CYS7 3.3 27.1 1.0 CB A:CYS37 3.3 29.7 1.0 CB A:HIS34 3.5 27.5 1.0 HB3 A:CYS37 3.6 35.6 1.0 HB2 A:PHE6 3.8 34.5 1.0 N A:CYS7 3.8 28.8 1.0 HZ1 A:LYS16 3.9 28.8 0.3 HD21 A:ASN14 3.9 41.8 1.0 ND2 A:ASN14 4.0 34.9 1.0 HB2 A:CYS7 4.1 32.6 1.0 N A:HIS34 4.1 28.7 1.0 NE2 A:HIS34 4.1 32.7 1.0 CA A:CYS7 4.1 27.7 1.0 CG A:ASN14 4.2 30.9 1.0 CD2 A:HIS34 4.2 31.0 1.0 HA A:ASN14 4.2 36.7 1.0 OD1 A:ASN14 4.3 32.5 1.0 HB3 A:HIS34 4.3 33.0 1.0 H A:GLY9 4.3 32.4 1.0 HD22 A:ASN14 4.4 41.8 1.0 CA A:HIS34 4.4 29.2 1.0 H A:PHE6 4.4 38.1 1.0 H A:LYS15 4.4 34.1 1.0 H A:CYS37 4.6 37.6 1.0 CA A:CYS4 4.6 26.8 1.0 CB A:PHE6 4.7 28.8 1.0 CA A:CYS37 4.7 29.7 1.0 NZ A:LYS16 4.7 24.0 0.3 C A:PHE6 4.8 30.3 1.0 H A:LEU8 4.8 31.0 1.0 HA2 A:GLY33 4.8 36.3 1.0 HD2 A:PHE6 4.8 42.6 1.0 H A:LYS16 4.8 37.2 0.7 HE2 A:HIS34 4.8 39.2 1.0 C A:CYS7 4.8 25.7 1.0 H A:LYS16 4.9 36.4 0.3 HA A:CYS7 4.9 33.2 1.0 HZ3 A:LYS16 4.9 28.8 0.3 HA A:CYS4 5.0 32.1 1.0 HA A:CYS37 5.0 35.6 1.0 HA3 A:GLY9 5.0 36.4 1.0 CA A:ASN14 5.0 30.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Human DPF2 Tandem Phd Finger 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 Human DPF2 Tandem Phd Finger Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:31.3 occ:1.00 SG A:CYS29 2.3 35.0 1.0 SG A:CYS55 2.3 31.1 1.0 SG A:CYS26 2.4 29.2 1.0 SG A:CYS58 2.4 33.5 1.0 H A:CYS29 2.9 43.3 1.0 HB2 A:CYS58 3.0 36.4 1.0 HB3 A:CYS29 3.2 41.1 1.0 H A:CYS55 3.3 33.8 1.0 CB A:CYS26 3.3 31.1 1.0 HB3 A:CYS26 3.3 37.3 1.0 CB A:CYS58 3.3 30.4 1.0 CB A:CYS29 3.3 34.3 1.0 HB2 A:CYS26 3.3 37.3 1.0 HB3 A:CYS55 3.4 33.2 1.0 CB A:CYS55 3.5 27.7 1.0 HB3 A:ASP28 3.6 50.0 0.4 HB3 A:ARG31 3.7 48.8 1.0 N A:CYS29 3.7 36.1 1.0 H A:CYS58 3.8 37.8 1.0 HB3 A:CYS58 3.9 36.4 1.0 HB2 A:ASP28 3.9 48.5 0.6 N A:CYS55 4.0 28.2 1.0 CA A:CYS29 4.0 33.7 1.0 HB2 A:CYS29 4.1 41.1 1.0 HB3 A:GLU57 4.1 43.1 1.0 H A:ARG31 4.2 45.5 1.0 N A:CYS58 4.2 31.5 1.0 CA A:CYS55 4.3 29.7 1.0 HB2 A:CYS55 4.3 33.2 1.0 H A:GLY30 4.4 44.2 1.0 H A:ASP28 4.4 42.0 0.6 CA A:CYS58 4.4 30.1 1.0 H A:ASP28 4.4 44.5 0.4 HB2 A:ARG31 4.4 48.8 1.0 CB A:ARG31 4.5 40.7 1.0 CB A:ASP28 4.5 41.6 0.4 O A:HOH316 4.6 50.5 1.0 C A:CYS29 4.7 35.1 1.0 CA A:CYS26 4.7 29.3 1.0 N A:GLY30 4.7 36.9 1.0 C A:CYS55 4.8 29.1 1.0 C A:ASP28 4.8 38.4 0.6 HA A:GLN54 4.8 31.0 1.0 O A:CYS55 4.8 29.4 1.0 CB A:ASP28 4.8 40.4 0.6 C A:ASP28 4.8 39.1 0.4 HA A:CYS29 4.9 40.4 1.0 HA A:CYS58 4.9 36.1 1.0 H A:GLU57 4.9 38.0 1.0 N A:ARG31 4.9 38.0 1.0 HB3 A:GLN54 5.0 30.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Human DPF2 Tandem Phd Finger 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 Human DPF2 Tandem Phd Finger Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:25.3 occ:1.00 SG A:CYS105 2.3 26.9 1.0 SG A:CYS76 2.3 24.6 1.0 SG A:CYS79 2.3 25.0 1.0 SG A:CYS102 2.3 26.0 1.0 HB2 A:CYS105 3.0 32.9 1.0 HB3 A:CYS79 3.0 27.4 1.0 HB3 A:CYS76 3.1 29.8 1.0 CB A:CYS76 3.1 24.8 1.0 H A:CYS79 3.2 28.2 1.0 H A:CYS102 3.2 31.0 1.0 HB2 A:CYS76 3.2 29.8 1.0 CB A:CYS79 3.3 22.8 1.0 CB A:CYS105 3.3 27.4 1.0 HB3 A:CYS102 3.4 32.1 1.0 CB A:CYS102 3.5 26.8 1.0 H A:CYS105 3.5 35.8 1.0 HB2 A:ASP78 3.6 34.3 1.0 N A:CYS79 3.7 23.5 1.0 HH21 A:ARG81 3.7 31.7 1.0 N A:CYS102 3.9 25.8 1.0 HB3 A:CYS105 3.9 32.9 1.0 HH A:TYR83 4.0 35.4 1.0 HB2 A:CYS79 4.1 27.4 1.0 CA A:CYS79 4.1 22.6 1.0 N A:CYS105 4.1 29.9 1.0 HE1 A:TYR83 4.2 29.9 1.0 CA A:CYS102 4.2 26.8 1.0 H A:ASP78 4.2 32.2 1.0 HB2 A:LEU104 4.3 36.0 1.0 CA A:CYS105 4.3 28.5 1.0 HB2 A:CYS102 4.3 32.1 1.0 HB2 A:ARG81 4.3 29.8 1.0 NH2 A:ARG81 4.4 26.4 1.0 HH22 A:ARG81 4.4 31.7 1.0 H A:ARG81 4.5 28.6 1.0 CB A:ASP78 4.5 28.6 1.0 HD2 A:ARG81 4.5 29.0 1.0 O A:HOH370 4.5 34.7 1.0 CA A:CYS76 4.6 23.4 1.0 HA A:CYS105 4.6 34.2 1.0 C A:ASP78 4.6 26.4 1.0 HA A:SER101 4.7 32.0 1.0 O A:CYS102 4.7 27.2 1.0 H A:ASP80 4.7 29.2 1.0 C A:CYS102 4.7 26.9 1.0 HB3 A:ASP78 4.8 34.3 1.0 OH A:TYR83 4.8 29.5 1.0 HA A:CYS79 4.8 27.1 1.0 C A:CYS79 4.9 23.3 1.0 N A:ASP78 4.9 26.8 1.0 CA A:ASP78 4.9 27.1 1.0 HA A:CYS76 5.0 28.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Human DPF2 Tandem Phd Finger 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 Human DPF2 Tandem Phd Finger Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:27.8 occ:1.00 ND1 A:HIS84 2.1 26.7 1.0 SG A:CYS87 2.2 29.3 1.0 SG A:CYS64 2.3 28.6 1.0 SG A:CYS61 2.4 24.8 1.0 HB2 A:HIS84 2.8 33.4 1.0 HB3 A:CYS61 2.9 30.5 1.0 H A:CYS64 3.0 33.4 1.0 CB A:CYS61 3.0 25.4 1.0 CE1 A:HIS84 3.0 29.7 1.0 HB3 A:CYS64 3.0 35.5 1.0 HB2 A:CYS61 3.1 30.5 1.0 CG A:HIS84 3.1 25.9 1.0 HE1 A:HIS84 3.2 35.7 1.0 HB2 A:CYS87 3.2 31.4 1.0 CB A:CYS64 3.2 29.6 1.0 CB A:CYS87 3.3 26.1 1.0 H A:HIS84 3.3 28.7 1.0 CB A:HIS84 3.4 27.9 1.0 HB3 A:CYS87 3.6 31.4 1.0 N A:CYS64 3.7 27.8 1.0 HB A:ILE63 3.8 33.1 1.0 HE2 A:TYR86 3.9 42.7 1.0 HB2 A:CYS64 4.0 35.5 1.0 CA A:CYS64 4.0 28.1 1.0 N A:HIS84 4.1 23.9 1.0 HB3 A:HIS84 4.1 33.4 1.0 NE2 A:HIS84 4.1 29.2 1.0 O A:HOH358 4.2 42.3 1.0 CD2 A:HIS84 4.2 27.8 1.0 CE2 A:TYR86 4.3 35.6 1.0 CA A:HIS84 4.4 25.5 1.0 HH A:TYR86 4.4 43.0 1.0 CA A:CYS61 4.5 26.7 1.0 H A:GLY65 4.5 34.7 1.0 H A:ILE63 4.5 28.2 1.0 H A:THR66 4.5 37.2 1.0 CA A:CYS87 4.7 28.4 1.0 CB A:ILE63 4.7 27.6 1.0 H A:CYS87 4.7 34.0 1.0 HA A:CYS64 4.8 33.7 1.0 CZ A:TYR86 4.8 34.0 1.0 OH A:TYR86 4.8 35.8 1.0 C A:ILE63 4.8 25.9 1.0 C A:CYS64 4.8 27.2 1.0 HG22 A:ILE63 4.9 36.6 1.0 O A:HOH412 4.9 44.4 1.0 HA A:CYS61 4.9 32.1 1.0 N A:GLY65 4.9 28.9 1.0 HE2 A:HIS84 4.9 35.0 1.0 CD2 A:TYR86 4.9 32.8 1.0 HA A:TYR83 5.0 28.3 1.0 HA A:CYS87 5.0 34.1 1.0 OG1 A:THR66 5.0 36.5 1.0 H A:CYS61 5.0 33.9 1.0 HD2 A:TYR86 5.0 39.4 1.0

F.M.Huber, S.M.Greenblatt, A.M.Davenport, C.Martinez, Y.Xu, L.P.Vu, S.D.Nimer, A.Hoelz. Histone-Binding of DPF2 Mediates Its Repressive Role in Myeloid Differentiation. Proc. Natl. Acad. Sci. V. 114 6016 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28533407
DOI: 10.1073/PNAS.1700328114