Zinc in PDB 4r2c: EGR1/ZIF268 Zinc Fingers in Complex with Hydroxymethylated Dna

The structure of EGR1/ZIF268 Zinc Fingers in Complex with Hydroxymethylated Dna, PDB code: 4r2c 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)	28.04 / 1.89
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	43.977, 56.076, 129.605, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 25

The structure of EGR1/ZIF268 Zinc Fingers in Complex with Hydroxymethylated Dna also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Zinc atom in the EGR1/ZIF268 Zinc Fingers in Complex with Hydroxymethylated Dna (pdb code 4r2c). 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 Hydroxymethylated Dna, PDB code: 4r2c:
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 Hydroxymethylated 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 Hydroxymethylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:38.8 occ:1.00 NE2 A:HIS362 2.0 27.6 1.0 NE2 A:HIS358 2.1 41.4 1.0 SG A:CYS340 2.3 36.5 1.0 SG A:CYS345 2.4 52.9 1.0 CB A:CYS345 2.8 52.9 1.0 CD2 A:HIS362 2.9 33.1 1.0 CD2 A:HIS358 3.0 32.1 1.0 CE1 A:HIS362 3.0 32.0 1.0 CE1 A:HIS358 3.0 42.5 1.0 CB A:CYS340 3.3 38.0 1.0 CG A:HIS362 4.1 30.2 1.0 ND1 A:HIS362 4.1 32.7 1.0 ND1 A:HIS358 4.1 32.4 1.0 CG A:HIS358 4.2 35.4 1.0 CA A:CYS345 4.3 58.3 1.0 CB A:VAL342 4.4 46.2 1.0 CG2 A:VAL342 4.5 38.1 1.0 CA A:CYS340 4.7 47.7 1.0 C A:CYS345 5.0 58.9 1.0

Zinc binding site 2 out of 3 in the EGR1/ZIF268 Zinc Fingers in Complex with Hydroxymethylated 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 Hydroxymethylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:21.8 occ:1.00 NE2 A:HIS386 2.0 17.6 1.0 NE2 A:HIS390 2.1 21.9 1.0 SG A:CYS373 2.3 21.6 1.0 SG A:CYS370 2.3 20.8 1.0 CD2 A:HIS390 2.9 19.8 1.0 CD2 A:HIS386 3.0 18.7 1.0 CE1 A:HIS386 3.0 14.6 1.0 CB A:CYS370 3.2 23.8 1.0 CE1 A:HIS390 3.2 26.8 1.0 CB A:CYS373 3.2 27.2 1.0 N A:CYS373 3.7 24.7 1.0 CA A:CYS373 4.0 26.3 1.0 CG A:HIS390 4.1 19.3 1.0 ND1 A:HIS386 4.1 14.9 1.0 CG A:HIS386 4.1 19.2 1.0 O A:HOH642 4.2 36.5 1.0 ND1 A:HIS390 4.2 25.2 1.0 CB A:ILE372 4.5 25.6 1.0 CA A:CYS370 4.6 24.9 1.0 C A:CYS373 4.7 29.6 1.0 C A:ILE372 4.7 27.8 1.0 N A:MET374 4.9 25.9 1.0 CB A:ARG375 4.9 25.5 1.0 CG2 A:ILE372 4.9 25.6 1.0

Zinc binding site 3 out of 3 in the EGR1/ZIF268 Zinc Fingers in Complex with Hydroxymethylated 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 Hydroxymethylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:14.8 occ:1.00 NE2 A:HIS418 2.0 16.2 1.0 NE2 A:HIS414 2.0 12.7 1.0 SG A:CYS401 2.3 15.5 1.0 SG A:CYS398 2.3 13.1 1.0 CD2 A:HIS414 2.9 15.3 1.0 CD2 A:HIS418 3.0 16.9 1.0 CE1 A:HIS418 3.0 19.2 1.0 CE1 A:HIS414 3.1 15.2 1.0 CB A:CYS398 3.1 11.4 1.0 CB A:CYS401 3.4 17.4 1.0 N A:CYS401 3.7 15.3 1.0 CA A:CYS401 4.1 13.7 1.0 CG A:HIS414 4.1 13.9 1.0 ND1 A:HIS418 4.1 17.3 1.0 CG A:HIS418 4.1 17.5 1.0 ND1 A:HIS414 4.1 11.8 1.0 CB A:ILE400 4.4 13.3 1.0 CA A:CYS398 4.6 15.0 1.0 O A:HOH636 4.6 33.6 1.0 C A:ILE400 4.7 20.5 1.0 CB A:ARG403 4.7 17.4 1.0 C A:CYS401 4.7 21.1 1.0 N A:GLY402 4.7 13.3 1.0 N A:ILE400 4.9 15.4 1.0 CA A:ILE400 4.9 15.3 1.0 N A:ARG403 4.9 16.3 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