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Nickel 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

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine, PDB code: 2oq7:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2oq7

Go back to Nickel Binding Sites List in 2oq7
Nickel 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 Nickel with other atoms in the Ni 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:Ni501

b:33.7
occ:1.00
O A:HOH653 1.8 21.6 1.0
NE2 A:HIS276 1.9 25.1 1.0
O2 A:OGA601 2.1 29.2 1.0
OE1 A:GLU190 2.2 28.6 1.0
O2' A:OGA601 2.2 33.3 1.0
NE2 A:HIS188 2.3 30.2 1.0
CE1 A:HIS276 2.8 38.3 1.0
C1 A:OGA601 2.9 48.8 1.0
C2 A:OGA601 2.9 35.3 1.0
CD2 A:HIS276 3.1 32.1 1.0
CE1 A:HIS188 3.1 24.5 1.0
CD A:GLU190 3.1 32.9 1.0
CD2 A:HIS188 3.3 35.7 1.0
OE2 A:GLU190 3.4 31.0 1.0
ND1 A:HIS276 4.0 33.5 1.0
O1 A:OGA601 4.1 34.5 1.0
CG A:HIS276 4.1 27.9 1.0
OG A:SER196 4.1 31.6 1.0
N1 A:OGA601 4.2 53.9 1.0
ND1 A:HIS188 4.2 36.9 1.0
O A:HOH642 4.3 38.4 1.0
CG A:HIS188 4.4 26.3 1.0
CG A:GLU190 4.5 31.4 1.0
NZ A:LYS241 4.7 28.4 0.5
CB A:SER196 4.8 30.6 1.0
C4 A:OGA601 4.8 34.3 1.0

Nickel binding site 2 out of 2 in 2oq7

Go back to Nickel Binding Sites List in 2oq7
Nickel 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 Nickel with other atoms in the Ni 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:Ni501

b:36.0
occ:1.00
O B:HOH678 2.0 19.1 1.0
NE2 B:HIS276 2.0 32.8 1.0
NE2 B:HIS188 2.1 31.4 1.0
O2 B:OGA601 2.2 31.3 1.0
OE1 B:GLU190 2.2 38.5 1.0
O2' B:OGA601 2.3 33.6 1.0
CE1 B:HIS276 2.9 32.1 1.0
C1 B:OGA601 3.0 54.0 1.0
C2 B:OGA601 3.0 30.9 1.0
CE1 B:HIS188 3.0 33.1 1.0
CD2 B:HIS276 3.1 34.2 1.0
CD B:GLU190 3.2 38.1 1.0
CD2 B:HIS188 3.2 35.5 1.0
OE2 B:GLU190 3.5 31.8 1.0
ND1 B:HIS276 4.0 33.1 1.0
ND1 B:HIS188 4.1 26.5 1.0
CG B:HIS276 4.2 28.1 1.0
O1 B:OGA601 4.2 41.5 1.0
OG B:SER196 4.2 40.6 1.0
N1 B:OGA601 4.2 51.5 1.0
CG B:HIS188 4.3 31.0 1.0
CG B:GLU190 4.5 30.4 1.0
CB B:SER196 4.9 34.5 1.0
C4 B:OGA601 4.9 44.4 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: Fri Sep 25 08:12:31 2020
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