Zinc in PDB 4l58: Crystal Structure of the MLL5 Phd Finger in Complex with H3K4ME3

All present enzymatic activity of Crystal Structure of the MLL5 Phd Finger in Complex with H3K4ME3:
2.1.1.43;

The structure of Crystal Structure of the MLL5 Phd Finger in Complex with H3K4ME3, PDB code: 4l58 was solved by Q.Tong, M.Ali, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.00 / 1.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	31.286, 43.638, 52.856, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / 14

The binding sites of Zinc atom in the Crystal Structure of the MLL5 Phd Finger in Complex with H3K4ME3 (pdb code 4l58). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the MLL5 Phd Finger in Complex with H3K4ME3, PDB code: 4l58:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the MLL5 Phd Finger in Complex with H3K4ME3


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 MLL5 Phd Finger in Complex with H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:10.0 occ:1.00 SG A:CYS22 2.3 10.0 1.0 SG A:CYS47 2.3 10.7 1.0 SG A:CYS19 2.3 8.4 1.0 SG A:CYS44 2.3 9.4 1.0 HB2 A:CYS47 2.9 12.3 1.0 HB3 A:CYS22 3.0 13.3 1.0 H A:CYS22 3.1 12.4 1.0 H A:CYS44 3.1 10.1 1.0 CB A:CYS47 3.2 10.3 1.0 CB A:CYS22 3.2 11.1 1.0 CB A:CYS19 3.3 8.0 1.0 HB3 A:CYS19 3.3 9.5 1.0 HB3 A:CYS44 3.3 9.6 1.0 HB2 A:CYS19 3.3 9.5 1.0 CB A:CYS44 3.4 8.0 1.0 H A:CYS47 3.6 13.1 1.0 HB3 A:LYS21 3.7 13.6 1.0 HG22 A:VAL24 3.7 10.4 1.0 N A:CYS22 3.7 10.3 1.0 HB3 A:CYS47 3.9 12.3 1.0 N A:CYS44 3.9 8.4 1.0 O A:HOH281 4.0 39.8 1.0 HB2 A:CYS22 4.0 13.3 1.0 CA A:CYS22 4.1 10.4 1.0 N A:CYS47 4.1 10.9 1.0 CA A:CYS44 4.2 9.2 1.0 HB2 A:CYS44 4.2 9.6 1.0 O A:HOH209 4.3 14.8 1.0 CA A:CYS47 4.3 10.1 1.0 HH21 A:ARG4 4.4 13.4 1.0 HB2 A:ARG46 4.4 19.7 1.0 H A:LYS21 4.5 11.5 1.0 H A:SER23 4.6 13.4 1.0 H A:VAL24 4.6 10.5 1.0 CG2 A:VAL24 4.6 8.7 1.0 HA A:LEU43 4.6 9.9 1.0 CB A:LYS21 4.7 11.3 1.0 HG21 A:VAL24 4.7 10.4 1.0 CA A:CYS19 4.7 7.5 1.0 HA A:CYS47 4.7 12.2 1.0 H A:ARG46 4.7 12.7 1.0 HG2 A:LYS21 4.8 13.9 1.0 C A:CYS22 4.8 11.0 1.0 C A:CYS44 4.8 9.8 1.0 HD22 A:LEU43 4.8 21.4 1.0 HD3 A:LYS21 4.8 15.7 1.0 C A:LYS21 4.9 10.8 1.0 HB3 A:LEU43 4.9 12.8 1.0 HA A:CYS22 4.9 12.5 1.0 N A:SER23 4.9 11.2 1.0 O A:CYS44 4.9 8.7 1.0 HA A:CYS19 5.0 9.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the MLL5 Phd Finger in Complex with H3K4ME3


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 MLL5 Phd Finger in Complex with H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:7.4 occ:1.00 ND1 A:HIS27 2.1 6.8 1.0 SG A:CYS30 2.3 7.2 1.0 SG A:CYS5 2.3 6.8 1.0 SG A:CYS7 2.3 7.1 1.0 HB2 A:HIS27 2.8 8.4 1.0 HB3 A:CYS5 2.9 9.1 1.0 HB3 A:CYS7 3.0 8.0 1.0 HG3 A:GLN61 3.0 9.5 1.0 HB2 A:CYS30 3.0 8.5 1.0 CE1 A:HIS27 3.1 7.4 1.0 CG A:HIS27 3.1 6.4 1.0 CB A:CYS30 3.1 7.1 1.0 CB A:CYS5 3.2 7.6 1.0 H A:CYS7 3.2 11.0 1.0 HE1 A:HIS27 3.2 8.8 1.0 CB A:CYS7 3.3 6.7 1.0 HB3 A:CYS30 3.3 8.5 1.0 H A:HIS27 3.4 7.8 1.0 CB A:HIS27 3.4 7.0 1.0 HB2 A:CYS5 3.6 9.1 1.0 HE21 A:GLN61 3.7 10.6 1.0 CG A:GLN61 3.8 7.9 1.0 HG2 A:GLN61 3.9 9.5 1.0 HB2 A:CYS7 4.0 8.0 1.0 N A:CYS7 4.0 9.1 1.0 HB1 A:ALA57 4.0 9.2 1.0 HB3 A:HIS27 4.1 8.4 1.0 NE2 A:GLN61 4.1 8.8 1.0 N A:HIS27 4.1 6.5 1.0 NE2 A:HIS27 4.2 6.9 1.0 CD2 A:HIS27 4.2 7.0 1.0 CD A:GLN61 4.2 8.1 1.0 CA A:CYS7 4.2 8.9 1.0 CA A:HIS27 4.4 6.9 1.0 H A:ILE6 4.4 10.1 1.0 H A:CYS30 4.4 8.7 1.0 CA A:CYS5 4.5 7.2 1.0 CA A:CYS30 4.6 7.1 1.0 N A:ILE6 4.7 8.4 1.0 HE22 A:GLN61 4.7 10.6 1.0 HB2 A:PHE9 4.7 9.0 1.0 C A:CYS5 4.7 8.5 1.0 H A:PHE9 4.7 9.8 1.0 HG12 A:ILE6 4.8 10.5 1.0 O A:HIS27 4.8 7.5 1.0 H A:GLY8 4.8 9.2 1.0 HG13 A:ILE6 4.9 10.5 1.0 HA A:CYS30 4.9 8.5 1.0 HA A:CYS5 4.9 8.7 1.0 CB A:ALA57 5.0 7.7 1.0 HE2 A:HIS27 5.0 8.3 1.0 HA A:CYS7 5.0 10.7 1.0 N A:CYS30 5.0 7.2 1.0

M.Ali, H.Rincon-Arano, W.Zhao, S.B.Rothbart, Q.Tong, S.M.Parkhurst, B.D.Strahl, L.W.Deng, M.Groudine, T.G.Kutateladze. Molecular Basis For Chromatin Binding and Regulation of MLL5. Proc.Natl.Acad.Sci.Usa V. 110 11296 2013.
ISSN: ISSN 0027-8424
PubMed: 23798402
DOI: 10.1073/PNAS.1310156110