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Zinc in PDB 5a80: Crystal Structure of Human JMJD2A in Complex with Compound 40

Protein crystallography data

The structure of Crystal Structure of Human JMJD2A in Complex with Compound 40, PDB code: 5a80 was solved by R.Nowak, S.Velupillai, T.Krojer, C.Gileadi, C.Johansson, M.Korczynska, D.D.Le, N.Younger, E.Gregori-Puigjane, A.Tumber, E.Iwasa, S.B.Pollock, I.Ortiz Torres, J.Kopec, C.Tallant, S.Froese, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, B.K.Shoichet, D.G.Fujimori, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.44 / 2.28
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.810, 149.190, 57.240, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 24.9

Other elements in 5a80:

The structure of Crystal Structure of Human JMJD2A in Complex with Compound 40 also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human JMJD2A in Complex with Compound 40 (pdb code 5a80). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human JMJD2A in Complex with Compound 40, PDB code: 5a80:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5a80

Go back to Zinc Binding Sites List in 5a80
Zinc binding site 1 out of 2 in the Crystal Structure of Human JMJD2A in Complex with Compound 40


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 JMJD2A in Complex with Compound 40 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1358

b:42.9
occ:1.00
NE2 A:HIS240 2.0 44.2 1.0
SG A:CYS306 2.2 49.5 1.0
SG A:CYS234 2.3 41.3 1.0
SG A:CYS308 2.4 44.4 1.0
CE1 A:HIS240 3.0 43.1 1.0
CD2 A:HIS240 3.0 42.7 1.0
CB A:CYS234 3.3 42.6 1.0
CB A:CYS306 3.4 47.5 1.0
CB A:CYS308 3.6 46.7 1.0
N A:CYS308 3.7 53.9 1.0
CA A:CYS306 3.9 47.9 1.0
N A:SER307 4.0 49.8 1.0
ND1 A:HIS240 4.1 46.7 1.0
CG A:ARG309 4.1 59.2 1.0
CA A:CYS308 4.1 50.8 1.0
CG A:HIS240 4.1 40.1 1.0
C A:CYS306 4.3 46.3 1.0
N A:ARG309 4.4 52.9 1.0
NE A:ARG309 4.5 75.4 1.0
C A:CYS308 4.5 55.5 1.0
CA A:CYS234 4.6 43.1 1.0
C A:SER307 4.7 52.1 1.0
O A:ALA236 4.8 35.9 1.0
CA A:PHE237 4.9 38.7 1.0
CD A:ARG309 4.9 62.2 1.0
CA A:SER307 4.9 53.0 1.0

Zinc binding site 2 out of 2 in 5a80

Go back to Zinc Binding Sites List in 5a80
Zinc binding site 2 out of 2 in the Crystal Structure of Human JMJD2A in Complex with Compound 40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human JMJD2A in Complex with Compound 40 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1357

b:49.7
occ:1.00
NE2 B:HIS240 2.1 48.8 1.0
SG B:CYS306 2.2 48.4 1.0
SG B:CYS234 2.3 45.7 1.0
SG B:CYS308 2.3 55.2 1.0
CE1 B:HIS240 3.0 49.7 1.0
CD2 B:HIS240 3.2 45.6 1.0
CB B:CYS308 3.4 55.6 1.0
CB B:CYS234 3.4 47.6 1.0
N B:CYS308 3.5 58.3 1.0
CB B:CYS306 3.5 50.4 1.0
N B:SER307 3.9 52.9 1.0
CA B:CYS308 3.9 54.8 1.0
CA B:CYS306 3.9 49.6 1.0
C B:CYS306 4.1 54.2 1.0
ND1 B:HIS240 4.2 49.6 1.0
N B:ARG309 4.3 55.5 1.0
CG B:HIS240 4.3 46.2 1.0
C B:CYS308 4.4 58.2 1.0
CG B:ARG309 4.5 61.6 1.0
C B:SER307 4.5 60.7 1.0
CA B:CYS234 4.7 52.5 1.0
CE B:MET312 4.8 55.6 1.0
O B:ALA236 4.8 37.0 1.0
CA B:SER307 4.8 55.8 1.0
CA B:PHE237 5.0 45.6 1.0

Reference:

M.Korczynska, D.D.Le, N.Younger, E.Gregori-Puigjane, A.Tumber, T.Krojer, S.Velupillai, C.Gileadi, R.P.Nowak, E.Iwasa, S.B.Pollock, I.Ortiz Torres, U.Oppermann, B.K.Shoichet, D.G.Fujimori. Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors. J.Med.Chem. V. 59 1580 2016.
ISSN: ISSN 0022-2623
PubMed: 26699912
DOI: 10.1021/ACS.JMEDCHEM.5B01527
Page generated: Wed Dec 16 06:01:53 2020

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