Zinc in PDB 4r2a: EGR1/ZIF268 Zinc Fingers in Complex with Methylated Dna

The structure of EGR1/ZIF268 Zinc Fingers in Complex with Methylated Dna, PDB code: 4r2a was solved by H.Hashimoto, Y.O.Olanrewaju, Y.Zheng, G.G.Wilson, X.Zhang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.10 / 1.59
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	43.990, 56.208, 130.219, 90.00, 90.00, 90.00
R / Rfree (%)	13.7 / 18.9

The binding sites of Zinc atom in the EGR1/ZIF268 Zinc Fingers in Complex with Methylated Dna (pdb code 4r2a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the EGR1/ZIF268 Zinc Fingers in Complex with Methylated Dna, PDB code: 4r2a:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the EGR1/ZIF268 Zinc Fingers in Complex with Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of EGR1/ZIF268 Zinc Fingers in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:34.2 occ:1.00 NE2 A:HIS358 2.1 29.4 1.0 NE2 A:HIS362 2.1 33.3 1.0 SG A:CYS345 2.2 39.1 1.0 SG A:CYS340 2.2 35.5 1.0 CE1 A:HIS358 3.0 30.4 1.0 CD2 A:HIS362 3.0 31.0 1.0 CE1 A:HIS362 3.0 33.8 1.0 CB A:CYS345 3.1 43.7 1.0 CD2 A:HIS358 3.1 27.1 1.0 CB A:CYS340 3.1 34.7 1.0 ND1 A:HIS358 4.1 27.9 1.0 ND1 A:HIS362 4.1 34.0 1.0 CG A:HIS362 4.2 31.9 1.0 CG A:HIS358 4.2 27.1 1.0 CB A:VAL342 4.5 43.0 1.0 CA A:CYS345 4.5 48.5 1.0 CA A:CYS340 4.6 35.1 1.0 CB A:ARG347 4.8 43.4 1.0 CG2 A:VAL342 4.8 41.1 1.0

Zinc binding site 2 out of 3 in the EGR1/ZIF268 Zinc Fingers in Complex with Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of EGR1/ZIF268 Zinc Fingers in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:21.7 occ:1.00 NE2 A:HIS390 2.0 20.4 1.0 NE2 A:HIS386 2.1 19.6 1.0 SG A:CYS370 2.3 21.4 1.0 SG A:CYS373 2.3 23.8 1.0 CD2 A:HIS390 3.0 19.4 1.0 CD2 A:HIS386 3.0 18.0 1.0 CE1 A:HIS390 3.1 22.0 1.0 CE1 A:HIS386 3.1 18.9 1.0 CB A:CYS370 3.1 21.3 1.0 CB A:CYS373 3.3 25.2 1.0 N A:CYS373 3.6 27.1 1.0 CA A:CYS373 4.0 27.3 1.0 CG A:HIS390 4.1 19.4 1.0 ND1 A:HIS390 4.2 22.9 1.0 CG A:HIS386 4.2 16.3 1.0 ND1 A:HIS386 4.2 16.7 1.0 O A:HOH647 4.3 41.3 1.0 CB A:ILE372 4.4 26.5 1.0 CA A:CYS370 4.6 22.2 1.0 C A:ILE372 4.6 28.8 1.0 C A:CYS373 4.7 28.8 1.0 N A:MET374 4.8 28.9 1.0 N A:ILE372 4.9 27.8 1.0 CA A:ILE372 4.9 27.0 1.0 CG2 A:ILE372 5.0 27.9 1.0

Zinc binding site 3 out of 3 in the EGR1/ZIF268 Zinc Fingers in Complex with Methylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of EGR1/ZIF268 Zinc Fingers in Complex with Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:15.7 occ:1.00 NE2 A:HIS418 2.0 16.5 1.0 NE2 A:HIS414 2.0 14.4 1.0 SG A:CYS398 2.3 15.5 1.0 SG A:CYS401 2.3 16.3 1.0 CD2 A:HIS414 3.0 13.2 1.0 CD2 A:HIS418 3.0 15.9 1.0 CE1 A:HIS418 3.0 16.8 1.0 CE1 A:HIS414 3.1 14.1 1.0 CB A:CYS398 3.1 14.7 1.0 CB A:CYS401 3.3 16.1 1.0 N A:CYS401 3.7 16.4 1.0 CA A:CYS401 4.0 15.4 1.0 CG A:HIS414 4.1 12.2 1.0 ND1 A:HIS418 4.1 18.5 1.0 CG A:HIS418 4.1 18.9 1.0 ND1 A:HIS414 4.2 14.1 1.0 O A:HOH639 4.3 43.4 1.0 CB A:ILE400 4.4 18.2 1.0 CA A:CYS398 4.6 13.8 1.0 C A:ILE400 4.7 16.8 1.0 C A:CYS401 4.7 15.0 1.0 N A:GLY402 4.7 15.8 1.0 CB A:ARG403 4.8 17.1 1.0 N A:ILE400 4.9 16.9 1.0 CA A:ILE400 4.9 18.2 1.0 N A:ARG403 4.9 16.6 1.0

H.Hashimoto, Y.O.Olanrewaju, Y.Zheng, G.G.Wilson, X.Zhang, X.Cheng. Wilms Tumor Protein Recognizes 5-Carboxylcytosine Within A Specific Dna Sequence. Genes Dev. 2014.
ISSN: ISSN 0890-9369
PubMed: 25258363
DOI: 10.1101/GAD.250746.114