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

Protein crystallography data

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

Zinc Binding Sites:

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 4k8v

Go back to Zinc Binding Sites List in 4k8v
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 4k8v

Go back to Zinc Binding Sites List in 4k8v
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 4k8v

Go back to Zinc Binding Sites List in 4k8v
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 4k8v

Go back to Zinc Binding Sites List in 4k8v
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

Reference:

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
Page generated: Sun Oct 27 01:48:58 2024

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