Atomistry » Zinc » PDB 5j1q-5jf1 » 5jcf
Atomistry »
  Zinc »
    PDB 5j1q-5jf1 »
      5jcf »

Zinc in PDB 5jcf: Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Orthorhombic Form).

Protein crystallography data

The structure of Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Orthorhombic Form)., PDB code: 5jcf was solved by S.Cusack, E.Uchikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.920, 132.470, 139.040, 90.00, 90.00, 90.00
R / Rfree (%) 27.7 / 31.2

Other elements in 5jcf:

The structure of Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Orthorhombic Form). also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Orthorhombic Form). (pdb code 5jcf). 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 Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Orthorhombic Form)., PDB code: 5jcf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5jcf

Go back to Zinc Binding Sites List in 5jcf
Zinc binding site 1 out of 2 in the Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Orthorhombic Form).


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 Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Orthorhombic Form). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:63.4
occ:1.00
SG A:CYS939 2.3 62.0 1.0
SG A:CYS884 2.3 67.9 1.0
SG A:CYS936 2.3 64.3 1.0
SG A:CYS881 2.3 62.1 1.0
CB A:CYS936 3.3 62.7 1.0
CB A:CYS884 3.4 68.3 1.0
CB A:CYS881 3.4 63.7 1.0
CB A:CYS939 3.4 64.1 1.0
N A:CYS884 3.9 65.6 1.0
CA A:CYS884 4.2 68.3 1.0
N A:CYS939 4.2 65.6 1.0
CA A:CYS939 4.4 64.7 1.0
CB A:GLN941 4.5 57.5 1.0
CB A:ASN883 4.7 62.5 1.0
CA A:CYS936 4.8 63.3 1.0
C A:CYS884 4.8 70.5 1.0
CA A:CYS881 4.8 64.0 1.0
CZ2 A:TRP943 4.9 62.7 1.0
NE1 A:TRP943 4.9 59.6 1.0
C A:ASN883 5.0 65.2 1.0
C A:CYS939 5.0 63.2 1.0
CB A:ASP938 5.0 70.3 1.0

Zinc binding site 2 out of 2 in 5jcf

Go back to Zinc Binding Sites List in 5jcf
Zinc binding site 2 out of 2 in the Crystal Structure of Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Orthorhombic Form).


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 Chicken MDA5 with 5'P 10-Mer Dsrna and Adp-MG2+ at 2.6 A Resolution (Orthorhombic Form). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:65.7
occ:1.00
SG B:CYS884 2.3 70.2 1.0
SG B:CYS939 2.3 64.5 1.0
SG B:CYS936 2.3 66.0 1.0
SG B:CYS881 2.3 64.2 1.0
CB B:CYS936 3.3 64.5 1.0
CB B:CYS884 3.4 71.0 1.0
CB B:CYS881 3.4 65.3 1.0
CB B:CYS939 3.4 66.7 1.0
N B:CYS884 3.9 68.0 1.0
CA B:CYS884 4.2 71.0 1.0
N B:CYS939 4.2 67.7 1.0
CA B:CYS939 4.4 67.2 1.0
CB B:GLN941 4.5 60.4 1.0
CB B:ASN883 4.7 64.7 1.0
CA B:CYS936 4.8 65.1 1.0
C B:CYS884 4.8 73.2 1.0
CA B:CYS881 4.8 65.2 1.0
CZ2 B:TRP943 4.9 64.5 1.0
NE1 B:TRP943 4.9 61.5 1.0
C B:ASN883 5.0 67.5 1.0
CB B:ASP938 5.0 72.1 1.0
C B:CYS939 5.0 65.8 1.0

Reference:

E.Uchikawa, M.Lethier, H.Malet, J.Brunel, D.Gerlier, S.Cusack. Structural Analysis of Dsrna Binding to Anti-Viral Pattern Recognition Receptors LGP2 and MDA5. Mol.Cell V. 62 586 2016.
ISSN: ISSN 1097-2765
PubMed: 27203181
DOI: 10.1016/J.MOLCEL.2016.04.021
Page generated: Sun Oct 27 18:43:55 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy