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Zinc in PDB 2wwj: Structure of JMJD2A Complexed with Inhibitor 10A

Enzymatic activity of Structure of JMJD2A Complexed with Inhibitor 10A

All present enzymatic activity of Structure of JMJD2A Complexed with Inhibitor 10A:
1.14.11.27;

Protein crystallography data

The structure of Structure of JMJD2A Complexed with Inhibitor 10A, PDB code: 2wwj was solved by N.R.Rose, I.J.Clifton, U.Oppermann, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.97 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.330, 148.970, 57.110, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 24.8

Other elements in 2wwj:

The structure of Structure of JMJD2A Complexed with Inhibitor 10A also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of JMJD2A Complexed with Inhibitor 10A (pdb code 2wwj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of JMJD2A Complexed with Inhibitor 10A, PDB code: 2wwj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2wwj

Go back to Zinc Binding Sites List in 2wwj
Zinc binding site 1 out of 2 in the Structure of JMJD2A Complexed with Inhibitor 10A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of JMJD2A Complexed with Inhibitor 10A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:33.7
occ:1.00
NE2 A:HIS240 2.1 32.1 1.0
SG A:CYS306 2.3 29.1 1.0
SG A:CYS234 2.3 32.1 1.0
SG A:CYS308 2.4 83.2 1.0
CE1 A:HIS240 2.9 28.5 1.0
CB A:CYS234 3.2 34.7 1.0
CD2 A:HIS240 3.2 29.7 1.0
CB A:CYS308 3.5 84.1 1.0
CB A:CYS306 3.6 26.9 1.0
N A:CYS308 3.7 87.0 1.0
CA A:CYS306 3.9 27.2 1.0
N A:SER307 3.9 92.4 1.0
ND1 A:HIS240 4.1 28.4 1.0
CA A:CYS308 4.1 85.6 1.0
C A:CYS306 4.1 27.1 1.0
CG A:HIS240 4.3 26.7 1.0
N A:ARG309 4.3 89.0 1.0
C A:CYS308 4.5 88.1 1.0
CG A:LYS310 4.5 0.8 1.0
N A:LYS310 4.6 83.9 1.0
CA A:CYS234 4.6 36.5 1.0
O A:ALA236 4.6 28.1 1.0
C A:SER307 4.7 89.6 1.0
CB A:LYS310 4.7 88.7 1.0
CA A:PHE237 4.8 25.5 1.0
C A:ALA236 4.8 28.7 1.0
CA A:SER307 4.9 91.4 1.0
N A:PHE237 4.9 27.4 1.0
O A:CYS306 5.0 27.7 1.0

Zinc binding site 2 out of 2 in 2wwj

Go back to Zinc Binding Sites List in 2wwj
Zinc binding site 2 out of 2 in the Structure of JMJD2A Complexed with Inhibitor 10A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of JMJD2A Complexed with Inhibitor 10A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:31.7
occ:1.00
NE2 B:HIS240 2.1 26.8 1.0
SG B:CYS234 2.3 41.5 1.0
SG B:CYS306 2.3 30.4 1.0
SG B:CYS308 2.4 51.2 1.0
CE1 B:HIS240 3.0 21.7 1.0
CD2 B:HIS240 3.1 17.1 1.0
CB B:CYS234 3.4 28.9 1.0
CB B:CYS306 3.5 24.6 1.0
CB B:CYS308 3.6 60.3 1.0
N B:CYS308 3.7 68.5 1.0
CA B:CYS306 4.0 35.8 1.0
CA B:CYS308 4.1 52.7 1.0
ND1 B:HIS240 4.1 29.9 1.0
N B:SER307 4.2 70.2 1.0
CG B:HIS240 4.2 28.9 1.0
C B:CYS306 4.3 40.5 1.0
CG B:ARG309 4.3 58.7 1.0
C B:CYS308 4.6 59.4 1.0
N B:ARG309 4.6 72.6 1.0
CA B:CYS234 4.6 32.4 1.0
CA B:PHE237 4.8 33.4 1.0
C B:SER307 4.8 89.5 1.0
O B:ALA236 4.8 24.8 1.0
NE B:ARG309 4.9 70.1 1.0
C B:ALA236 4.9 30.9 1.0
N B:PHE237 4.9 27.0 1.0
CD B:ARG309 5.0 65.5 1.0

Reference:

N.R.Rose, E.C.Woon, G.L.Kingham, O.N.King, J.Mecinovic, I.J.Clifton, S.S.Ng, J.Talib-Hardy, U.Oppermann, M.A.Mcdonough, C.J.Schofield. Selective Inhibitors of the JMJD2 Histone Demethylases: Combined Nondenaturing Mass Spectrometric Screening and Crystallographic Approaches. J. Med. Chem. V. 53 1810 2010.
ISSN: ISSN 1520-4804
PubMed: 20088513
DOI: 10.1021/JM901680B
Page generated: Wed Dec 16 03:58:30 2020

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