Iron in PDB 2p5b: The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide

The structure of The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide, PDB code: 2p5b was solved by G.Zhang, Z.Chen, J.Zang, X.Hong, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.34 / 1.99
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.915, 150.844, 57.346, 90.00, 90.00, 90.00
R / Rfree (%)	23.8 / 26.3

The structure of The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Iron atom in the The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide (pdb code 2p5b). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide, PDB code: 2p5b:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe352 b:34.3 occ:1.00 OE1 A:GLU190 2.1 26.1 1.0 NE2 A:HIS276 2.1 26.7 1.0 NE2 A:HIS188 2.2 31.1 1.0 O2' A:OGA401 2.3 51.5 1.0 O1 A:OXY502 2.4 42.4 0.5 O2 A:OGA401 2.4 51.3 1.0 O2 A:OXY502 2.4 43.5 0.5 CE1 A:HIS188 2.9 31.1 1.0 CE1 A:HIS276 3.0 24.6 1.0 C2 A:OGA401 3.0 53.7 1.0 CD A:GLU190 3.0 23.7 1.0 C1 A:OGA401 3.1 52.3 1.0 CD2 A:HIS276 3.2 23.9 1.0 CD2 A:HIS188 3.3 30.7 1.0 OE2 A:GLU190 3.4 21.7 1.0 ND1 A:HIS188 4.1 31.7 1.0 O1 A:OXY501 4.1 34.1 0.5 ND1 A:HIS276 4.1 27.5 1.0 OG A:SER196 4.2 31.4 1.0 CG A:HIS276 4.3 22.9 1.0 O1 A:OGA401 4.3 50.2 1.0 N1 A:OGA401 4.3 56.1 1.0 CG A:HIS188 4.3 29.6 1.0 CG A:GLU190 4.4 23.0 1.0 O2 A:OXY501 4.7 39.3 0.5 CB A:SER196 4.7 30.1 1.0 CG2 A:THR270 4.8 30.4 1.0 OG1 A:THR270 4.9 28.3 1.0 C4 A:OGA401 5.0 58.6 1.0

Iron binding site 2 out of 2 in the The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Complex Structure of JMJD2A and Trimethylated H3K36 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe352 b:35.0 occ:1.00 OE1 B:GLU190 2.1 32.8 1.0 NE2 B:HIS276 2.1 29.3 1.0 O2 B:OGA402 2.2 44.3 1.0 NE2 B:HIS188 2.2 25.0 1.0 O2' B:OGA402 2.3 47.6 1.0 O2 B:OXY503 2.4 41.8 0.5 O1 B:OXY503 2.4 41.6 0.5 CE1 B:HIS188 3.0 24.3 1.0 C1 B:OGA402 3.0 49.0 1.0 CE1 B:HIS276 3.0 26.6 1.0 C2 B:OGA402 3.0 50.8 1.0 CD B:GLU190 3.1 32.8 1.0 CD2 B:HIS276 3.1 24.9 1.0 CD2 B:HIS188 3.4 25.1 1.0 OE2 B:GLU190 3.5 30.8 1.0 O B:HOH593 4.1 65.1 1.0 ND1 B:HIS276 4.1 28.1 1.0 ND1 B:HIS188 4.2 27.7 1.0 O1 B:OGA402 4.2 47.9 1.0 OG B:SER196 4.2 32.3 1.0 CG B:HIS276 4.2 26.2 1.0 N1 B:OGA402 4.3 53.8 1.0 CG B:HIS188 4.4 25.4 1.0 CG B:GLU190 4.4 30.1 1.0 CB B:SER196 4.7 32.6 1.0 CG2 B:THR270 4.8 26.6 1.0 OG1 B:THR270 4.9 29.6 1.0 CM2 J:M3L10 5.0 86.2 1.0

Z.Chen, J.Zang, J.Kappler, X.Hong, F.Crawford, Q.Wang, F.Lan, C.Jiang, J.Whetstine, S.Dai, K.Hansen, Y.Shi, G.Zhang. Structural Basis of the Recognition of A Methylated Histone Tail By JMJD2A. Proc.Natl.Acad.Sci.Usa V. 104 10818 2007.
ISSN: ISSN 0027-8424
PubMed: 17567753
DOI: 10.1073/PNAS.0704525104