Zinc in PDB 8ytf: Crystal Structures of Human IRF2BP2 Ring Domain in Complex with VGLL4 Peptide

The structure of Crystal Structures of Human IRF2BP2 Ring Domain in Complex with VGLL4 Peptide, PDB code: 8ytf was solved by G.C.Wang, J.P.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.43 / 1.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	33.372, 43.209, 55.761, 90, 90, 90
R / Rfree (%)	15.3 / 17.3

The binding sites of Zinc atom in the Crystal Structures of Human IRF2BP2 Ring Domain in Complex with VGLL4 Peptide (pdb code 8ytf). 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 Structures of Human IRF2BP2 Ring Domain in Complex with VGLL4 Peptide, PDB code: 8ytf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structures of Human IRF2BP2 Ring Domain in Complex with VGLL4 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structures of Human IRF2BP2 Ring Domain in Complex with VGLL4 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:10.0 occ:1.00 SG A:CYS533 2.3 9.8 1.0 SG A:CYS509 2.3 9.3 1.0 SG A:CYS506 2.3 8.4 1.0 SG A:CYS530 2.4 10.8 1.0 CB A:CYS533 3.2 7.7 1.0 CB A:CYS509 3.2 9.1 1.0 CB A:CYS506 3.2 9.6 1.0 CB A:CYS530 3.6 10.9 1.0 N A:CYS509 3.7 9.3 1.0 N A:CYS530 4.0 9.6 1.0 CA A:CYS509 4.0 9.6 1.0 N A:CYS533 4.3 9.7 1.0 CA A:CYS533 4.3 9.0 1.0 CA A:CYS530 4.4 9.4 1.0 CA A:CYS506 4.7 9.6 1.0 C A:LEU508 4.7 10.6 1.0 C A:CYS509 4.8 10.8 1.0 CB A:LEU508 4.8 8.7 1.0 O A:CYS530 4.9 9.8 1.0 C A:CYS530 4.9 9.3 1.0 N A:HIS510 5.0 8.9 1.0

Zinc binding site 2 out of 3 in the Crystal Structures of Human IRF2BP2 Ring Domain in Complex with VGLL4 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structures of Human IRF2BP2 Ring Domain in Complex with VGLL4 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:9.1 occ:1.00 ND1 A:HIS527 2.1 7.7 1.0 SG A:CYS555 2.3 9.7 1.0 SG A:CYS521 2.4 7.8 1.0 SG A:CYS549 2.4 8.6 1.0 CE1 A:HIS527 3.0 8.8 1.0 CG A:HIS527 3.2 9.5 1.0 CB A:CYS555 3.2 8.7 1.0 CB A:CYS521 3.2 9.2 1.0 CB A:CYS549 3.3 7.8 1.0 CB A:HIS527 3.5 9.2 1.0 OG A:SER551 3.6 9.4 1.0 CG2 A:VAL524 4.0 11.4 1.0 CB A:VAL524 4.1 10.6 1.0 NE2 A:HIS527 4.2 9.8 1.0 CD2 A:HIS527 4.3 9.1 1.0 NE1 A:TRP564 4.3 7.9 1.0 CB A:SER551 4.5 9.5 1.0 CA A:CYS555 4.6 9.4 1.0 CA A:CYS521 4.6 7.8 1.0 CA A:CYS549 4.7 7.2 1.0 N A:CYS555 4.8 8.5 1.0 O A:HOH711 4.8 13.6 1.0 CG1 A:VAL524 5.0 9.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structures of Human IRF2BP2 Ring Domain in Complex with VGLL4 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structures of Human IRF2BP2 Ring Domain in Complex with VGLL4 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:15.5 occ:1.00 N A:SER497 2.0 11.8 1.0 O A:SER497 2.1 11.2 1.0 O A:HOH744 2.1 18.4 1.0 O A:HOH741 2.2 22.6 1.0 O A:HOH774 2.3 17.8 1.0 C A:SER497 2.7 13.2 1.0 CA A:SER497 2.8 13.1 1.0 OG A:SER497 3.6 35.2 1.0 CB A:SER497 3.8 23.2 1.0 O A:HOH782 4.0 35.0 1.0 N A:LEU498 4.0 13.3 1.0 O A:HOH793 4.3 26.9 1.0 O A:HOH794 4.5 36.1 1.0 CA A:LEU498 4.8 12.0 1.0

G.C.Wang, J.P.Ding. IRF2BP2 Recognizes and Bind to A Conserved Rxsvi Sequence Motif of Protein Partners and Interacts with ZBTB16 to Regulate Megakaryocytic Differentiation To Be Published.