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Zinc in PDB 5fp7: Crystal Structure of Human KDM4D in Complex with 3-4-Methylthiophen-2- Yl Methylaminopyridine-4-Carboxylic Acid

Protein crystallography data

The structure of Crystal Structure of Human KDM4D in Complex with 3-4-Methylthiophen-2- Yl Methylaminopyridine-4-Carboxylic Acid, PDB code: 5fp7 was solved by C.Chung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.52 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.410, 71.410, 150.590, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 20.7

Other elements in 5fp7:

The structure of Crystal Structure of Human KDM4D in Complex with 3-4-Methylthiophen-2- Yl Methylaminopyridine-4-Carboxylic Acid also contains other interesting chemical elements:

Iron (Fe) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human KDM4D in Complex with 3-4-Methylthiophen-2- Yl Methylaminopyridine-4-Carboxylic Acid (pdb code 5fp7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human KDM4D in Complex with 3-4-Methylthiophen-2- Yl Methylaminopyridine-4-Carboxylic Acid, PDB code: 5fp7:

Zinc binding site 1 out of 1 in 5fp7

Go back to Zinc Binding Sites List in 5fp7
Zinc binding site 1 out of 1 in the Crystal Structure of Human KDM4D in Complex with 3-4-Methylthiophen-2- Yl Methylaminopyridine-4-Carboxylic Acid


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 Human KDM4D in Complex with 3-4-Methylthiophen-2- Yl Methylaminopyridine-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn350

b:26.3
occ:1.00
NE2 A:HIS244 2.0 25.5 1.0
SG A:CYS238 2.2 28.6 1.0
SG A:CYS310 2.2 32.0 1.0
SG A:CYS312 2.3 31.1 1.0
CE1 A:HIS244 2.9 24.8 1.0
CB A:CYS238 3.0 30.6 1.0
CD2 A:HIS244 3.1 25.1 1.0
CB A:CYS310 3.3 30.4 1.0
CB A:CYS312 3.3 33.5 1.0
N A:CYS312 3.9 37.2 1.0
CA A:CYS310 4.0 31.2 1.0
ND1 A:HIS244 4.1 24.1 1.0
CA A:CYS312 4.1 36.2 1.0
CG A:HIS244 4.2 22.9 1.0
CB A:GLU314 4.3 51.1 1.0
O A:HOH2370 4.4 40.1 1.0
CA A:CYS238 4.4 31.4 1.0
C A:CYS310 4.5 33.4 1.0
N A:GLU314 4.6 47.4 1.0
N A:SER311 4.6 33.2 1.0
C A:CYS312 4.6 37.8 1.0
N A:ALA315 4.6 51.0 1.0
O A:ALA240 4.7 24.6 1.0
N A:GLY313 4.7 40.9 1.0
CA A:PHE241 4.8 21.5 1.0
O A:HOH2369 4.9 40.8 1.0
C A:ALA240 4.9 25.0 1.0
CG A:GLU314 4.9 55.4 1.0
CA A:GLU314 4.9 49.5 1.0

Reference:

S.M.Westaway, A.G.Preston, M.D.Barker, F.Brown, J.A.Brown, M.Campbell, C.W.Chung, G.Drewes, R.Eagle, N.Garton, L.Gordon, C.Haslam, T.G.Hayhow, P.G.Humphreys, G.Joberty, R.Katso, L.Kruidenier, M.Leveridge, M.Pemberton, I.Rioja, G.A.Seal, T.Shipley, O.Singh, C.J.Suckling, J.Taylor, P.Thomas, D.M.Wilson, K.Lee, R.K.Prinjha. Cell Penetrant Inhibitors of the KDM4 and KDM5 Families of Histone Lysine Demethylases. 2. Pyrido[3,4-D]Pyrimidin-4(3H)-One Derivatives. J. Med. Chem. V. 59 1370 2016.
ISSN: ISSN 1520-4804
PubMed: 26771203
DOI: 10.1021/ACS.JMEDCHEM.5B01538
Page generated: Wed Dec 16 06:15:33 2020

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