Atomistry » Zinc » PDB 2omg-2ovx » 2oq7
Atomistry »
  Zinc »
    PDB 2omg-2ovx »
      2oq7 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy