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Zinc in PDB 2ox0: Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Dimethylated at LYS9

Protein crystallography data

The structure of Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Dimethylated at LYS9, PDB code: 2ox0 was solved by E.S.Pilka, S.S.Ng, K.L.Kavanagh, M.A.Mcdonough, P.Savitsky, F.Von Delft, C.H.Arrowsmith, J.Weigelt, A.Edwards, M.Sundstrom, C.J.Schofield, U.Oppermann, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.49 / 1.95
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.210, 150.004, 57.228, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21

Other elements in 2ox0:

The structure of Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Dimethylated at LYS9 also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Dimethylated at LYS9 (pdb code 2ox0). 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 JMJD2A Complexed with Histone H3 Peptide Dimethylated at LYS9, PDB code: 2ox0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2ox0

Go back to Zinc Binding Sites List in 2ox0
Zinc binding site 1 out of 2 in the Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Dimethylated at LYS9


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 JMJD2A Complexed with Histone H3 Peptide Dimethylated at LYS9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:40.5
occ:1.00
NE2 A:HIS240 2.1 38.4 1.0
SG A:CYS234 2.3 41.2 1.0
SG A:CYS306 2.3 41.1 1.0
SG A:CYS308 2.4 40.9 1.0
CE1 A:HIS240 3.1 34.5 1.0
CD2 A:HIS240 3.1 41.9 1.0
CB A:CYS234 3.1 47.3 1.0
CB A:CYS306 3.3 41.8 1.0
CB A:CYS308 3.5 47.1 1.0
N A:CYS308 3.8 49.1 1.0
CA A:CYS306 4.0 43.2 1.0
CA A:CYS308 4.1 47.2 1.0
ND1 A:HIS240 4.2 33.5 1.0
CG A:ARG309 4.2 57.0 1.0
CG A:HIS240 4.2 34.5 1.0
N A:SER307 4.4 50.2 1.0
N A:ARG309 4.4 49.1 1.0
C A:CYS306 4.5 46.0 1.0
C A:CYS308 4.5 47.8 1.0
CA A:CYS234 4.6 49.9 1.0
O A:HOH649 4.7 38.1 1.0
O A:ALA236 4.7 36.4 1.0
O A:HOH659 4.7 38.0 1.0
CA A:PHE237 4.8 35.5 1.0
NE A:ARG309 4.9 64.2 1.0
C A:ALA236 4.9 36.6 1.0
CD A:ARG309 4.9 58.0 1.0
C A:SER307 4.9 54.6 1.0

Zinc binding site 2 out of 2 in 2ox0

Go back to Zinc Binding Sites List in 2ox0
Zinc binding site 2 out of 2 in the Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Dimethylated at LYS9


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 JMJD2A Complexed with Histone H3 Peptide Dimethylated at LYS9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:40.2
occ:1.00
NE2 B:HIS240 2.2 43.1 1.0
SG B:CYS306 2.3 41.8 1.0
SG B:CYS234 2.3 38.9 1.0
SG B:CYS308 2.4 40.1 1.0
CE1 B:HIS240 3.1 46.0 1.0
CB B:CYS234 3.2 47.1 1.0
CD2 B:HIS240 3.2 39.5 1.0
CB B:CYS306 3.5 42.5 1.0
N B:CYS308 3.6 49.6 1.0
CB B:CYS308 3.6 45.1 1.0
CA B:CYS306 4.0 42.7 1.0
N B:SER307 4.1 51.7 1.0
CA B:CYS308 4.1 47.1 1.0
ND1 B:HIS240 4.3 38.2 1.0
C B:CYS306 4.3 47.4 1.0
CG B:HIS240 4.3 34.0 1.0
N B:ARG309 4.3 53.5 1.0
C B:CYS308 4.6 49.5 1.0
CA B:CYS234 4.6 47.5 1.0
CG B:ARG309 4.6 57.7 1.0
O B:HOH725 4.7 44.4 1.0
O B:ALA236 4.7 35.1 1.0
C B:SER307 4.7 55.3 1.0
CD B:ARG309 4.8 60.3 1.0
O B:HOH627 4.8 47.4 1.0
CA B:PHE237 4.8 33.9 1.0
OG B:SER307 4.9 59.8 1.0
C B:ALA236 4.9 36.0 1.0
CA B:SER307 5.0 55.4 1.0

Reference:

S.S.Ng, K.L.Kavanagh, M.A.Mcdonough, D.Butler, E.S.Pilka, B.M.Lienard, J.E.Bray, P.Savitsky, O.Gileadi, F.Von Delft, N.R.Rose, J.Offer, J.C.Scheinost, T.Borowski, M.Sundstrom, C.J.Schofield, U.Oppermann. Crystal Structures of Histone Demethylase JMJD2A Reveal Basis For Substrate Specificity. Nature V. 448 87 2007.
ISSN: ISSN 0028-0836
PubMed: 17589501
DOI: 10.1038/NATURE05971
Page generated: Wed Dec 16 03:47:19 2020

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