Atomistry » Zinc » PDB 5a0s-5a8a » 5a7s
Atomistry »
  Zinc »
    PDB 5a0s-5a8a »
      5a7s »

Zinc in PDB 5a7s: Crystal Structure of Human JMJD2A in Complex with Compound 44

Enzymatic activity of Crystal Structure of Human JMJD2A in Complex with Compound 44

All present enzymatic activity of Crystal Structure of Human JMJD2A in Complex with Compound 44:
1.14.11.27;

Protein crystallography data

The structure of Crystal Structure of Human JMJD2A in Complex with Compound 44, PDB code: 5a7s 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) 31.19 / 2.20
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.070, 100.760, 149.000, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 22.8

Other elements in 5a7s:

The structure of Crystal Structure of Human JMJD2A in Complex with Compound 44 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 44 (pdb code 5a7s). 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 44, PDB code: 5a7s:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5a7s

Go back to Zinc Binding Sites List in 5a7s
Zinc binding site 1 out of 2 in the Crystal Structure of Human JMJD2A in Complex with Compound 44


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 44 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1356

b:38.7
occ:1.00
NE2 A:HIS240 2.1 44.2 1.0
SG A:CYS306 2.1 41.9 1.0
SG A:CYS234 2.2 41.0 1.0
SG A:CYS308 2.3 47.0 1.0
CE1 A:HIS240 3.0 42.7 1.0
CD2 A:HIS240 3.1 36.0 1.0
CB A:CYS234 3.2 39.3 1.0
CB A:CYS306 3.4 34.1 1.0
CB A:CYS308 3.5 46.3 1.0
N A:CYS308 3.6 48.4 1.0
CA A:CYS306 3.9 44.5 1.0
N A:SER307 3.9 40.2 1.0
CA A:CYS308 4.0 48.4 1.0
ND1 A:HIS240 4.1 38.9 1.0
CG A:HIS240 4.2 34.6 1.0
C A:CYS306 4.2 40.0 1.0
N A:ARG309 4.4 49.0 1.0
C A:CYS308 4.5 49.5 1.0
CA A:CYS234 4.5 42.9 1.0
CG A:ARG309 4.7 52.2 1.0
C A:SER307 4.7 60.2 1.0
O A:ALA236 4.8 31.9 1.0
CA A:PHE237 4.8 35.9 1.0
CD A:ARG309 4.9 53.3 1.0
CE A:MET312 4.9 56.8 1.0
CA A:SER307 4.9 52.8 1.0

Zinc binding site 2 out of 2 in 5a7s

Go back to Zinc Binding Sites List in 5a7s
Zinc binding site 2 out of 2 in the Crystal Structure of Human JMJD2A in Complex with Compound 44


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 44 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1356

b:37.0
occ:1.00
NE2 B:HIS240 2.0 36.9 1.0
SG B:CYS306 2.1 37.9 1.0
SG B:CYS234 2.3 32.8 1.0
SG B:CYS308 2.4 37.8 1.0
CE1 B:HIS240 3.0 37.7 1.0
CD2 B:HIS240 3.1 35.0 1.0
CB B:CYS306 3.3 32.8 1.0
CB B:CYS234 3.3 36.9 1.0
CB B:CYS308 3.6 41.5 1.0
N B:CYS308 3.6 49.3 1.0
N B:SER307 3.8 37.6 1.0
CA B:CYS306 3.9 39.5 1.0
CA B:CYS308 4.1 45.8 1.0
ND1 B:HIS240 4.1 34.4 1.0
C B:CYS306 4.1 41.4 1.0
CG B:HIS240 4.2 33.3 1.0
N B:ARG309 4.3 47.3 1.0
CG B:ARG309 4.5 53.9 1.0
C B:CYS308 4.5 48.8 1.0
CA B:CYS234 4.6 34.4 1.0
C B:SER307 4.6 51.4 1.0
O B:HOH2142 4.7 43.7 1.0
CA B:SER307 4.8 47.7 1.0
CD B:ARG309 4.8 58.5 1.0
CA B:PHE237 4.9 31.6 1.0
O B:ALA236 4.9 27.7 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 06:01:52 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy