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Iron in PDB 2pxj: The Complex Structure of JMJD2A and Monomethylated H3K36 Peptide

Protein crystallography data

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

Resolution Low / High (Å) 45.56 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.863, 150.172, 57.317, 90.00, 90.00, 90.00
R / Rfree (%) 25.6 / 27.6

Other elements in 2pxj:

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

Zinc (Zn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the The Complex Structure of JMJD2A and Monomethylated H3K36 Peptide (pdb code 2pxj). 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 Monomethylated H3K36 Peptide, PDB code: 2pxj:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 2pxj

Go back to Iron Binding Sites List in 2pxj
Iron binding site 1 out of 2 in the The Complex Structure of JMJD2A and Monomethylated 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 Monomethylated H3K36 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:26.3
occ:1.00
OE1 A:GLU190 2.1 22.9 1.0
NE2 A:HIS276 2.2 24.8 1.0
O2' A:OGA5001 2.4 39.3 1.0
NE2 A:HIS188 2.4 30.0 1.0
O2 A:OGA5001 2.6 41.5 1.0
O A:HOH5077 2.7 37.9 1.0
CE1 A:HIS188 3.0 29.4 1.0
CE1 A:HIS276 3.1 23.7 1.0
CD A:GLU190 3.1 25.5 1.0
C2 A:OGA5001 3.2 42.5 1.0
CD2 A:HIS276 3.2 23.2 1.0
C1 A:OGA5001 3.3 42.3 1.0
OE2 A:GLU190 3.5 22.7 1.0
CD2 A:HIS188 3.6 29.4 1.0
ND1 A:HIS188 4.2 30.1 1.0
ND1 A:HIS276 4.2 25.5 1.0
CG A:HIS276 4.3 23.9 1.0
OG A:SER196 4.3 28.9 1.0
CG A:GLU190 4.5 23.8 1.0
CG A:HIS188 4.5 28.1 1.0
O1 A:OGA5001 4.5 40.7 1.0
N1 A:OGA5001 4.6 43.1 1.0
CG2 A:THR270 4.7 26.5 1.0
CB A:SER196 4.8 26.4 1.0
OG1 A:THR270 4.8 25.3 1.0

Iron binding site 2 out of 2 in 2pxj

Go back to Iron Binding Sites List in 2pxj
Iron binding site 2 out of 2 in the The Complex Structure of JMJD2A and Monomethylated 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 Monomethylated H3K36 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:33.0
occ:1.00
OE1 B:GLU190 2.2 25.8 1.0
NE2 B:HIS276 2.2 25.9 1.0
NE2 B:HIS188 2.2 27.7 1.0
O2 B:OGA6001 2.4 39.4 1.0
O2' B:OGA6001 2.5 37.1 1.0
O B:HOH6043 2.7 38.2 1.0
CE1 B:HIS188 2.8 28.3 1.0
C1 B:OGA6001 3.0 41.0 1.0
C2 B:OGA6001 3.1 40.0 1.0
CE1 B:HIS276 3.1 24.9 1.0
CD B:GLU190 3.2 27.5 1.0
CD2 B:HIS276 3.2 25.0 1.0
CD2 B:HIS188 3.4 30.4 1.0
OE2 B:GLU190 3.5 25.4 1.0
ND1 B:HIS188 4.0 30.9 1.0
O1 B:OGA6001 4.2 45.2 1.0
ND1 B:HIS276 4.2 25.8 1.0
CG B:HIS188 4.3 26.8 1.0
CG B:HIS276 4.3 24.4 1.0
OG B:SER196 4.5 30.6 1.0
N1 B:OGA6001 4.5 40.1 1.0
CG B:GLU190 4.5 26.0 1.0
CG2 B:THR270 4.9 25.4 1.0
CB B:SER196 4.9 26.2 1.0
OG1 B:THR270 4.9 27.2 1.0
O B:HIS188 5.0 22.3 1.0

Reference:

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
Page generated: Sun Dec 13 14:51:29 2020

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