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Cobalt in PDB 4ask: Crystal Structure of JMJD3 with Gsk-J1

Protein crystallography data

The structure of Crystal Structure of JMJD3 with Gsk-J1, PDB code: 4ask was solved by C.Chung, J.Mosley, J.Liddle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.37 / 1.86
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.359, 65.554, 77.392, 85.98, 67.69, 68.42
R / Rfree (%) 16.471 / 20.882

Other elements in 4ask:

The structure of Crystal Structure of JMJD3 with Gsk-J1 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of JMJD3 with Gsk-J1 (pdb code 4ask). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of JMJD3 with Gsk-J1, PDB code: 4ask:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 4ask

Go back to Cobalt Binding Sites List in 4ask
Cobalt binding site 1 out of 2 in the Crystal Structure of JMJD3 with Gsk-J1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of JMJD3 with Gsk-J1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co3000

b:20.7
occ:1.00
N4 A:K0I2639 2.1 16.8 1.0
OE2 A:GLU1392 2.2 14.1 1.0
O A:HOH2327 2.2 14.4 1.0
NE2 A:HIS1390 2.2 14.3 1.0
O A:HOH2335 2.2 18.3 1.0
N3 A:K0I2639 2.2 16.4 1.0
C8 A:K0I2639 3.0 19.0 1.0
C7 A:K0I2639 3.0 18.9 1.0
CD2 A:HIS1390 3.1 14.9 1.0
C12 A:K0I2639 3.1 17.7 1.0
CD A:GLU1392 3.2 15.3 1.0
C4 A:K0I2639 3.3 17.7 1.0
CE1 A:HIS1390 3.3 14.6 1.0
OE1 A:GLU1392 3.4 16.2 1.0
N1 A:K0I2639 3.4 17.4 1.0
NE2 A:HIS1470 3.9 14.6 1.0
O A:HOH2322 4.1 23.1 1.0
CE1 A:HIS1470 4.3 14.1 1.0
CG A:HIS1390 4.3 15.1 1.0
O A:HOH2625 4.3 38.7 1.0
O A:HOH2342 4.3 15.9 1.0
N2 A:K0I2639 4.3 18.4 1.0
C9 A:K0I2639 4.3 20.4 1.0
ND1 A:HIS1390 4.3 14.6 1.0
C11 A:K0I2639 4.4 18.5 1.0
C5 A:K0I2639 4.5 17.8 1.0
CG A:GLU1392 4.5 15.4 1.0
C3 A:K0I2639 4.9 17.5 1.0
C10 A:K0I2639 4.9 20.2 1.0
C6 A:K0I2639 4.9 19.1 1.0

Cobalt binding site 2 out of 2 in 4ask

Go back to Cobalt Binding Sites List in 4ask
Cobalt binding site 2 out of 2 in the Crystal Structure of JMJD3 with Gsk-J1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of JMJD3 with Gsk-J1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co3000

b:22.5
occ:1.00
N4 B:K0I2639 2.1 18.4 1.0
OE2 B:GLU1392 2.1 15.7 1.0
NE2 B:HIS1390 2.1 14.2 1.0
O B:HOH2262 2.2 13.9 1.0
N3 B:K0I2639 2.2 18.1 1.0
O B:HOH2270 2.3 19.7 1.0
C8 B:K0I2639 3.0 20.2 1.0
C7 B:K0I2639 3.0 19.2 1.0
CD2 B:HIS1390 3.0 14.0 1.0
C12 B:K0I2639 3.1 19.3 1.0
CD B:GLU1392 3.1 15.5 1.0
CE1 B:HIS1390 3.2 14.2 1.0
C4 B:K0I2639 3.3 18.9 1.0
OE1 B:GLU1392 3.4 16.2 1.0
N1 B:K0I2639 3.5 19.0 1.0
NE2 B:HIS1470 3.9 14.4 1.0
O B:HOH2257 4.2 26.4 1.0
CG B:HIS1390 4.2 14.2 1.0
ND1 B:HIS1390 4.3 14.7 1.0
CE1 B:HIS1470 4.3 14.7 1.0
O B:HOH2256 4.3 41.3 1.0
C9 B:K0I2639 4.3 21.9 1.0
N2 B:K0I2639 4.3 20.4 1.0
O B:HOH2277 4.3 17.5 1.0
C11 B:K0I2639 4.4 21.3 1.0
CG B:GLU1392 4.5 14.9 1.0
C5 B:K0I2639 4.5 18.9 1.0
C10 B:K0I2639 4.9 21.8 1.0
C3 B:K0I2639 4.9 18.2 1.0
C6 B:K0I2639 4.9 19.4 1.0

Reference:

L.Kruidenier, C.Chung, Z.Cheng, J.Liddle, K.Che, G.Joberty, M.Bantscheff, C.Bountra, A.Bridges, H.Diallo, D.Eberhard, S.Hutchinson, E.Jones, R.Katso, M.Leveridge, P.K.Mander, J.Mosley, C.Ramirez-Molina, P.Rowland, C.J.Schofield, R.J.Sheppard, J.E.Smith, C.Swales, R.Tanner, P.Thomas, A.Tumber, G.Drewes, U.Oppermann, D.J.Patel, K.Lee, D.M.Wilson. A Selective Jumonji H3K27 Demethylase Inhibitor Modulates the Proinflammatory Macrophage Response Nature V. 488 404 2012.
ISSN: ISSN 0028-0836
PubMed: 22842901
DOI: 10.1038/NATURE11262
Page generated: Sun Dec 13 10:43:47 2020

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