Magnesium in PDB 3kqi: Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide

The structure of Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide, PDB code: 3kqi was solved by H.Wen, J.Z.Li, T.Song, M.Lu, M.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.99 / 1.78
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.757, 77.758, 72.116, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 21.8

The structure of Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide (pdb code 3kqi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide, PDB code: 3kqi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg74 b:35.9 occ:1.00 O A:HOH102 3.6 39.0 1.0 OG1 A:THR67 3.6 27.9 1.0 N A:THR67 3.7 25.9 1.0 NE A:ARG66 3.8 25.3 1.0 NZ A:LYS63 4.0 24.8 1.0 CB A:THR67 4.0 28.1 1.0 O A:HOH92 4.4 38.8 1.0 CA A:THR67 4.5 28.3 1.0 CA A:ARG66 4.5 24.3 1.0 CD A:ARG66 4.6 24.1 1.0 C A:ARG66 4.6 24.6 1.0 NH2 A:ARG66 4.6 28.2 1.0 CD A:LYS63 4.6 24.2 1.0 CZ A:ARG66 4.7 25.2 1.0 CE A:LYS63 4.7 23.9 1.0 O A:HOH128 4.9 55.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of PHF2 Phd Domain Complexed with H3K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg75 b:42.5 occ:1.00 O A:HOH139 3.5 52.9 1.0 OG A:SER33 3.5 27.8 1.0 O A:HOH133 3.7 27.3 1.0 O A:HOH134 3.7 29.4 1.0 NE A:ARG18 3.8 23.2 1.0 CB A:SER33 4.0 26.6 1.0 CG A:ARG18 4.2 23.1 1.0 CD A:ARG18 4.5 22.8 1.0 CB A:ARG18 4.5 23.2 1.0 NH2 A:ARG18 4.6 23.1 1.0 CZ A:ARG18 4.7 23.4 1.0 CA A:ARG18 4.9 23.1 1.0 O A:HOH140 5.0 43.8 1.0

H.Wen, J.Li, T.Song, M.Lu, P.Y.Kan, M.G.Lee, B.Sha, X.Shi. Recognition of Histone H3K4 Trimethylation By the Plant Homeodomain of PHF2 Modulates Histone Demethylation. J.Biol.Chem. V. 285 9322 2010.
ISSN: ISSN 0021-9258
PubMed: 20129925
DOI: 10.1074/JBC.C109.097667