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Zinc in PDB 5vds: Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 3',3'-Cdump

Enzymatic activity of Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 3',3'-Cdump

All present enzymatic activity of Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 3',3'-Cdump:
2.7.7.86;

Protein crystallography data

The structure of Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 3',3'-Cdump, PDB code: 5vds was solved by L.J.Byrnes, J.D.Hall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.17 / 2.77
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 215.450, 48.408, 86.086, 90.00, 104.81, 90.00
R / Rfree (%) 20.6 / 24.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 3',3'-Cdump (pdb code 5vds). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 3',3'-Cdump, PDB code: 5vds:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5vds

Go back to Zinc Binding Sites List in 5vds
Zinc binding site 1 out of 2 in the Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 3',3'-Cdump


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 3',3'-Cdump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:38.9
occ:1.00
NE2 A:HIS390 2.2 35.5 1.0
SG A:CYS397 2.3 41.1 1.0
SG A:CYS404 2.3 29.8 1.0
SG A:CYS396 2.4 25.9 1.0
CD2 A:HIS390 2.9 32.7 1.0
CB A:CYS397 3.3 40.1 1.0
CE1 A:HIS390 3.4 39.0 1.0
CB A:CYS404 3.5 22.7 1.0
N A:CYS397 3.7 29.9 1.0
CB A:CYS396 3.8 26.8 1.0
O A:HOH735 3.8 17.9 1.0
N A:CYS404 3.9 37.9 1.0
C A:CYS396 3.9 24.6 1.0
CA A:CYS397 4.1 35.6 1.0
CG A:HIS390 4.2 33.9 1.0
CA A:CYS404 4.2 29.2 1.0
O A:CYS396 4.2 25.7 1.0
NH1 A:ARG406 4.3 32.9 1.0
ND1 A:HIS390 4.3 37.8 1.0
CA A:CYS396 4.4 24.0 1.0
O A:GLU402 4.5 50.2 1.0
O A:HOH719 4.5 52.3 1.0
C A:CYS404 4.8 27.3 1.0
O A:CYS404 4.9 30.0 1.0
C A:LYS403 5.0 43.1 1.0

Zinc binding site 2 out of 2 in 5vds

Go back to Zinc Binding Sites List in 5vds
Zinc binding site 2 out of 2 in the Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 3',3'-Cdump


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 3',3'-Cdump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:33.1
occ:1.00
NE2 B:HIS390 2.2 35.9 1.0
SG B:CYS404 2.3 22.7 1.0
SG B:CYS397 2.3 30.9 1.0
SG B:CYS396 2.5 21.9 1.0
CD2 B:HIS390 2.9 32.4 1.0
CB B:CYS397 3.3 33.3 1.0
CE1 B:HIS390 3.4 38.2 1.0
O B:HOH744 3.4 25.5 1.0
CB B:CYS404 3.5 18.1 1.0
N B:CYS397 3.8 25.6 1.0
CB B:CYS396 3.8 26.3 1.0
N B:CYS404 3.9 21.5 1.0
C B:CYS396 3.9 25.1 1.0
CA B:CYS397 4.1 29.2 1.0
CG B:HIS390 4.1 29.8 1.0
CA B:CYS404 4.2 19.3 1.0
O B:CYS396 4.2 26.4 1.0
NH1 B:ARG406 4.3 15.9 1.0
ND1 B:HIS390 4.4 36.0 1.0
CA B:CYS396 4.4 25.8 1.0
O B:GLU402 4.6 43.1 1.0
C B:CYS404 4.7 22.1 1.0
O B:CYS404 4.8 26.5 1.0
O B:HOH748 4.9 24.2 1.0

Reference:

J.Hall, E.C.Ralph, S.Shanker, H.Wang, L.J.Byrnes, R.Horst, J.Wong, A.Brault, D.Dumlao, J.F.Smith, L.A.Dakin, D.C.Schmitt, J.Trujillo, F.Vincent, M.Griffor, A.E.Aulabaugh. The Catalytic Mechanism of Cyclic Gmp-Amp Synthase (Cgas) and Implications For Innate Immunity and Inhibition. Protein Sci. V. 26 2367 2017.
ISSN: ESSN 1469-896X
PubMed: 28940468
DOI: 10.1002/PRO.3304
Page generated: Wed Dec 16 11:08:29 2020

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