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Zinc 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:

Cobalt (Co) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of JMJD3 with Gsk-J1 (pdb code 4ask). 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 JMJD3 with Gsk-J1, PDB code: 4ask:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4ask

Go back to Zinc Binding Sites List in 4ask
Zinc 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 Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of JMJD3 with Gsk-J1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2000

b:23.0
occ:1.00
SG A:CYS1575 2.3 21.7 1.0
SG A:CYS1578 2.4 21.9 1.0
SG A:CYS1605 2.4 22.2 1.0
SG A:CYS1602 2.4 20.4 1.0
CB A:CYS1575 3.2 20.4 1.0
CB A:CYS1605 3.2 21.7 1.0
CB A:CYS1578 3.3 24.7 1.0
CB A:CYS1602 3.5 19.8 1.0
N A:CYS1578 3.8 26.6 1.0
N A:CYS1602 4.0 19.5 1.0
O A:HOH2553 4.1 36.9 1.0
CA A:CYS1578 4.1 24.8 1.0
N A:CYS1605 4.3 20.9 1.0
CA A:CYS1602 4.3 19.8 1.0
CG1 A:VAL1580 4.3 19.2 1.0
CA A:CYS1605 4.4 21.6 1.0
O A:HOH2550 4.5 37.1 1.0
CB A:GLU1577 4.6 32.3 1.0
CA A:CYS1575 4.6 20.8 1.0
C A:GLU1577 4.8 29.9 1.0
C A:CYS1578 4.8 24.6 1.0
C A:CYS1602 4.9 20.1 1.0
O A:CYS1602 4.9 19.8 1.0
N A:GLU1577 4.9 29.6 1.0

Zinc binding site 2 out of 2 in 4ask

Go back to Zinc Binding Sites List in 4ask
Zinc 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 Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of JMJD3 with Gsk-J1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2000

b:24.8
occ:1.00
SG B:CYS1575 2.2 22.5 1.0
SG B:CYS1602 2.3 22.2 1.0
SG B:CYS1578 2.3 23.4 1.0
SG B:CYS1605 2.4 25.2 1.0
CB B:CYS1575 3.1 22.9 1.0
CB B:CYS1605 3.2 25.6 1.0
CB B:CYS1578 3.4 24.3 1.0
CB B:CYS1602 3.5 22.5 1.0
N B:CYS1578 3.8 26.4 1.0
N B:CYS1602 4.0 22.1 1.0
CA B:CYS1578 4.2 25.1 1.0
O B:HOH2472 4.2 39.7 1.0
CG2 B:VAL1580 4.2 20.4 0.7
CG1 B:VAL1580 4.3 20.3 0.3
CA B:CYS1602 4.3 22.1 1.0
N B:CYS1605 4.3 24.9 1.0
CA B:CYS1605 4.4 25.2 1.0
O B:HOH2468 4.4 44.4 1.0
O B:HOH2456 4.5 42.7 1.0
CA B:CYS1575 4.6 23.9 1.0
CB B:GLU1577 4.6 33.7 1.0
C B:GLU1577 4.8 29.5 1.0
OE1 B:GLU1577 4.8 40.2 1.0
C B:CYS1578 4.8 24.3 1.0
C B:CYS1602 4.9 23.0 1.0
N B:GLU1577 4.9 31.9 1.0
O B:CYS1602 5.0 22.7 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: Wed Dec 16 05:03:44 2020

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