Zinc in PDB 2v87: Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2SK4ME3 Peptide

The structure of Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2SK4ME3 Peptide, PDB code: 2v87 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)	20.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.407, 46.630, 57.005, 90.00, 95.13, 90.00
R / Rfree (%)	18.1 / 20.8

The binding sites of Zinc atom in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2SK4ME3 Peptide (pdb code 2v87). 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 H3R2ME2SK4ME3 Peptide, PDB code: 2v87:
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 H3R2ME2SK4ME3 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 H3R2ME2SK4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1487 b:18.4 occ:1.00 ND1 A:HIS455 2.1 15.9 1.0 SG A:CYS419 2.3 17.8 1.0 SG A:CYS423 2.3 17.6 1.0 SG A:CYS458 2.3 17.4 1.0 CG A:HIS455 3.1 15.8 1.0 CE1 A:HIS455 3.1 16.9 1.0 CB A:CYS423 3.2 15.2 1.0 CB A:CYS458 3.2 14.8 1.0 CB A:HIS455 3.4 14.0 1.0 CB A:CYS419 3.4 20.5 1.0 CA A:CYS423 3.7 18.0 1.0 N A:CYS419 3.9 23.4 1.0 CG2 A:VAL425 4.1 23.9 1.0 CB A:VAL425 4.1 23.1 1.0 N A:HIS455 4.1 15.1 1.0 CA A:CYS419 4.2 22.5 1.0 NE2 A:HIS455 4.2 17.3 1.0 CD2 A:HIS455 4.2 15.8 1.0 N A:ASP424 4.3 20.2 1.0 N A:VAL425 4.3 21.9 1.0 CA A:HIS455 4.4 15.1 1.0 C A:CYS423 4.4 20.4 1.0 CA A:CYS458 4.7 15.0 1.0 N A:CYS420 4.7 21.0 1.0 C A:CYS419 4.8 23.2 1.0 O A:HIS455 4.9 15.0 1.0 CA A:VAL425 4.9 22.9 1.0 SG A:CYS420 4.9 18.8 1.0 O A:ILE417 4.9 24.2 1.0 N A:CYS423 4.9 18.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2SK4ME3 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 H3R2ME2SK4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1488 b:22.0 occ:1.00 NE2 A:HIS452 2.0 19.1 1.0 ND1 A:HIS481 2.1 27.7 1.0 SG A:CYS446 2.2 19.1 1.0 SG A:CYS478 2.3 20.9 1.0 CE1 A:HIS452 2.9 20.5 1.0 CE1 A:HIS481 3.0 28.2 1.0 CD2 A:HIS452 3.1 18.6 1.0 CB A:CYS446 3.2 15.7 1.0 CG A:HIS481 3.2 27.1 1.0 CB A:CYS478 3.4 20.7 1.0 CB A:HIS481 3.6 24.9 1.0 N A:CYS478 3.9 19.8 1.0 CB A:HIS448 4.1 27.4 1.0 ND1 A:HIS452 4.1 19.8 1.0 NE2 A:HIS481 4.1 27.4 1.0 CG A:HIS452 4.2 19.6 1.0 CA A:CYS478 4.2 20.2 1.0 CD2 A:HIS481 4.3 26.8 1.0 N A:HIS481 4.5 26.0 1.0 CA A:CYS446 4.6 17.0 1.0 CA A:HIS481 4.7 26.4 1.0 CG A:HIS448 4.8 30.2 1.0 C A:CYS478 4.8 21.5 1.0 O A:CYS478 4.9 20.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2SK4ME3 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 H3R2ME2SK4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1488 b:24.2 occ:1.00 ND1 B:HIS455 2.2 19.6 1.0 SG B:CYS458 2.3 21.7 1.0 SG B:CYS419 2.3 20.4 1.0 SG B:CYS423 2.4 23.5 1.0 CE1 B:HIS455 3.1 19.4 1.0 CB B:CYS423 3.1 27.2 1.0 CG B:HIS455 3.2 19.4 1.0 CB B:CYS458 3.3 19.4 1.0 CB B:CYS419 3.3 23.0 1.0 CB B:HIS455 3.5 18.6 1.0 CA B:CYS423 3.9 31.1 1.0 N B:CYS419 3.9 27.6 1.0 CG2 B:VAL425 4.0 34.4 1.0 N B:HIS455 4.1 19.1 1.0 CA B:CYS419 4.2 25.8 1.0 CB B:VAL425 4.2 35.5 1.0 NE2 B:HIS455 4.2 21.3 1.0 CD2 B:HIS455 4.3 16.8 1.0 CA B:HIS455 4.4 18.4 1.0 C B:CYS423 4.6 33.9 1.0 N B:ASP424 4.6 36.0 1.0 CA B:CYS458 4.7 21.4 1.0 N B:VAL425 4.7 36.3 1.0 N B:CYS420 4.8 27.0 1.0 C B:CYS419 4.8 27.2 1.0 SG B:CYS420 4.8 26.2 1.0 O B:ILE417 4.8 28.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2SK4ME3 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 H3R2ME2SK4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1489 b:22.3 occ:1.00 ND1 B:HIS481 2.1 22.8 1.0 NE2 B:HIS452 2.1 18.6 1.0 SG B:CYS478 2.3 21.5 1.0 SG B:CYS446 2.3 18.8 1.0 CE1 B:HIS481 2.9 25.1 1.0 CE1 B:HIS452 3.1 21.3 1.0 CD2 B:HIS452 3.1 20.1 1.0 CB B:CYS446 3.1 18.3 1.0 CG B:HIS481 3.2 23.6 1.0 CB B:CYS478 3.4 18.5 1.0 CB B:HIS481 3.6 21.1 1.0 N B:CYS478 3.9 19.7 1.0 CB B:HIS448 4.0 21.9 1.0 NE2 B:HIS481 4.1 22.8 1.0 ND1 B:HIS452 4.2 19.9 1.0 CA B:CYS478 4.2 19.5 1.0 CG B:HIS452 4.2 20.4 1.0 CD2 B:HIS481 4.2 22.9 1.0 N B:HIS481 4.4 21.8 1.0 CA B:CYS446 4.6 18.1 1.0 CA B:HIS481 4.7 21.7 1.0 CG B:HIS448 4.7 25.8 1.0 C B:CYS478 4.8 20.7 1.0 N B:HIS448 5.0 21.3 1.0 O B:CYS478 5.0 19.1 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