Zinc in PDB 6hgt: Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation

The structure of Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation, PDB code: 6hgt was solved by J.Maw, Y.V.Le Bihan, R.L.M.Van Montfort, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.16 / 2.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.440, 103.410, 144.520, 90.00, 99.63, 90.00
R / Rfree (%)	25.1 / 28

The binding sites of Zinc atom in the Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation (pdb code 6hgt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation, PDB code: 6hgt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation


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 Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:39.2 occ:1.00 OE2 A:GLU190 2.1 39.3 1.0 O2 A:OGA403 2.1 48.5 0.9 NE2 A:HIS276 2.2 31.0 1.0 NE2 A:HIS188 2.3 25.2 1.0 O2' A:OGA403 2.5 47.6 0.9 C1 A:OGA403 3.0 49.4 0.9 C2 A:OGA403 3.1 49.2 0.9 CE1 A:HIS188 3.2 24.0 1.0 CE1 A:HIS276 3.2 31.0 1.0 CD2 A:HIS276 3.3 30.7 1.0 CD2 A:HIS188 3.3 25.8 1.0 CD A:GLU190 3.3 44.1 1.0 OE1 A:GLU190 3.8 62.6 1.0 O1 A:OGA403 4.2 49.6 0.9 ND1 A:HIS188 4.3 24.4 1.0 OG A:SER196 4.3 34.8 1.0 ND1 A:HIS276 4.3 31.3 1.0 CG A:HIS188 4.4 23.8 1.0 CG A:HIS276 4.4 28.5 1.0 N1 A:OGA403 4.4 49.4 0.9 NH2 E:ARG9 4.4 30.4 1.0 CG A:GLU190 4.5 31.5 1.0 O A:HOH606 4.6 32.3 1.0 O A:HOH532 4.6 34.6 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation


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 Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:49.2 occ:1.00 NE2 A:HIS240 2.1 43.2 1.0 SG A:CYS234 2.2 51.6 1.0 SG A:CYS306 2.2 46.6 1.0 SG A:CYS308 2.5 60.3 1.0 CE1 A:HIS240 3.0 43.0 1.0 CB A:CYS234 3.2 48.7 1.0 CD2 A:HIS240 3.2 42.1 1.0 CB A:CYS306 3.4 43.0 1.0 N A:CYS308 3.7 58.4 1.0 CB A:CYS308 3.9 58.9 1.0 N A:SER307 3.9 54.3 1.0 CA A:CYS306 3.9 44.8 1.0 ND1 A:HIS240 4.2 42.3 1.0 CG A:HIS240 4.3 39.8 1.0 CA A:CYS308 4.3 59.3 1.0 C A:CYS306 4.3 54.3 1.0 O A:ALA236 4.4 39.8 1.0 N A:ARG309 4.5 57.7 1.0 CA A:CYS234 4.5 50.3 1.0 C A:SER307 4.8 63.5 1.0 CG A:ARG309 4.8 58.0 1.0 C A:ALA236 4.8 40.4 1.0 C A:CYS308 4.8 63.2 1.0 CA A:PHE237 4.9 33.7 1.0 CA A:SER307 4.9 57.2 1.0 CD A:ARG309 5.0 56.5 1.0 OG A:SER307 5.0 66.6 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation


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 Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:36.3 occ:1.00 O1 B:OGA403 2.0 21.5 0.7 OE2 B:GLU190 2.1 39.1 1.0 NE2 B:HIS276 2.3 28.9 1.0 NE2 B:HIS188 2.3 22.6 1.0 O2' B:OGA403 2.6 29.6 0.7 O B:HOH582 2.6 28.9 1.0 C1 B:OGA403 3.0 22.0 0.7 C2 B:OGA403 3.1 26.6 0.7 CD B:GLU190 3.2 37.6 1.0 CE1 B:HIS276 3.2 28.5 1.0 CE1 B:HIS188 3.3 21.6 1.0 CD2 B:HIS276 3.3 30.0 1.0 CD2 B:HIS188 3.3 23.0 1.0 OE1 B:GLU190 3.7 40.8 1.0 O2 B:OGA403 4.1 18.8 0.7 OG B:SER196 4.2 33.0 1.0 ND1 B:HIS276 4.4 30.1 1.0 N1 B:OGA403 4.4 28.2 0.7 CG B:HIS276 4.4 28.7 1.0 CG B:GLU190 4.4 25.7 1.0 ND1 B:HIS188 4.4 22.7 1.0 CG B:HIS188 4.4 22.2 1.0 NH2 F:ARG9 4.5 21.3 1.0 O F:HOH104 4.9 45.9 1.0 OG1 B:THR270 5.0 27.5 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation


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 Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:34.4 occ:0.84 SG B:CYS306 2.2 39.1 1.0 NE2 B:HIS240 2.2 32.9 1.0 SG B:CYS234 2.2 37.0 1.0 SG B:CYS308 2.3 47.9 1.0 CE1 B:HIS240 3.1 32.7 1.0 CB B:CYS234 3.2 34.5 1.0 CD2 B:HIS240 3.3 32.1 1.0 CB B:CYS306 3.5 34.3 1.0 N B:CYS308 3.6 44.1 1.0 CB B:CYS308 3.7 45.5 1.0 N B:SER307 3.9 40.2 1.0 CA B:CYS306 4.0 34.9 1.0 CA B:CYS308 4.1 44.9 1.0 C B:CYS306 4.3 40.3 1.0 N B:ARG309 4.3 44.5 1.0 ND1 B:HIS240 4.3 32.6 1.0 CG B:HIS240 4.4 30.0 1.0 O B:ALA236 4.5 37.9 1.0 CA B:CYS234 4.5 36.3 1.0 C B:SER307 4.6 48.4 1.0 C B:CYS308 4.6 49.5 1.0 CG B:ARG309 4.7 65.2 1.0 CA B:SER307 4.8 42.3 1.0 OG B:SER307 4.9 57.1 1.0 C B:ALA236 4.9 38.4 1.0 CA B:PHE237 4.9 32.5 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation


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 Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:42.7 occ:1.00 OE2 C:GLU190 2.1 45.9 1.0 O1 C:OGA403 2.1 26.4 0.8 NE2 C:HIS276 2.2 35.7 1.0 NE2 C:HIS188 2.2 31.5 1.0 O2' C:OGA403 2.6 31.9 0.8 O C:HOH530 2.8 34.0 1.0 C1 C:OGA403 3.1 26.9 0.8 CE1 C:HIS276 3.1 35.8 1.0 CE1 C:HIS188 3.1 30.6 1.0 C2 C:OGA403 3.2 30.6 0.8 CD2 C:HIS276 3.2 35.7 1.0 CD2 C:HIS188 3.2 32.7 1.0 CD C:GLU190 3.3 42.0 1.0 OE1 C:GLU190 3.8 34.0 1.0 O2 C:OGA403 4.2 25.3 0.8 ND1 C:HIS276 4.2 36.6 1.0 CG C:HIS276 4.3 34.4 1.0 ND1 C:HIS188 4.3 31.9 1.0 CG C:HIS188 4.3 31.6 1.0 OG C:SER196 4.3 32.2 1.0 N1 C:OGA403 4.4 32.2 0.8 O C:HOH579 4.5 28.4 1.0 CG C:GLU190 4.5 34.8 1.0 NH1 G:ARG9 4.5 29.3 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation


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 Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:51.0 occ:0.83 NE2 C:HIS240 2.1 44.9 1.0 SG C:CYS306 2.1 62.3 1.0 SG C:CYS234 2.3 58.7 1.0 SG C:CYS308 2.4 74.6 1.0 CE1 C:HIS240 3.1 44.4 1.0 CD2 C:HIS240 3.2 43.5 1.0 CB C:CYS234 3.2 56.2 1.0 CB C:CYS306 3.5 57.3 1.0 N C:CYS308 3.7 70.1 1.0 CB C:CYS308 3.8 72.7 1.0 N C:SER307 4.0 65.2 1.0 CA C:CYS306 4.0 57.8 1.0 CA C:CYS308 4.2 71.7 1.0 ND1 C:HIS240 4.2 43.7 1.0 CG C:HIS240 4.3 41.0 1.0 C C:CYS306 4.3 65.2 1.0 N C:ARG309 4.3 71.7 1.0 O C:ALA236 4.5 52.1 1.0 CA C:CYS234 4.6 58.6 1.0 C C:CYS308 4.7 76.0 1.0 C C:SER307 4.8 72.7 1.0 CA C:SER307 4.9 67.0 1.0 C C:ALA236 4.9 52.5 1.0 CB C:ARG309 5.0 70.3 1.0 CA C:PHE237 5.0 44.1 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:40.4 occ:1.00 OE2 D:GLU190 2.1 33.7 1.0 O1 D:OGA403 2.1 33.2 0.8 NE2 D:HIS188 2.3 31.4 1.0 NE2 D:HIS276 2.3 30.8 1.0 O2' D:OGA403 2.5 34.0 0.8 C1 D:OGA403 3.0 35.8 0.8 C2 D:OGA403 3.1 37.3 0.8 CE1 D:HIS188 3.2 31.1 1.0 CE1 D:HIS276 3.2 30.9 1.0 CD2 D:HIS276 3.3 30.8 1.0 CD2 D:HIS188 3.3 31.6 1.0 CD D:GLU190 3.3 40.7 1.0 OE1 D:GLU190 3.8 54.2 1.0 NH2 H:ARG9 4.2 34.3 1.0 O2 D:OGA403 4.2 35.7 0.8 ND1 D:HIS188 4.3 31.8 1.0 OG D:SER196 4.3 51.8 1.0 ND1 D:HIS276 4.4 31.6 1.0 CG D:HIS188 4.4 30.5 1.0 CG D:HIS276 4.4 29.6 1.0 N1 D:OGA403 4.4 40.1 0.8 CG D:GLU190 4.5 32.8 1.0 O D:HOH514 4.6 36.0 1.0 O D:HOH586 4.6 38.2 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Human KDM4A Complexed with Co-Substrate Analog Nog and Histone H3 Peptide with K9R Mutation within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:39.1 occ:0.70 NE2 D:HIS240 2.1 41.2 1.0 SG D:CYS234 2.2 54.0 1.0 SG D:CYS306 2.3 59.8 1.0 SG D:CYS308 2.3 70.3 1.0 CE1 D:HIS240 3.0 41.2 1.0 CB D:CYS234 3.0 51.2 1.0 CD2 D:HIS240 3.3 41.0 1.0 CB D:CYS306 3.6 55.3 1.0 N D:CYS308 3.7 69.6 1.0 CB D:CYS308 3.7 69.7 1.0 N D:SER307 4.0 65.6 1.0 CA D:CYS306 4.1 57.3 1.0 ND1 D:HIS240 4.2 41.8 1.0 CA D:CYS308 4.2 70.2 1.0 CG D:HIS240 4.3 39.6 1.0 C D:CYS306 4.4 65.9 1.0 CA D:CYS234 4.4 52.4 1.0 O D:ALA236 4.5 41.5 1.0 N D:ARG309 4.5 66.9 1.0 CG D:ARG309 4.5 70.1 1.0 C D:SER307 4.7 75.5 1.0 NE D:ARG309 4.8 75.8 1.0 C D:CYS308 4.8 72.5 1.0 CA D:PHE237 4.9 37.1 1.0 CA D:SER307 4.9 69.0 1.0 C D:ALA236 4.9 42.8 1.0 OG D:SER307 5.0 82.2 1.0

J.Maw, Y.V.Le Bihan, V.Bavetsias, J.Blagg. Structure-Based Design of Selective, Histone Substrate-Based Inhibitors of Histone Lysine Demethylases 4 (KDM4) Subfamily To Be Published.