Zinc in PDB 3kv6: Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate

The structure of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate, PDB code: 3kv6 was solved by J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.54 / 2.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.400, 125.200, 206.000, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 25.3

The structure of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate (pdb code 3kv6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate, PDB code: 3kv6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn489 b:21.5 occ:1.00 SG A:CYS85 2.2 19.9 1.0 SG A:CYS58 2.3 19.8 1.0 SG A:CYS55 2.3 20.6 1.0 SG A:CYS82 2.3 22.3 1.0 CB A:CYS55 3.3 20.3 1.0 CB A:CYS58 3.3 16.0 1.0 CB A:CYS85 3.3 22.7 1.0 CB A:CYS82 3.5 19.7 1.0 O A:HOH505 3.6 13.4 1.0 N A:CYS58 3.7 17.8 1.0 N A:CYS82 4.1 20.9 1.0 CA A:CYS58 4.1 17.6 1.0 CZ A:PHE62 4.2 18.5 1.0 CE1 A:PHE62 4.3 18.8 1.0 CA A:CYS82 4.4 20.4 1.0 CB A:ILE57 4.4 20.7 1.0 N A:CYS85 4.4 23.9 1.0 CA A:CYS85 4.5 24.1 1.0 CA A:CYS55 4.7 22.1 1.0 C A:ILE57 4.7 19.6 1.0 O A:CYS82 4.9 21.4 1.0 CA A:ILE57 5.0 20.1 1.0

Zinc binding site 2 out of 4 in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn490 b:26.4 occ:1.00 ND1 A:HIS63 1.8 19.9 1.0 SG A:CYS66 2.2 23.1 1.0 SG A:CYS40 2.2 24.6 1.0 SG A:CYS42 2.2 30.2 1.0 CE1 A:HIS63 2.8 20.8 1.0 CG A:HIS63 2.9 20.1 1.0 CB A:CYS40 3.0 22.5 1.0 CB A:HIS63 3.2 19.3 1.0 CB A:CYS66 3.3 22.2 1.0 CB A:CYS42 3.7 26.2 1.0 NE2 A:HIS63 3.9 22.0 1.0 CD2 A:HIS63 4.0 20.8 1.0 N A:HIS63 4.0 20.0 1.0 N A:CYS42 4.3 24.6 1.0 CA A:HIS63 4.3 19.7 1.0 NH2 A:ARG50 4.4 38.2 1.0 CA A:CYS40 4.4 23.5 1.0 CA A:CYS42 4.6 26.3 1.0 CA A:CYS66 4.6 21.1 1.0 N A:VAL41 4.7 23.5 1.0 C A:CYS40 4.7 24.0 1.0 N A:CYS66 5.0 20.6 1.0 CG2 A:VAL41 5.0 21.4 1.0

Zinc binding site 3 out of 4 in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn489 b:30.6 occ:1.00 SG D:CYS85 2.1 21.9 1.0 SG D:CYS58 2.2 21.3 1.0 SG D:CYS55 2.2 20.9 1.0 SG D:CYS82 2.4 18.5 1.0 CB D:CYS85 3.1 23.0 1.0 CB D:CYS58 3.2 20.8 1.0 CB D:CYS55 3.3 22.2 1.0 CB D:CYS82 3.5 16.9 1.0 N D:CYS58 3.6 22.3 1.0 N D:CYS82 3.9 17.9 1.0 CA D:CYS58 4.0 21.5 1.0 N D:CYS85 4.2 25.4 1.0 CA D:CYS85 4.2 25.1 1.0 CA D:CYS82 4.2 18.2 1.0 CB D:ILE57 4.4 24.5 1.0 CE1 D:PHE62 4.5 16.5 1.0 CZ D:PHE62 4.5 17.0 1.0 O D:CYS82 4.7 19.3 1.0 C D:ILE57 4.7 23.4 1.0 CA D:CYS55 4.7 21.6 1.0 C D:CYS82 4.8 19.4 1.0 CG2 D:ILE57 4.8 25.0 1.0 C D:CYS58 4.9 21.7 1.0 CA D:ILE57 5.0 23.8 1.0

Zinc binding site 4 out of 4 in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn490 b:27.4 occ:1.00 ND1 D:HIS63 2.0 14.9 1.0 SG D:CYS42 2.1 22.1 1.0 SG D:CYS40 2.1 18.6 1.0 SG D:CYS66 2.2 16.7 1.0 CG D:HIS63 3.0 15.8 1.0 CB D:CYS40 3.0 17.8 1.0 CE1 D:HIS63 3.0 15.3 1.0 CB D:CYS66 3.2 15.9 1.0 CB D:HIS63 3.3 15.6 1.0 CB D:CYS42 3.4 21.8 1.0 N D:HIS63 4.1 17.4 1.0 NH2 D:ARG50 4.1 34.5 1.0 NE2 D:HIS63 4.1 16.6 1.0 CD2 D:HIS63 4.1 15.3 1.0 N D:CYS42 4.1 20.4 1.0 CA D:HIS63 4.3 16.4 1.0 CA D:CYS42 4.4 21.1 1.0 CA D:CYS40 4.4 18.9 1.0 OE1 D:GLN44 4.4 43.4 1.0 CA D:CYS66 4.6 16.8 1.0 N D:VAL41 4.6 18.3 1.0 NH1 D:ARG50 4.7 33.7 1.0 CZ D:ARG50 4.7 34.2 1.0 O D:HIS63 4.9 15.4 1.0 C D:CYS40 4.9 18.6 1.0 CG D:GLN44 5.0 38.0 1.0

J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng. Enzymatic and Structural Insights For Substrate Specificity of A Family of Jumonji Histone Lysine Demethylases. Nat.Struct.Mol.Biol. V. 17 38 2010.
ISSN: ISSN 1545-9993
PubMed: 20023638
DOI: 10.1038/NSMB.1753