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

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

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

Protein crystallography data

The structure of Human Cyclic Gmp-Amp Synthase (Cgas) in Complex with 3',3'-Cdimp, PDB code: 5vdr 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) 55.90 / 3.04
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 215.528, 48.395, 89.099, 90.00, 109.89, 90.00
R / Rfree (%) 20.8 / 25.4

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 5vdr

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


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'-Cdimp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:55.8
occ:1.00
NE2 A:HIS390 2.2 51.9 1.0
SG A:CYS404 2.4 55.0 1.0
SG A:CYS397 2.4 67.3 1.0
SG A:CYS396 2.4 60.6 1.0
CD2 A:HIS390 2.9 49.7 1.0
CE1 A:HIS390 3.4 54.3 1.0
CB A:CYS404 3.4 54.2 1.0
CB A:CYS397 3.5 73.5 1.0
CB A:CYS396 3.8 53.9 1.0
N A:CYS397 3.9 66.2 1.0
N A:CYS404 4.0 64.7 1.0
C A:CYS396 4.1 60.8 1.0
NH1 A:ARG406 4.1 45.5 1.0
O A:GLU402 4.2 0.0 1.0
CG A:HIS390 4.2 47.9 1.0
CA A:CYS404 4.2 57.1 1.0
CA A:CYS397 4.3 73.4 1.0
ND1 A:HIS390 4.3 51.8 1.0
CA A:CYS396 4.5 52.2 1.0
O A:CYS396 4.5 63.1 1.0
C A:CYS404 4.8 55.4 1.0

Zinc binding site 2 out of 2 in 5vdr

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


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'-Cdimp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:55.9
occ:1.00
NE2 B:HIS390 2.2 46.7 1.0
SG B:CYS397 2.3 66.2 1.0
SG B:CYS404 2.4 48.4 1.0
SG B:CYS396 2.4 54.1 1.0
CD2 B:HIS390 2.8 41.5 1.0
CE1 B:HIS390 3.3 47.5 1.0
CB B:CYS397 3.4 69.0 1.0
CB B:CYS404 3.6 49.0 1.0
CB B:CYS396 3.7 46.5 1.0
N B:CYS397 3.9 65.1 1.0
C B:CYS396 3.9 59.0 1.0
NH1 B:ARG406 4.0 32.4 1.0
CG B:HIS390 4.0 39.2 1.0
CA B:CYS397 4.2 69.5 1.0
N B:CYS404 4.2 63.1 1.0
O B:CYS396 4.3 62.0 1.0
ND1 B:HIS390 4.3 43.6 1.0
CA B:CYS396 4.4 48.7 1.0
CA B:CYS404 4.4 50.1 1.0
O B:GLU402 4.6 86.1 1.0
C B:CYS404 4.9 45.8 1.0
N B:GLY391 5.0 42.5 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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