Zinc in PDB 4k8v: Structure of Cyclic Gmp-Amp Synthase (Cgas)

The structure of Structure of Cyclic Gmp-Amp Synthase (Cgas), PDB code: 4k8v was solved by P.Gao, Y.Wu, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.07 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.563, 84.147, 124.716, 90.00, 92.74, 90.00
R / Rfree (%)	17.5 / 20.8

The binding sites of Zinc atom in the Structure of Cyclic Gmp-Amp Synthase (Cgas) (pdb code 4k8v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Cyclic Gmp-Amp Synthase (Cgas), PDB code: 4k8v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Cyclic Gmp-Amp Synthase (Cgas)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Cyclic Gmp-Amp Synthase (Cgas) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:13.5 occ:1.00 NE2 C:HIS378 2.1 12.2 1.0 SG C:CYS384 2.3 12.5 1.0 SG C:CYS392 2.3 12.2 1.0 SG C:CYS385 2.3 13.2 1.0 CD2 C:HIS378 3.0 10.5 1.0 CE1 C:HIS378 3.2 16.0 1.0 CB C:CYS385 3.3 9.4 1.0 CB C:CYS392 3.4 8.9 1.0 CB C:CYS384 3.6 12.2 1.0 N C:CYS392 3.7 11.3 1.0 N C:CYS385 3.7 16.0 1.0 C C:CYS384 3.8 12.2 1.0 O C:HOH704 4.0 13.4 1.0 CA C:CYS385 4.1 13.3 1.0 CA C:CYS392 4.1 10.9 1.0 O C:CYS384 4.1 11.7 1.0 CG C:HIS378 4.2 9.8 1.0 CA C:CYS384 4.2 9.3 1.0 ND1 C:HIS378 4.2 14.1 1.0 NH1 C:ARG394 4.3 11.0 1.0 O C:HOH713 4.5 11.8 1.0 O C:HOH725 4.6 16.1 1.0 C C:LYS391 4.6 15.1 1.0 C C:CYS392 4.7 11.3 1.0 O C:ALA390 4.7 17.2 1.0 O C:HOH845 4.7 24.4 1.0 O C:CYS392 4.7 12.8 1.0 CA C:LYS391 5.0 18.3 1.0

Zinc binding site 2 out of 4 in the Structure of Cyclic Gmp-Amp Synthase (Cgas)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Cyclic Gmp-Amp Synthase (Cgas) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:11.9 occ:1.00 NE2 A:HIS378 2.1 11.9 1.0 SG A:CYS385 2.3 12.7 1.0 SG A:CYS384 2.3 11.4 1.0 SG A:CYS392 2.4 9.4 1.0 CD2 A:HIS378 3.0 10.5 1.0 CE1 A:HIS378 3.2 13.7 1.0 CB A:CYS392 3.3 13.3 1.0 CB A:CYS385 3.3 14.2 1.0 CB A:CYS384 3.6 8.5 1.0 N A:CYS385 3.6 15.4 1.0 C A:CYS384 3.7 14.6 1.0 N A:CYS392 3.8 11.8 1.0 CA A:CYS385 4.0 11.8 1.0 CA A:CYS392 4.1 11.8 1.0 O A:HOH728 4.1 13.1 1.0 O A:CYS384 4.1 13.2 1.0 CA A:CYS384 4.2 9.9 1.0 CG A:HIS378 4.2 13.7 1.0 ND1 A:HIS378 4.3 14.1 1.0 NH1 A:ARG394 4.3 8.2 1.0 O A:HOH713 4.6 14.7 1.0 C A:CYS392 4.6 9.5 1.0 O A:HOH796 4.7 25.4 1.0 O A:CYS392 4.7 12.0 1.0 C A:LYS391 4.8 13.3 1.0 O A:ALA390 4.8 13.9 1.0 O A:HOH1060 4.8 23.9 1.0

Zinc binding site 3 out of 4 in the Structure of Cyclic Gmp-Amp Synthase (Cgas)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Cyclic Gmp-Amp Synthase (Cgas) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:15.6 occ:1.00 NE2 B:HIS378 2.2 12.1 1.0 SG B:CYS385 2.3 17.6 1.0 SG B:CYS384 2.3 14.9 1.0 SG B:CYS392 2.4 15.1 1.0 CD2 B:HIS378 3.0 9.5 1.0 CE1 B:HIS378 3.2 15.9 1.0 CB B:CYS385 3.3 20.4 1.0 CB B:CYS392 3.4 13.6 1.0 CB B:CYS384 3.6 15.3 1.0 N B:CYS385 3.6 10.9 1.0 C B:CYS384 3.8 15.0 1.0 N B:CYS392 3.8 17.0 1.0 O B:HOH723 4.0 23.2 1.0 CA B:CYS385 4.0 15.9 1.0 CA B:CYS392 4.1 15.0 1.0 O B:CYS384 4.2 12.4 1.0 CA B:CYS384 4.2 14.0 1.0 CG B:HIS378 4.2 12.1 1.0 ND1 B:HIS378 4.3 16.1 1.0 NH1 B:ARG394 4.3 10.9 1.0 O B:HOH707 4.5 14.7 1.0 C B:CYS392 4.6 19.8 1.0 O B:CYS392 4.7 16.7 1.0 O B:HOH779 4.7 30.0 1.0 O B:HOH733 4.7 23.2 1.0 O B:ALA390 4.8 15.8 1.0 C B:LYS391 4.8 16.9 1.0

Zinc binding site 4 out of 4 in the Structure of Cyclic Gmp-Amp Synthase (Cgas)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Cyclic Gmp-Amp Synthase (Cgas) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:14.2 occ:1.00 NE2 D:HIS378 2.0 15.0 1.0 SG D:CYS385 2.3 14.9 1.0 SG D:CYS392 2.3 12.2 1.0 SG D:CYS384 2.4 13.9 1.0 CD2 D:HIS378 2.9 13.3 1.0 CE1 D:HIS378 3.0 16.6 1.0 CB D:CYS385 3.3 14.0 1.0 CB D:CYS392 3.3 17.4 1.0 CB D:CYS384 3.6 10.8 1.0 N D:CYS385 3.7 12.4 1.0 C D:CYS384 3.8 14.0 1.0 N D:CYS392 3.8 11.2 1.0 CG D:HIS378 4.0 13.6 1.0 CA D:CYS385 4.1 16.1 1.0 ND1 D:HIS378 4.1 18.5 1.0 CA D:CYS392 4.1 15.6 1.0 O D:CYS384 4.1 13.3 1.0 O D:HOH707 4.2 11.5 1.0 CA D:CYS384 4.2 12.8 1.0 NH1 D:ARG394 4.3 11.7 1.0 O D:HOH705 4.6 14.9 1.0 C D:CYS392 4.7 13.4 1.0 O D:HOH725 4.7 23.2 1.0 O D:ALA390 4.7 16.7 1.0 O D:CYS392 4.7 14.1 1.0 O D:HOH780 4.8 31.6 1.0 C D:LYS391 4.8 15.4 1.0

P.Gao, M.Ascano, Y.Wu, W.Barchet, B.L.Gaffney, T.Zillinger, A.A.Serganov, Y.Liu, R.A.Jones, G.Hartmann, T.Tuschl, D.J.Patel. Cyclic [G(2',5')Pa(3',5')P] Is the Metazoan Second Messenger Produced By Dna-Activated Cyclic Gmp-Amp Synthase. Cell(Cambridge,Mass.) V. 153 1094 2013.
ISSN: ISSN 0092-8674
PubMed: 23647843
DOI: 10.1016/J.CELL.2013.04.046