Zinc in PDB 6mlc: PHD6 Domain of MLL3 in Complex with Histone H4

All present enzymatic activity of PHD6 Domain of MLL3 in Complex with Histone H4:
2.1.1.43;

The structure of PHD6 Domain of MLL3 in Complex with Histone H4, PDB code: 6mlc was solved by A.Dong, Y.Liu, S.Qin, M.Lei, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.00 / 1.80
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	85.939, 85.939, 98.733, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 21.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the PHD6 Domain of MLL3 in Complex with Histone H4 (pdb code 6mlc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the PHD6 Domain of MLL3 in Complex with Histone H4, PDB code: 6mlc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the PHD6 Domain of MLL3 in Complex with Histone H4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PHD6 Domain of MLL3 in Complex with Histone H4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:21.9 occ:1.00 ND1 B:HIS1059 2.1 25.0 1.0 SG A:CYS1081 2.2 21.6 1.0 SG A:CYS1069 2.3 22.8 1.0 SG A:CYS1078 2.3 21.6 1.0 CE1 B:HIS1059 3.0 25.1 1.0 CB A:CYS1081 3.1 25.7 1.0 CG B:HIS1059 3.2 22.8 1.0 CB A:CYS1069 3.3 24.2 1.0 CB A:CYS1078 3.5 21.8 1.0 CB B:HIS1059 3.6 24.6 1.0 CA B:HIS1059 3.8 22.3 1.0 N A:CYS1078 3.9 22.4 1.0 CB A:TRP1071 4.1 24.3 1.0 NE2 A:HIS1059 4.1 21.3 1.0 NE2 B:HIS1059 4.2 22.6 1.0 N A:CYS1081 4.2 22.6 1.0 CA A:CYS1081 4.2 23.6 1.0 CA A:CYS1078 4.2 21.4 1.0 CD2 B:HIS1059 4.3 26.5 1.0 CA A:CYS1069 4.6 23.4 1.0 O B:HIS1059 4.6 20.9 1.0 O A:CYS1078 4.7 21.1 1.0 CD2 A:HIS1059 4.7 22.3 1.0 CG A:TRP1071 4.7 23.7 1.0 CE1 A:HIS1059 4.8 22.4 1.0 C B:HIS1059 4.8 21.9 1.0 C A:CYS1078 4.8 20.8 1.0 N B:HIS1059 4.8 23.9 1.0 O3 A:GOL2005 5.0 31.3 1.0

Zinc binding site 2 out of 14 in the PHD6 Domain of MLL3 in Complex with Histone H4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PHD6 Domain of MLL3 in Complex with Histone H4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:25.7 occ:1.00 ND1 A:HIS1111 2.2 32.6 1.0 SG A:CYS1114 2.2 29.9 1.0 SG A:CYS1090 2.3 28.3 1.0 SG A:CYS1087 2.3 24.8 1.0 CB A:CYS1087 2.9 26.3 1.0 CG A:HIS1111 3.1 29.1 1.0 CE1 A:HIS1111 3.2 33.3 1.0 CB A:CYS1090 3.2 26.0 1.0 CB A:CYS1114 3.3 28.7 1.0 CB A:HIS1111 3.3 25.1 1.0 N A:CYS1090 3.7 28.9 1.0 CA A:CYS1090 4.1 27.6 1.0 CD2 A:HIS1111 4.3 28.5 1.0 NE2 A:HIS1111 4.3 28.2 1.0 N A:HIS1111 4.3 25.1 1.0 CB A:VAL1089 4.4 27.5 1.0 CA A:CYS1087 4.4 28.4 1.0 CA A:HIS1111 4.4 24.6 1.0 CA A:CYS1114 4.7 28.7 1.0 C A:VAL1089 4.7 28.4 1.0 CA A:VAL1089 4.9 28.2 1.0 N A:VAL1089 4.9 23.6 1.0 C A:CYS1090 4.9 28.2 1.0 C A:CYS1087 5.0 26.4 1.0

Zinc binding site 3 out of 14 in the PHD6 Domain of MLL3 in Complex with Histone H4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of PHD6 Domain of MLL3 in Complex with Histone H4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2003 b:23.9 occ:1.00 SG A:CYS1103 2.3 24.6 1.0 SG A:CYS1133 2.3 24.0 1.0 SG A:CYS1136 2.3 26.3 1.0 SG A:CYS1106 2.4 23.7 1.0 CB A:CYS1103 3.1 23.3 1.0 CB A:CYS1136 3.3 27.4 1.0 CB A:CYS1106 3.3 22.1 1.0 CB A:CYS1133 3.5 25.1 1.0 N A:CYS1106 3.6 21.5 1.0 N A:CYS1133 4.0 25.6 1.0 CA A:CYS1106 4.1 22.4 1.0 N A:CYS1136 4.1 30.0 1.0 CA A:CYS1133 4.2 25.7 1.0 CB A:GLN1105 4.3 26.5 0.5 CA A:CYS1136 4.3 29.6 1.0 CB A:GLN1105 4.4 24.9 0.5 NH2 A:ARG1108 4.4 26.7 1.0 CA A:CYS1103 4.6 23.5 1.0 O A:CYS1133 4.6 24.1 1.0 C A:GLN1105 4.6 23.7 0.5 C A:GLN1105 4.7 24.5 0.5 CE A:MET1110 4.7 24.8 1.0 C A:CYS1133 4.7 26.8 1.0 CA A:GLN1105 4.9 25.3 0.5 CA A:GLN1105 4.9 24.4 0.5 C A:MET1135 4.9 30.1 0.5 N A:GLN1105 4.9 24.2 0.5 CB A:MET1135 4.9 32.3 0.5 C A:CYS1106 5.0 23.4 1.0 CG A:GLN1105 5.0 26.1 0.5 N A:GLN1105 5.0 24.7 0.5 CB A:MET1135 5.0 29.7 0.5

Zinc binding site 4 out of 14 in the PHD6 Domain of MLL3 in Complex with Histone H4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of PHD6 Domain of MLL3 in Complex with Histone H4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2004 b:23.9 occ:1.00 SG A:CYS1060 2.3 25.0 1.0 SG A:CYS1057 2.4 26.4 1.0 SG B:CYS1057 2.4 24.2 1.0 SG B:CYS1060 2.4 25.3 1.0 CB A:CYS1057 3.0 26.9 1.0 CB B:CYS1057 3.0 24.8 1.0 CB A:CYS1060 3.3 25.8 1.0 CB B:CYS1060 3.4 24.6 1.0 N A:CYS1060 3.8 25.6 1.0 N B:CYS1060 4.0 22.4 1.0 CA A:CYS1060 4.1 26.4 1.0 CA B:CYS1060 4.3 24.0 1.0 CB A:HIS1059 4.3 22.1 1.0 CA A:CYS1057 4.4 27.3 1.0 CA B:CYS1057 4.5 25.0 1.0 CB B:HIS1059 4.6 24.6 1.0 C A:HIS1059 4.7 27.8 1.0 O A:CYS1057 4.8 24.4 1.0 O B:CYS1057 4.8 25.3 1.0 C A:CYS1057 4.8 27.5 1.0 CB B:ALA1062 4.8 27.9 1.0 C B:HIS1059 4.9 21.9 1.0 CA A:HIS1059 4.9 24.9 1.0 C B:CYS1057 4.9 23.8 1.0 N A:HIS1059 5.0 26.7 1.0 C B:CYS1060 5.0 23.7 1.0

Zinc binding site 5 out of 14 in the PHD6 Domain of MLL3 in Complex with Histone H4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of PHD6 Domain of MLL3 in Complex with Histone H4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2008 b:22.3 occ:1.00 ND1 A:HIS1059 2.1 21.1 1.0 SG B:CYS1081 2.3 25.0 1.0 SG B:CYS1069 2.3 24.8 1.0 SG B:CYS1078 2.3 22.5 1.0 CE1 A:HIS1059 2.9 22.4 1.0 CB B:CYS1081 3.1 24.3 1.0 CG A:HIS1059 3.2 21.1 1.0 CB B:CYS1069 3.4 27.1 1.0 CB B:CYS1078 3.5 22.5 1.0 CB A:HIS1059 3.7 22.1 1.0 CA A:HIS1059 4.0 24.9 1.0 CB B:TRP1071 4.0 26.0 1.0 N B:CYS1078 4.0 22.9 1.0 NE2 A:HIS1059 4.1 21.3 1.0 NE2 B:HIS1059 4.1 22.6 1.0 CA B:CYS1081 4.2 20.9 1.0 N B:CYS1081 4.2 23.5 1.0 CA B:CYS1078 4.3 23.1 1.0 CD2 A:HIS1059 4.3 22.3 1.0 CD2 B:HIS1059 4.6 26.5 1.0 O A:HIS1059 4.6 25.1 1.0 CA B:CYS1069 4.6 26.7 1.0 CG B:TRP1071 4.7 26.5 1.0 CE1 B:HIS1059 4.7 25.1 1.0 O B:CYS1078 4.7 21.4 1.0 C B:CYS1078 4.8 21.8 1.0 C A:HIS1059 4.8 27.8 1.0 N A:HIS1059 5.0 26.7 1.0

Zinc binding site 6 out of 14 in the PHD6 Domain of MLL3 in Complex with Histone H4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of PHD6 Domain of MLL3 in Complex with Histone H4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:25.5 occ:1.00 ND1 B:HIS1111 2.0 25.4 1.0 SG B:CYS1087 2.3 23.1 1.0 SG B:CYS1114 2.3 27.9 1.0 SG B:CYS1090 2.3 25.7 1.0 CB B:CYS1087 2.9 23.9 1.0 CG B:HIS1111 3.0 23.7 1.0 CE1 B:HIS1111 3.1 24.9 1.0 CB B:HIS1111 3.3 24.9 1.0 CB B:CYS1090 3.3 24.0 1.0 CB B:CYS1114 3.4 26.6 1.0 N B:CYS1090 3.7 24.8 1.0 CA B:CYS1090 4.1 24.6 1.0 CD2 B:HIS1111 4.2 25.5 1.0 NE2 B:HIS1111 4.2 23.3 1.0 N B:HIS1111 4.3 21.9 1.0 CA B:CYS1087 4.4 26.2 1.0 CA B:HIS1111 4.4 23.6 1.0 CB B:VAL1089 4.6 28.2 1.0 CA B:CYS1114 4.7 28.4 1.0 C B:VAL1089 4.8 26.2 1.0 N B:VAL1089 4.9 24.1 1.0 C B:CYS1087 4.9 23.7 1.0 C B:CYS1090 4.9 27.1 1.0 CA B:VAL1089 5.0 27.0 1.0 N B:CYS1114 5.0 28.6 1.0

Zinc binding site 7 out of 14 in the PHD6 Domain of MLL3 in Complex with Histone H4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of PHD6 Domain of MLL3 in Complex with Histone H4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1202 b:24.5 occ:1.00 SG B:CYS1133 2.3 23.3 1.0 SG B:CYS1103 2.3 23.7 1.0 SG B:CYS1106 2.4 23.4 1.0 SG B:CYS1136 2.4 26.9 1.0 CB B:CYS1103 3.1 22.7 1.0 CB B:CYS1136 3.3 27.7 1.0 CB B:CYS1106 3.3 21.7 1.0 CB B:CYS1133 3.4 24.1 1.0 N B:CYS1106 3.7 22.7 1.0 N B:CYS1133 3.9 24.2 1.0 CA B:CYS1106 4.1 24.0 1.0 N B:CYS1136 4.1 25.8 1.0 CA B:CYS1133 4.1 25.2 1.0 CB B:GLN1105 4.2 26.6 0.5 NH2 B:ARG1108 4.3 26.3 1.0 CA B:CYS1136 4.3 28.5 1.0 CB B:GLN1105 4.4 27.1 0.5 C B:GLN1105 4.6 23.1 0.5 O B:CYS1133 4.6 24.5 1.0 CA B:CYS1103 4.6 22.6 1.0 C B:CYS1133 4.6 25.2 1.0 CE B:MET1110 4.7 23.9 1.0 C B:GLN1105 4.7 25.4 0.5 CA B:GLN1105 4.9 24.9 0.5 CA B:GLN1105 4.9 25.7 0.5 N B:GLN1105 4.9 25.4 0.5 NE B:ARG1108 4.9 24.9 1.0 C B:MET1135 5.0 28.5 1.0 CG B:GLN1105 5.0 28.0 0.5 N B:GLN1105 5.0 25.8 0.5

Zinc binding site 8 out of 14 in the PHD6 Domain of MLL3 in Complex with Histone H4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of PHD6 Domain of MLL3 in Complex with Histone H4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2001 b:22.8 occ:1.00 ND1 D:HIS1059 2.1 25.9 1.0 SG C:CYS1081 2.2 22.7 1.0 SG C:CYS1078 2.3 21.9 1.0 SG C:CYS1069 2.3 22.6 1.0 CE1 D:HIS1059 2.9 25.8 1.0 CB C:CYS1081 3.1 23.3 1.0 CG D:HIS1059 3.3 23.9 1.0 CB C:CYS1069 3.4 25.4 1.0 CB C:CYS1078 3.5 23.1 1.0 CB D:HIS1059 3.7 22.9 1.0 N C:CYS1078 3.9 24.2 1.0 CA D:HIS1059 4.0 24.1 1.0 CB C:TRP1071 4.1 25.6 1.0 NE2 D:HIS1059 4.2 26.1 1.0 NE2 C:HIS1059 4.2 23.0 1.0 CA C:CYS1078 4.2 23.0 1.0 CA C:CYS1081 4.2 21.3 1.0 N C:CYS1081 4.2 22.1 1.0 CD2 D:HIS1059 4.3 23.0 1.0 O C:CYS1078 4.6 24.0 1.0 CA C:CYS1069 4.7 25.4 1.0 CE1 C:HIS1059 4.7 22.3 1.0 CD2 C:HIS1059 4.7 24.6 1.0 CG C:TRP1071 4.7 25.7 1.0 C C:CYS1078 4.8 25.0 1.0 O D:HIS1059 4.8 26.2 1.0 C D:HIS1059 5.0 26.0 1.0

Zinc binding site 9 out of 14 in the PHD6 Domain of MLL3 in Complex with Histone H4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of PHD6 Domain of MLL3 in Complex with Histone H4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2002 b:23.9 occ:1.00 ND1 C:HIS1111 2.0 28.7 1.0 SG C:CYS1114 2.2 26.6 1.0 SG C:CYS1090 2.3 27.6 1.0 SG C:CYS1087 2.3 22.8 1.0 CB C:CYS1087 3.0 23.7 1.0 CE1 C:HIS1111 3.0 28.2 1.0 CG C:HIS1111 3.1 25.1 1.0 CB C:CYS1090 3.2 27.1 1.0 CB C:CYS1114 3.4 25.5 1.0 CB C:HIS1111 3.4 24.0 1.0 N C:CYS1090 3.7 26.6 1.0 CA C:CYS1090 4.1 28.5 1.0 NE2 C:HIS1111 4.1 26.8 1.0 CD2 C:HIS1111 4.2 26.1 1.0 N C:HIS1111 4.3 22.7 1.0 CA C:CYS1087 4.4 23.5 1.0 CA C:HIS1111 4.5 23.6 1.0 CB C:VAL1089 4.5 25.0 1.0 CA C:CYS1114 4.7 24.8 1.0 C C:VAL1089 4.7 26.5 1.0 C C:CYS1090 4.9 28.4 1.0 N C:VAL1089 5.0 22.7 1.0 C C:CYS1087 5.0 22.9 1.0 CA C:VAL1089 5.0 24.3 1.0

Zinc binding site 10 out of 14 in the PHD6 Domain of MLL3 in Complex with Histone H4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of PHD6 Domain of MLL3 in Complex with Histone H4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2003 b:22.9 occ:1.00 SG C:CYS1103 2.3 21.2 1.0 SG C:CYS1133 2.3 23.5 1.0 SG C:CYS1106 2.4 22.5 1.0 SG C:CYS1136 2.4 23.7 1.0 CB C:CYS1103 3.2 21.1 1.0 CB C:CYS1136 3.3 25.0 1.0 CB C:CYS1106 3.3 19.8 1.0 CB C:CYS1133 3.5 23.3 1.0 N C:CYS1106 3.6 22.0 1.0 N C:CYS1133 4.0 22.6 1.0 CA C:CYS1106 4.1 21.0 1.0 N C:CYS1136 4.1 24.4 1.0 CA C:CYS1133 4.2 24.1 1.0 CA C:CYS1136 4.3 27.3 1.0 CB C:GLN1105 4.3 25.4 0.5 NH2 C:ARG1108 4.4 25.9 1.0 CB C:GLN1105 4.5 21.4 0.5 O C:CYS1133 4.6 23.3 1.0 CE C:MET1110 4.6 24.4 1.0 CA C:CYS1103 4.6 20.4 1.0 C C:CYS1133 4.7 26.7 1.0 C C:GLN1105 4.7 24.6 0.5 C C:GLN1105 4.7 23.3 0.5 CA C:GLN1105 4.9 25.8 0.5 C C:MET1135 4.9 24.8 0.5 CB C:MET1135 4.9 27.8 0.5 CA C:GLN1105 5.0 23.5 0.5 C C:CYS1106 5.0 21.9 1.0 N C:GLN1105 5.0 23.6 0.5 N C:GLN1105 5.0 25.1 0.5

Y.Liu, S.Qin, T.Y.Chen, M.Lei, S.S.Dhar, J.C.Ho, A.Dong, P.Loppnau, Y.Li, M.G.Lee, J.Min. Structural Insights Into Trans-Histone Regulation of H3K4 Methylation By Unique Histone H4 Binding of MLL3/4. Nat Commun V. 10 36 2019.
ISSN: ESSN 2041-1723
PubMed: 30604749
DOI: 10.1038/S41467-018-07906-3