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Zinc in PDB 5vdp: Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 2',3'-Cgamp

Enzymatic activity of Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 2',3'-Cgamp

All present enzymatic activity of Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 2',3'-Cgamp:
2.7.7.86;

Protein crystallography data

The structure of Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 2',3'-Cgamp, PDB code: 5vdp 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) 32.45 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 215.886, 46.733, 88.165, 90.00, 110.45, 90.00
R / Rfree (%) 19.7 / 24.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 2',3'-Cgamp (pdb code 5vdp). 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 2',3'-Cgamp, PDB code: 5vdp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5vdp

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


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 2',3'-Cgamp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:44.2
occ:1.00
SG A:CYS397 2.1 43.7 1.0
NE2 A:HIS390 2.2 34.0 1.0
SG A:CYS396 2.3 37.0 1.0
SG A:CYS404 2.4 35.6 1.0
CD2 A:HIS390 3.0 31.7 1.0
CE1 A:HIS390 3.3 34.9 1.0
CB A:CYS404 3.3 36.5 1.0
CB A:CYS397 3.4 41.9 1.0
CB A:CYS396 3.5 35.7 1.0
O A:HOH733 3.6 31.1 1.0
N A:CYS397 3.7 40.3 1.0
C A:CYS396 3.8 38.4 1.0
N A:CYS404 3.8 44.4 1.0
CA A:CYS404 4.1 39.5 1.0
CA A:CYS397 4.1 41.9 1.0
CA A:CYS396 4.2 37.3 1.0
CG A:HIS390 4.2 32.4 1.0
O A:CYS396 4.2 38.0 1.0
NH1 A:ARG406 4.3 27.9 1.0
ND1 A:HIS390 4.3 34.1 1.0
O A:CYS404 4.4 37.5 1.0
O A:GLU402 4.5 67.8 1.0
C A:CYS404 4.5 37.7 1.0

Zinc binding site 2 out of 2 in 5vdp

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


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 2',3'-Cgamp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:42.1
occ:1.00
NE2 B:HIS390 2.2 28.8 1.0
SG B:CYS397 2.2 52.2 1.0
SG B:CYS396 2.4 40.6 1.0
SG B:CYS404 2.6 31.6 1.0
CD2 B:HIS390 3.0 28.1 1.0
CE1 B:HIS390 3.2 29.1 1.0
CB B:CYS397 3.3 49.7 1.0
CB B:CYS404 3.4 33.8 1.0
CB B:CYS396 3.5 38.1 1.0
C B:CYS396 3.7 40.8 1.0
N B:CYS397 3.7 49.6 1.0
O B:HOH732 3.9 35.2 1.0
N B:CYS404 3.9 39.3 1.0
O B:CYS396 4.0 38.9 1.0
CA B:CYS397 4.1 51.1 1.0
CA B:CYS396 4.1 39.1 1.0
CA B:CYS404 4.2 37.5 1.0
NH1 B:ARG406 4.2 33.3 1.0
CG B:HIS390 4.2 27.2 1.0
ND1 B:HIS390 4.3 27.8 1.0
O B:GLU402 4.4 59.9 1.0
O B:CYS404 4.5 34.4 1.0
C B:CYS404 4.6 34.6 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 11:08:33 2020

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