Zinc in PDB 2v88: Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2SK4ME2 Peptide

The structure of Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2SK4ME2 Peptide, PDB code: 2v88 was solved by S.Ramon-Maiques, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.200, 46.685, 56.869, 90.00, 97.20, 90.00
R / Rfree (%)	19.6 / 23.2

The binding sites of Zinc atom in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2SK4ME2 Peptide (pdb code 2v88). 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 RAG2-Phd Finger in Complex with H3R2ME2SK4ME2 Peptide, PDB code: 2v88:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2SK4ME2 Peptide


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 RAG2-Phd Finger in Complex with H3R2ME2SK4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1488 b:17.8 occ:1.00 ND1 A:HIS455 2.1 13.0 1.0 SG A:CYS458 2.3 14.8 1.0 SG A:CYS419 2.4 15.9 1.0 SG A:CYS423 2.4 16.9 1.0 CG A:HIS455 3.1 12.2 1.0 CE1 A:HIS455 3.1 16.5 1.0 CB A:CYS423 3.2 17.6 1.0 CB A:CYS458 3.3 16.0 1.0 CB A:CYS419 3.3 16.8 1.0 CB A:HIS455 3.3 12.7 1.0 CA A:CYS423 3.7 18.5 1.0 N A:CYS419 3.9 18.9 1.0 N A:HIS455 4.1 15.2 1.0 CG2 A:VAL425 4.1 23.8 1.0 CA A:CYS419 4.1 17.5 1.0 CB A:VAL425 4.1 20.6 1.0 CD2 A:HIS455 4.2 14.0 1.0 NE2 A:HIS455 4.2 16.2 1.0 N A:ASP424 4.3 19.1 1.0 CA A:HIS455 4.3 15.9 1.0 N A:VAL425 4.3 22.5 1.0 C A:CYS423 4.4 19.4 1.0 CA A:CYS458 4.7 14.4 1.0 N A:CYS420 4.7 17.2 1.0 C A:CYS419 4.8 17.8 1.0 SG A:CYS420 4.9 17.2 1.0 CA A:VAL425 4.9 22.7 1.0 O A:HIS455 4.9 16.1 1.0 N A:CYS423 4.9 17.8 1.0 O A:ILE417 5.0 23.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2SK4ME2 Peptide


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 RAG2-Phd Finger in Complex with H3R2ME2SK4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1489 b:20.4 occ:1.00 NE2 A:HIS452 2.0 17.3 1.0 ND1 A:HIS481 2.2 24.4 1.0 SG A:CYS446 2.3 15.0 1.0 SG A:CYS478 2.3 19.3 1.0 CE1 A:HIS481 2.9 20.5 1.0 CE1 A:HIS452 3.0 16.4 1.0 CD2 A:HIS452 3.1 17.7 1.0 CB A:CYS446 3.2 12.9 1.0 CG A:HIS481 3.2 21.4 1.0 CB A:CYS478 3.4 18.5 1.0 CB A:HIS481 3.7 21.4 1.0 N A:CYS478 3.9 19.6 1.0 NE2 A:HIS481 4.0 24.9 1.0 ND1 A:HIS452 4.1 17.7 1.0 CB A:HIS448 4.2 20.4 1.0 CG A:HIS452 4.2 17.6 1.0 CD2 A:HIS481 4.2 22.7 1.0 CA A:CYS478 4.2 19.7 1.0 N A:HIS481 4.5 23.8 1.0 CA A:CYS446 4.6 15.8 1.0 CA A:HIS481 4.8 22.1 1.0 C A:CYS478 4.8 20.6 1.0 O A:CYS478 4.9 19.2 1.0 CG A:HIS448 4.9 25.5 1.0 C A:TYR477 5.0 17.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2SK4ME2 Peptide


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 RAG2-Phd Finger in Complex with H3R2ME2SK4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1488 b:23.4 occ:1.00 ND1 B:HIS455 2.2 18.8 1.0 SG B:CYS419 2.3 22.2 1.0 SG B:CYS458 2.3 20.8 1.0 SG B:CYS423 2.4 27.2 1.0 CG B:HIS455 3.1 17.6 1.0 CE1 B:HIS455 3.1 15.8 1.0 CB B:CYS419 3.3 26.1 1.0 CB B:CYS458 3.3 19.6 1.0 CB B:CYS423 3.3 30.8 1.0 CB B:HIS455 3.4 17.7 1.0 CA B:CYS423 3.8 32.6 1.0 N B:CYS419 3.8 28.2 1.0 N B:HIS455 4.1 17.7 1.0 CA B:CYS419 4.1 27.2 1.0 NE2 B:HIS455 4.2 15.9 1.0 CD2 B:HIS455 4.3 16.1 1.0 N B:ASP424 4.3 35.9 1.0 CB B:VAL425 4.3 35.0 1.0 CA B:HIS455 4.4 15.9 1.0 CG2 B:VAL425 4.4 34.6 1.0 N B:VAL425 4.4 36.8 1.0 C B:CYS423 4.5 34.2 1.0 N B:CYS420 4.7 28.2 1.0 CA B:CYS458 4.7 21.5 1.0 C B:CYS419 4.7 27.6 1.0 O B:ILE417 4.8 30.6 1.0 C B:THR418 5.0 30.0 1.0 SG B:CYS420 5.0 25.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2SK4ME2 Peptide


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 RAG2-Phd Finger in Complex with H3R2ME2SK4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1489 b:19.8 occ:1.00 NE2 B:HIS452 2.0 19.9 1.0 ND1 B:HIS481 2.1 14.6 1.0 SG B:CYS446 2.2 20.4 1.0 SG B:CYS478 2.3 18.8 1.0 CE1 B:HIS452 2.9 18.4 1.0 CE1 B:HIS481 3.0 18.6 1.0 CD2 B:HIS452 3.1 17.8 1.0 CB B:CYS446 3.1 20.2 1.0 CG B:HIS481 3.2 19.2 1.0 CB B:CYS478 3.3 17.2 1.0 CB B:HIS481 3.7 19.6 1.0 N B:CYS478 3.9 17.3 1.0 CB B:HIS448 4.1 19.8 1.0 ND1 B:HIS452 4.1 17.7 1.0 NE2 B:HIS481 4.1 19.2 1.0 CA B:CYS478 4.2 17.6 1.0 CG B:HIS452 4.2 17.6 1.0 CD2 B:HIS481 4.3 18.7 1.0 N B:HIS481 4.5 23.8 1.0 CA B:CYS446 4.6 17.8 1.0 CA B:HIS481 4.7 23.0 1.0 CG B:HIS448 4.8 21.9 1.0 C B:CYS478 4.9 17.3 1.0

S.Ramon-Maiques, A.J.Kuo, D.Carney, A.G.W.Matthews, M.A.Oettinger, O.Gozani, W.Yang. The Plant Homeodomain Finger of RAG2 Recognizes Histone H3 Methylated at Both Lysine-4 and Arginine-2. Proc.Natl.Acad.Sci.Usa V. 104 18993 2007.
ISSN: ISSN 0027-8424
PubMed: 18025461
DOI: 10.1073/PNAS.0709170104