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Zinc in PDB 2oq7: The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine

Enzymatic activity of The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine

All present enzymatic activity of The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine:
1.14.11.27;

Protein crystallography data

The structure of The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine, PDB code: 2oq7 was solved by K.L.Kavanagh, S.S.Ng, E.Pilka, 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) 50.00 / 2.15
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.120, 148.531, 57.333, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.8

Other elements in 2oq7:

The structure of The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine (pdb code 2oq7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine, PDB code: 2oq7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2oq7

Go back to Zinc Binding Sites List in 2oq7
Zinc binding site 1 out of 2 in the The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:37.6
occ:1.00
NE2 A:HIS240 2.2 33.8 1.0
SG A:CYS306 2.2 35.5 1.0
SG A:CYS234 2.3 34.7 1.0
SG A:CYS308 2.5 34.8 1.0
CE1 A:HIS240 3.0 30.2 1.0
CD2 A:HIS240 3.2 37.9 1.0
CB A:CYS306 3.3 36.4 1.0
CB A:CYS234 3.3 33.7 1.0
CB A:CYS308 3.7 35.7 1.0
N A:CYS308 3.7 40.5 1.0
CA A:CYS306 3.9 37.0 1.0
N A:SER307 4.0 36.2 1.0
CA A:CYS308 4.2 39.7 1.0
C A:CYS306 4.2 37.8 1.0
ND1 A:HIS240 4.2 28.1 1.0
CG A:HIS240 4.3 41.9 1.0
N A:ARG309 4.4 43.9 1.0
C A:CYS308 4.5 42.8 1.0
CB A:LYS310 4.5 51.9 1.0
O A:ALA236 4.6 32.9 1.0
N A:LYS310 4.6 49.1 1.0
CA A:CYS234 4.7 40.2 1.0
CG A:LYS310 4.7 52.9 1.0
CA A:PHE237 4.8 36.3 1.0
C A:SER307 4.8 41.8 1.0
C A:ALA236 4.9 37.1 1.0
CA A:SER307 5.0 43.5 1.0

Zinc binding site 2 out of 2 in 2oq7

Go back to Zinc Binding Sites List in 2oq7
Zinc binding site 2 out of 2 in the The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:38.9
occ:1.00
NE2 B:HIS240 2.2 30.7 1.0
SG B:CYS234 2.2 35.0 1.0
SG B:CYS306 2.3 39.1 1.0
SG B:CYS308 2.3 38.5 1.0
CE1 B:HIS240 3.0 33.7 1.0
CB B:CYS234 3.2 41.9 1.0
CD2 B:HIS240 3.3 32.7 1.0
CB B:CYS306 3.5 43.0 1.0
CB B:CYS308 3.6 50.8 1.0
N B:CYS308 3.8 48.4 1.0
CA B:CYS306 3.9 41.1 1.0
N B:SER307 4.0 43.5 1.0
ND1 B:HIS240 4.2 32.5 1.0
CA B:CYS308 4.2 49.3 1.0
C B:CYS306 4.2 44.6 1.0
CG B:HIS240 4.3 31.4 1.0
N B:ARG309 4.5 51.9 1.0
CG B:ARG309 4.5 53.5 1.0
CA B:CYS234 4.5 44.1 1.0
O B:ALA236 4.6 33.2 1.0
CD B:ARG309 4.7 52.2 1.0
C B:SER307 4.7 51.2 1.0
C B:CYS308 4.7 52.1 1.0
CA B:PHE237 4.8 34.6 1.0
CA B:SER307 4.9 49.4 1.0
C B:ALA236 4.9 34.1 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: Thu Oct 17 02:44:05 2024

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