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Manganese in PDB 5iw0: Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid]

Protein crystallography data

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid], PDB code: 5iw0 was solved by J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.97 / 1.63
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.320, 62.741, 46.609, 90.00, 91.93, 90.00
R / Rfree (%) 15.7 / 19.2

Other elements in 5iw0:

The structure of Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid] also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid] (pdb code 5iw0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid], PDB code: 5iw0:

Manganese binding site 1 out of 1 in 5iw0

Go back to Manganese Binding Sites List in 5iw0
Manganese binding site 1 out of 1 in the Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid]


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-Chloro-2- Methylbenzyl)Oxy)-1H-Pyrazol-1-Yl)Isonicotinic Acid] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn603

b:13.9
occ:1.00
OE1 A:GLU485 2.1 17.4 1.0
O A:HOH776 2.2 18.1 1.0
N08 A:6EP601 2.3 17.0 1.0
N22 A:6EP601 2.3 13.2 1.0
NE2 A:HIS483 2.3 12.6 1.0
NE2 A:HIS571 2.3 15.1 1.0
N07 A:6EP601 3.0 16.2 1.0
C06 A:6EP601 3.1 12.0 1.0
CE1 A:HIS571 3.1 14.2 1.0
CD A:GLU485 3.2 16.9 1.0
CE1 A:HIS483 3.2 15.6 1.0
CD2 A:HIS483 3.3 11.6 1.0
C23 A:6EP601 3.3 12.0 1.0
CD2 A:HIS571 3.4 12.0 1.0
C09 A:6EP601 3.4 18.0 1.0
OE2 A:GLU485 3.6 21.5 1.0
C11 A:6EP601 4.2 17.1 1.0
O A:HOH770 4.3 25.6 1.0
ND1 A:HIS571 4.3 11.7 1.0
ND1 A:HIS483 4.3 12.9 1.0
CG A:HIS483 4.4 12.2 1.0
C10 A:6EP601 4.4 16.7 1.0
CG A:GLU485 4.4 10.7 1.0
CG A:HIS571 4.4 10.9 1.0
C05 A:6EP601 4.5 12.1 1.0
OG A:SER491 4.5 16.6 1.0
C24 A:6EP601 4.6 12.3 1.0

Reference:

J.R.Horton, X.Liu, M.Gale, L.Wu, J.R.Shanks, X.Zhang, P.J.Webber, J.S.Bell, S.C.Kales, B.T.Mott, G.Rai, D.J.Jansen, M.J.Henderson, D.J.Urban, M.D.Hall, A.Simeonov, D.J.Maloney, M.A.Johns, H.Fu, A.Jadhav, P.M.Vertino, Q.Yan, X.Cheng. Structural Basis For KDM5A Histone Lysine Demethylase Inhibition By Diverse Compounds. Cell Chem Biol V. 23 769 2016.
ISSN: ESSN 2451-9456
PubMed: 27427228
DOI: 10.1016/J.CHEMBIOL.2016.06.006
Page generated: Tue Dec 15 04:42:04 2020

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