Zinc in PDB 3kv5: Structure of KIAA1718, Human Jumonji Demethylase, in Complex with N-Oxalylglycine

The structure of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with N-Oxalylglycine, PDB code: 3kv5 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)	34.82 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.700, 125.600, 206.100, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24.5

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

Iron

(Fe)

3 atoms

The binding sites of Zinc atom in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with N-Oxalylglycine (pdb code 3kv5). 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 N-Oxalylglycine, PDB code: 3kv5:
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 N-Oxalylglycine


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 N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn489 b:29.0 occ:1.00 SG D:CYS85 2.3 30.0 1.0 SG D:CYS55 2.3 24.1 1.0 SG D:CYS82 2.3 25.6 1.0 SG D:CYS58 2.4 28.0 1.0 CB D:CYS55 3.2 24.7 1.0 CB D:CYS58 3.3 27.8 1.0 CB D:CYS85 3.3 30.1 1.0 CB D:CYS82 3.4 25.5 1.0 N D:CYS58 3.7 29.2 1.0 N D:CYS82 4.0 23.9 1.0 CA D:CYS58 4.1 27.9 1.0 CA D:CYS82 4.2 25.4 1.0 N D:CYS85 4.3 30.7 1.0 CA D:CYS85 4.4 30.0 1.0 CZ D:PHE62 4.4 18.5 1.0 CE1 D:PHE62 4.5 18.4 1.0 CB D:ILE57 4.5 31.2 1.0 CA D:CYS55 4.7 25.0 1.0 C D:ILE57 4.8 29.8 1.0 O D:CYS82 4.8 25.4 1.0 C D:CYS82 4.9 26.1 1.0 C D:CYS58 5.0 27.6 1.0

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


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 N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn490 b:29.7 occ:1.00 ND1 D:HIS63 1.9 23.6 1.0 SG D:CYS40 2.3 29.9 1.0 SG D:CYS66 2.3 32.6 1.0 SG D:CYS42 2.4 39.7 1.0 CE1 D:HIS63 2.8 23.2 1.0 CG D:HIS63 3.0 24.3 1.0 CB D:CYS40 3.1 30.6 1.0 CB D:CYS66 3.3 30.8 1.0 CB D:HIS63 3.5 23.4 1.0 CB D:CYS42 3.5 35.6 1.0 O D:HOH496 3.7 30.7 1.0 NE2 D:HIS63 3.9 25.2 1.0 CD2 D:HIS63 4.1 24.1 1.0 N D:CYS42 4.1 34.1 1.0 N D:HIS63 4.1 23.5 1.0 NH2 D:ARG50 4.4 38.6 1.0 CA D:CYS42 4.4 35.4 1.0 CA D:HIS63 4.4 23.6 1.0 CA D:CYS40 4.6 30.5 1.0 N D:VAL41 4.6 31.6 1.0 CA D:CYS66 4.7 30.1 1.0 C D:CYS40 4.9 31.1 1.0 O D:HIS63 4.9 22.8 1.0 CG2 D:VAL41 4.9 33.0 1.0

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


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 N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn489 b:26.1 occ:1.00 SG A:CYS55 2.3 23.4 1.0 SG A:CYS85 2.4 28.9 1.0 SG A:CYS82 2.4 23.1 1.0 SG A:CYS58 2.4 24.6 1.0 CB A:CYS55 3.2 24.1 1.0 CB A:CYS85 3.3 27.5 1.0 CB A:CYS58 3.4 25.9 1.0 CB A:CYS82 3.5 21.6 1.0 N A:CYS58 3.7 28.0 1.0 N A:CYS82 4.0 20.4 1.0 CA A:CYS58 4.2 27.0 1.0 CZ A:PHE62 4.2 24.1 1.0 N A:CYS85 4.3 27.9 1.0 CA A:CYS82 4.3 21.6 1.0 CA A:CYS85 4.4 27.8 1.0 CE1 A:PHE62 4.4 24.1 1.0 CB A:ILE57 4.4 29.7 1.0 CA A:CYS55 4.6 25.4 1.0 C A:ILE57 4.8 28.4 1.0 O A:CYS82 4.9 20.7 1.0 C A:CYS82 4.9 21.9 1.0

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


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 N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn490 b:28.9 occ:1.00 ND1 A:HIS63 2.0 28.6 1.0 SG A:CYS42 2.2 34.5 1.0 SG A:CYS40 2.3 31.5 1.0 SG A:CYS66 2.3 30.3 1.0 CE1 A:HIS63 2.9 27.7 1.0 CG A:HIS63 2.9 27.8 1.0 CB A:CYS40 3.2 32.1 1.0 CB A:CYS66 3.3 27.6 1.0 CB A:HIS63 3.4 26.9 1.0 CB A:CYS42 3.5 35.2 1.0 O A:HOH573 3.7 49.7 1.0 NE2 A:HIS63 4.0 28.3 1.0 CD2 A:HIS63 4.0 28.1 1.0 N A:CYS42 4.1 34.4 1.0 N A:HIS63 4.2 26.3 1.0 NH2 A:ARG50 4.4 39.3 1.0 CA A:HIS63 4.4 26.1 1.0 CA A:CYS42 4.4 35.0 1.0 N A:VAL41 4.6 32.7 1.0 CA A:CYS40 4.6 32.3 1.0 CA A:CYS66 4.7 27.3 1.0 CG2 A:VAL41 4.7 32.5 1.0 C A:CYS40 4.9 32.2 1.0 NH1 A:ARG50 5.0 39.0 1.0 CZ A:ARG50 5.0 39.8 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