Zinc in PDB 4qen: Crystal Structure of Kryptonite in Complex with Mchh Dna and Sah

All present enzymatic activity of Crystal Structure of Kryptonite in Complex with Mchh Dna and Sah:
2.1.1.43;

The structure of Crystal Structure of Kryptonite in Complex with Mchh Dna and Sah, PDB code: 4qen was solved by J.Du, S.Li, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.68 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.395, 98.009, 122.581, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.1

The binding sites of Zinc atom in the Crystal Structure of Kryptonite in Complex with Mchh Dna and Sah (pdb code 4qen). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Kryptonite in Complex with Mchh Dna and Sah, PDB code: 4qen:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Kryptonite in Complex with Mchh Dna and Sah


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 Kryptonite in Complex with Mchh Dna and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:38.8 occ:1.00 SG A:CYS397 2.3 27.8 1.0 SG A:CYS383 2.3 29.3 1.0 SG A:CYS425 2.4 26.5 1.0 SG A:CYS429 2.5 28.1 1.0 CB A:CYS425 3.1 27.4 1.0 CB A:CYS383 3.3 29.6 1.0 CB A:CYS429 3.3 29.2 1.0 CB A:CYS397 3.3 37.4 1.0 CA A:CYS425 3.5 23.2 1.0 N A:CYS383 3.6 30.1 1.0 ZN A:ZN804 3.8 41.2 1.0 ZN A:ZN803 3.9 39.0 1.0 CA A:CYS383 4.0 35.2 1.0 SG A:CYS389 4.3 31.1 1.0 N A:CYS425 4.4 21.4 1.0 SG A:CYS395 4.5 33.6 1.0 CA A:CYS429 4.5 30.3 1.0 SG A:CYS431 4.5 30.5 1.0 C A:GLY382 4.6 36.9 1.0 CA A:CYS397 4.6 36.2 1.0 C A:CYS425 4.7 26.0 1.0 N A:GLY426 4.7 25.9 1.0 CA A:GLY382 4.7 42.1 1.0 N A:CYS397 4.7 40.1 1.0 O A:HOH986 4.8 43.2 1.0 C A:CYS383 4.8 33.3 1.0 O A:CYS383 4.9 34.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Kryptonite in Complex with Mchh Dna and Sah


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 Kryptonite in Complex with Mchh Dna and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:39.0 occ:1.00 SG A:CYS431 2.3 30.5 1.0 SG A:CYS425 2.3 26.5 1.0 SG A:CYS435 2.4 29.8 1.0 SG A:CYS389 2.4 31.1 1.0 CB A:CYS431 3.2 34.9 1.0 CB A:CYS425 3.2 27.4 1.0 CB A:CYS435 3.3 29.6 1.0 CB A:CYS389 3.4 28.1 1.0 ZN A:ZN802 3.9 38.8 1.0 N A:CYS389 4.0 34.8 1.0 ZN A:ZN804 4.2 41.2 1.0 SG A:CYS383 4.3 29.3 1.0 CA A:CYS389 4.3 35.6 1.0 CB A:ASN437 4.5 29.0 1.0 NE A:ARG438 4.6 24.7 1.0 CA A:CYS431 4.6 34.7 1.0 CA A:CYS425 4.6 23.2 1.0 CA A:CYS435 4.7 32.9 1.0 CG A:ARG438 4.8 24.2 1.0 CB A:CYS429 4.9 29.2 1.0 C A:SER388 5.0 44.4 1.0 N A:CYS431 5.0 31.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Kryptonite in Complex with Mchh Dna and Sah


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 Kryptonite in Complex with Mchh Dna and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:41.2 occ:1.00 SG A:CYS389 2.3 31.1 1.0 SG A:CYS395 2.4 33.6 1.0 SG A:CYS385 2.4 35.3 1.0 SG A:CYS383 2.4 29.3 1.0 CB A:CYS383 3.1 29.6 1.0 CB A:CYS389 3.1 28.1 1.0 CB A:CYS385 3.2 36.0 1.0 CB A:CYS395 3.2 38.9 1.0 ZN A:ZN802 3.8 38.8 1.0 CA A:CYS395 3.9 39.4 1.0 ZN A:ZN803 4.2 39.0 1.0 CA A:CYS389 4.2 35.6 1.0 SG A:CYS425 4.3 26.5 1.0 N A:CYS385 4.3 45.3 1.0 CA A:CYS385 4.4 45.9 1.0 CA A:CYS383 4.6 35.2 1.0 C A:CYS395 4.7 41.3 1.0 O A:HOH1055 4.7 39.0 1.0 CB A:CYS397 4.8 37.4 1.0 N A:ALA396 4.9 35.1 1.0 C A:CYS383 4.9 33.3 1.0 SG A:CYS397 4.9 27.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Kryptonite in Complex with Mchh Dna and Sah


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 Kryptonite in Complex with Mchh Dna and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:48.9 occ:1.00 SG A:CYS612 2.3 37.0 1.0 SG A:CYS614 2.4 37.4 1.0 SG A:CYS619 2.4 40.5 1.0 SG A:CYS554 2.4 41.5 1.0 O A:CYS619 3.2 75.8 1.0 CB A:CYS612 3.3 39.7 1.0 CB A:CYS614 3.4 39.2 1.0 CB A:CYS619 3.4 47.9 1.0 CB A:CYS554 3.5 37.9 1.0 CA A:CYS619 3.7 57.0 1.0 C A:CYS619 3.9 65.5 1.0 N A:CYS614 3.9 36.7 1.0 N A:CYS554 3.9 37.7 1.0 CA A:CYS614 4.2 42.9 1.0 CA A:CYS554 4.4 40.0 1.0 O A:HOH1032 4.4 39.6 1.0 NE2 A:HIS552 4.5 42.8 1.0 C A:CYS612 4.5 41.3 1.0 CA A:CYS612 4.5 41.0 1.0 N A:LYS621 4.7 44.5 1.0 CD2 A:HIS552 4.7 37.8 1.0 O A:CYS612 4.8 43.0 1.0 N A:GLY615 4.8 38.2 1.0 C A:CYS614 4.8 40.0 1.0 N A:TYR613 4.9 46.4 1.0 C A:SER553 4.9 29.5 1.0 CB A:ALA616 5.0 50.9 1.0

J.Du, L.M.Johnson, M.Groth, S.Feng, C.J.Hale, S.Li, A.A.Vashisht, J.Gallego-Bartolome, J.A.Wohlschlegel, D.J.Patel, S.E.Jacobsen. Mechanism of Dna Methylation-Directed Histone Methylation By Kryptonite. Mol.Cell V. 55 495 2014.
ISSN: ISSN 1097-2765
PubMed: 25018018
DOI: 10.1016/J.MOLCEL.2014.06.009