Zinc in PDB 3lqi: Crystal Structure of MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide

The structure of Crystal Structure of MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide, PDB code: 3lqi was solved by Z.Wang, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.744, 90.584, 125.085, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.1

The binding sites of Zinc atom in the Crystal Structure of MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide (pdb code 3lqi). 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 MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide, PDB code: 3lqi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide


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 MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:24.9 occ:1.00 ND1 A:HIS1596 2.2 16.3 1.0 SG A:CYS1569 2.3 14.4 1.0 SG A:CYS1599 2.4 14.3 1.0 SG A:CYS1572 2.4 16.5 1.0 CB A:CYS1569 3.1 16.1 1.0 CE1 A:HIS1596 3.2 16.0 1.0 CG A:HIS1596 3.2 17.9 1.0 CB A:CYS1572 3.3 18.1 1.0 CB A:HIS1596 3.5 15.8 1.0 CB A:CYS1599 3.5 13.9 1.0 N A:CYS1572 3.7 16.4 1.0 N A:HIS1596 3.9 14.2 1.0 CA A:CYS1572 4.1 17.9 1.0 NZ A:LYS1598 4.1 19.4 1.0 CA A:HIS1596 4.3 14.3 1.0 NE2 A:HIS1596 4.3 15.8 1.0 CD2 A:HIS1596 4.3 16.5 1.0 CA A:CYS1569 4.6 16.3 1.0 CB A:LEU1571 4.7 31.8 1.0 C A:LEU1571 4.8 18.2 1.0 CE A:LYS1598 4.8 20.1 1.0 CA A:CYS1599 4.8 13.4 1.0 C A:CYS1572 4.8 19.0 1.0 N A:ASP1573 4.9 22.1 1.0 N A:LEU1571 4.9 17.1 1.0 C A:CYS1569 5.0 16.5 1.0 C A:VAL1595 5.0 13.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide


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 MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:24.6 occ:1.00 SG A:CYS1591 2.4 16.2 1.0 SG A:CYS1624 2.4 15.4 1.0 SG A:CYS1621 2.4 15.6 1.0 SG A:CYS1588 2.4 14.8 1.0 CB A:CYS1588 3.1 15.2 1.0 CB A:CYS1624 3.2 17.9 1.0 CB A:CYS1591 3.2 16.5 1.0 CB A:CYS1621 3.6 16.9 1.0 N A:CYS1591 3.7 18.7 1.0 CA A:CYS1591 4.0 18.2 1.0 N A:CYS1621 4.0 14.5 1.0 N A:CYS1624 4.1 17.4 1.0 CA A:CYS1624 4.3 17.8 1.0 CA A:CYS1621 4.4 13.9 1.0 CA A:CYS1588 4.6 14.3 1.0 CB A:LYS1590 4.7 23.4 1.0 C A:LYS1590 4.7 19.6 1.0 C A:CYS1591 4.8 20.1 1.0 C A:CYS1621 4.9 15.3 1.0 N A:LYS1590 5.0 18.1 1.0 O A:CYS1621 5.0 14.7 1.0 CA A:LYS1590 5.0 20.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide


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 MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3 b:26.5 occ:1.00 ND1 B:HIS1596 2.3 19.7 1.0 SG B:CYS1569 2.3 20.1 1.0 SG B:CYS1599 2.4 18.4 1.0 SG B:CYS1572 2.4 19.4 1.0 CB B:CYS1569 3.0 21.7 1.0 CG B:HIS1596 3.2 19.7 1.0 CE1 B:HIS1596 3.2 15.3 1.0 CB B:CYS1572 3.3 22.2 1.0 CB B:HIS1596 3.4 19.1 1.0 CB B:CYS1599 3.5 15.9 1.0 N B:CYS1572 3.7 21.1 1.0 N B:HIS1596 3.9 18.4 1.0 CA B:CYS1572 4.1 21.3 1.0 CA B:HIS1596 4.2 18.2 1.0 NE2 B:HIS1596 4.3 19.2 1.0 CD2 B:HIS1596 4.3 19.2 1.0 O B:HOH291 4.3 40.2 1.0 CA B:CYS1569 4.5 20.3 1.0 CB B:LEU1571 4.6 23.8 1.0 C B:LEU1571 4.7 26.9 1.0 NZ B:LYS1598 4.7 24.5 1.0 CA B:CYS1599 4.9 13.9 1.0 C B:CYS1569 4.9 20.3 1.0 O B:HIS1596 4.9 18.1 1.0 C B:CYS1572 4.9 21.7 1.0 N B:LEU1571 5.0 25.9 1.0 O B:CYS1569 5.0 21.4 1.0 CA B:LEU1571 5.0 26.5 1.0 C B:VAL1595 5.0 17.3 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide


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 MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4 b:38.3 occ:1.00 SG B:CYS1621 2.4 25.1 1.0 SG B:CYS1624 2.4 30.3 1.0 SG B:CYS1588 2.4 24.0 1.0 SG B:CYS1591 2.5 31.4 1.0 CB B:CYS1588 3.2 23.0 1.0 CB B:CYS1624 3.2 30.5 1.0 CB B:CYS1591 3.3 33.9 1.0 CB B:CYS1621 3.5 23.2 1.0 N B:CYS1591 3.7 34.7 1.0 N B:CYS1621 4.0 22.6 1.0 CA B:CYS1591 4.1 33.4 1.0 CA B:CYS1621 4.3 22.8 1.0 N B:CYS1624 4.3 28.4 1.0 O B:HOH253 4.4 43.8 1.0 CA B:CYS1624 4.4 30.2 1.0 CA B:CYS1588 4.6 24.6 1.0 CB B:LYS1590 4.7 45.7 1.0 C B:LYS1590 4.7 38.5 1.0 C B:CYS1591 4.8 33.2 1.0 O B:CYS1621 4.9 21.1 1.0 C B:CYS1621 4.9 22.6 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide


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 MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn5 b:31.5 occ:1.00 ND1 C:HIS1596 2.2 20.3 1.0 SG C:CYS1599 2.4 23.3 1.0 SG C:CYS1572 2.4 19.9 1.0 SG C:CYS1569 2.4 23.4 1.0 CG C:HIS1596 3.1 21.7 1.0 CB C:CYS1569 3.1 23.5 1.0 CE1 C:HIS1596 3.2 20.2 1.0 CB C:CYS1572 3.3 20.8 1.0 CB C:HIS1596 3.4 20.9 1.0 CB C:CYS1599 3.5 23.4 1.0 N C:CYS1572 3.7 20.2 1.0 N C:HIS1596 4.0 19.2 1.0 CA C:CYS1572 4.1 20.4 1.0 CD2 C:HIS1596 4.2 21.6 1.0 NE2 C:HIS1596 4.2 22.5 1.0 CA C:HIS1596 4.3 19.1 1.0 NZ C:LYS1598 4.5 55.2 1.0 CA C:CYS1569 4.5 25.2 1.0 CB C:LEU1571 4.6 26.8 1.0 C C:LEU1571 4.6 27.9 1.0 CA C:CYS1599 4.8 21.5 1.0 O C:CYS1569 4.8 23.2 1.0 C C:CYS1569 4.9 24.4 1.0 N C:LEU1571 4.9 28.6 1.0 CA C:LEU1571 4.9 27.5 1.0 C C:CYS1572 5.0 21.6 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide


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 MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn6 b:52.2 occ:1.00 SG C:CYS1621 2.5 52.7 1.0 SG C:CYS1591 2.5 39.7 1.0 SG C:CYS1588 2.6 38.5 1.0 SG C:CYS1624 2.6 49.2 1.0 CB C:CYS1621 3.1 52.2 1.0 CB C:CYS1588 3.3 38.1 1.0 CB C:CYS1624 3.5 50.7 1.0 CB C:CYS1591 3.5 42.8 1.0 N C:CYS1621 3.8 42.9 1.0 N C:CYS1591 3.9 52.4 1.0 CA C:CYS1621 4.0 44.8 1.0 N C:CYS1624 4.1 53.3 1.0 CA C:CYS1591 4.3 51.5 1.0 CA C:CYS1624 4.4 52.5 1.0 C C:CYS1621 4.5 45.3 1.0 CB C:LYS1590 4.5 55.8 1.0 O C:CYS1621 4.7 45.3 1.0 CB C:ASN1623 4.7 56.2 1.0 C C:ASN1623 4.7 54.5 1.0 N C:ASN1623 4.7 53.8 1.0 CA C:CYS1588 4.8 32.7 1.0 C C:LYS1590 4.9 51.5 1.0 C C:CYS1591 4.9 52.0 1.0 CB C:ARG1593 5.0 49.0 1.0 C C:THR1620 5.0 38.6 1.0 CA C:ASN1623 5.0 54.6 1.0

Z.Wang, J.Song, T.A.Milne, G.G.Wang, H.Li, C.D.Allis, D.J.Patel. Pro Isomerization in MLL1 PHD3-Bromo Cassette Connects H3K4ME Readout to CYP33 and Hdac-Mediated Repression. Cell(Cambridge,Mass.) V. 141 1183 2010.
ISSN: ISSN 0092-8674
PubMed: 20541251
DOI: 10.1016/J.CELL.2010.05.016