Zinc in PDB 2v85: Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME1K4ME3 Peptide

The structure of Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME1K4ME3 Peptide, PDB code: 2v85 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)	50.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	76.711, 46.936, 56.955, 90.00, 103.65, 90.00
R / Rfree (%)	18.7 / 19.7

The binding sites of Zinc atom in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME1K4ME3 Peptide (pdb code 2v85). 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 H3R2ME1K4ME3 Peptide, PDB code: 2v85:
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 H3R2ME1K4ME3 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 H3R2ME1K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1488 b:9.8 occ:1.00 ND1 A:HIS455 2.1 5.3 1.0 SG A:CYS419 2.3 9.8 1.0 SG A:CYS458 2.4 10.7 1.0 SG A:CYS423 2.4 11.3 1.0 CG A:HIS455 3.1 6.1 1.0 CE1 A:HIS455 3.1 6.8 1.0 CB A:CYS423 3.2 9.8 1.0 CB A:CYS458 3.3 8.3 1.0 CB A:HIS455 3.4 6.0 1.0 CB A:CYS419 3.4 14.0 1.0 CA A:CYS423 3.7 14.5 1.0 N A:CYS419 3.9 17.5 1.0 N A:HIS455 4.1 6.7 1.0 CA A:CYS419 4.2 14.9 1.0 NE2 A:HIS455 4.2 6.6 1.0 CD2 A:HIS455 4.2 5.9 1.0 N A:ASP424 4.2 14.9 1.0 CB A:VAL425 4.3 17.4 1.0 CG2 A:VAL425 4.3 17.0 1.0 CA A:HIS455 4.3 7.0 1.0 N A:VAL425 4.4 17.9 1.0 C A:CYS423 4.4 14.6 1.0 CA A:CYS458 4.7 9.2 1.0 N A:CYS420 4.7 14.3 1.0 O A:HIS455 4.8 4.8 1.0 C A:CYS419 4.9 15.4 1.0 SG A:CYS420 4.9 15.1 1.0 O A:ILE417 4.9 18.0 1.0 CA A:VAL425 4.9 17.6 1.0 N A:CYS423 4.9 14.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME1K4ME3 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 H3R2ME1K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1489 b:11.2 occ:1.00 NE2 A:HIS452 2.1 11.4 1.0 ND1 A:HIS481 2.2 16.3 1.0 SG A:CYS446 2.3 10.4 1.0 SG A:CYS478 2.3 12.7 1.0 CE1 A:HIS452 3.0 11.1 1.0 CE1 A:HIS481 3.1 17.1 1.0 CD2 A:HIS452 3.1 12.0 1.0 CB A:CYS446 3.1 9.7 1.0 CG A:HIS481 3.2 15.1 1.0 CB A:CYS478 3.3 13.7 1.0 CB A:HIS481 3.6 15.6 1.0 N A:CYS478 3.9 13.4 1.0 ND1 A:HIS452 4.1 12.5 1.0 CA A:CYS478 4.2 14.1 1.0 CB A:HIS448 4.2 11.3 1.0 CG A:HIS452 4.2 11.4 1.0 NE2 A:HIS481 4.2 17.6 1.0 CD2 A:HIS481 4.3 15.8 1.0 N A:HIS481 4.5 16.8 1.0 CA A:CYS446 4.6 8.7 1.0 O A:HOH2071 4.7 40.8 1.0 CA A:HIS481 4.7 16.6 1.0 C A:CYS478 4.8 14.6 1.0 O A:CYS478 4.8 12.8 1.0 CG A:HIS448 5.0 13.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME1K4ME3 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 H3R2ME1K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1487 b:16.4 occ:1.00 ND1 B:HIS455 2.0 8.7 1.0 SG B:CYS458 2.3 16.9 1.0 SG B:CYS419 2.3 17.3 1.0 SG B:CYS423 2.4 20.1 1.0 CE1 B:HIS455 3.0 9.5 1.0 CG B:HIS455 3.1 11.2 1.0 CB B:CYS423 3.2 24.4 1.0 CB B:CYS458 3.3 15.3 1.0 CB B:CYS419 3.4 21.8 1.0 CB B:HIS455 3.5 11.0 1.0 CA B:CYS423 3.8 28.3 1.0 N B:CYS419 3.9 24.7 1.0 NE2 B:HIS455 4.1 11.9 1.0 N B:HIS455 4.1 10.3 1.0 CA B:CYS419 4.2 23.9 1.0 CD2 B:HIS455 4.2 9.9 1.0 CB B:VAL425 4.3 31.6 1.0 CG2 B:VAL425 4.4 30.2 1.0 CA B:HIS455 4.4 11.4 1.0 N B:ASP424 4.6 33.4 1.0 C B:CYS423 4.6 31.4 1.0 N B:VAL425 4.6 33.5 1.0 CA B:CYS458 4.7 15.3 1.0 N B:CYS420 4.8 26.1 1.0 C B:CYS419 4.8 24.6 1.0 SG B:CYS420 4.8 22.9 1.0 O B:ILE417 4.9 23.5 1.0 O B:HIS455 5.0 11.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME1K4ME3 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 H3R2ME1K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1488 b:12.1 occ:1.00 NE2 B:HIS452 2.1 13.2 1.0 ND1 B:HIS481 2.2 18.8 1.0 SG B:CYS446 2.3 11.1 1.0 SG B:CYS478 2.3 14.8 1.0 CE1 B:HIS452 3.0 12.3 1.0 CE1 B:HIS481 3.1 19.1 1.0 CD2 B:HIS452 3.1 13.1 1.0 CB B:CYS446 3.2 11.1 1.0 CG B:HIS481 3.2 19.8 1.0 CB B:CYS478 3.4 12.7 1.0 CB B:HIS481 3.6 16.8 1.0 N B:CYS478 3.9 12.0 1.0 CB B:HIS448 4.0 15.3 1.0 ND1 B:HIS452 4.1 13.4 1.0 CA B:CYS478 4.2 12.8 1.0 NE2 B:HIS481 4.2 18.1 1.0 CG B:HIS452 4.2 13.9 1.0 CD2 B:HIS481 4.3 17.2 1.0 N B:HIS481 4.4 19.3 1.0 CA B:CYS446 4.6 9.9 1.0 CA B:HIS481 4.7 18.2 1.0 CG B:HIS448 4.8 15.8 1.0 C B:CYS478 4.9 13.5 1.0 O B:CYS478 5.0 12.7 1.0 N B:HIS448 5.0 12.0 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