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Magnesium in PDB 4ty0: Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg

Enzymatic activity of Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg

All present enzymatic activity of Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg:
2.7.7.86;

Protein crystallography data

The structure of Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg, PDB code: 4ty0 was solved by P.J.Kranzusch, A.S.Y.Lee, S.C.Wilson, M.S.Solovykh, R.E.Vance, J.M.Berger, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.35 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.329, 59.596, 102.163, 90.00, 96.47, 90.00
R / Rfree (%) 17.3 / 20.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg (pdb code 4ty0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg, PDB code: 4ty0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4ty0

Go back to Magnesium Binding Sites List in 4ty0
Magnesium binding site 1 out of 4 in the Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:24.4
occ:1.00
 OD2 A:ASP194 1.9 26.3 1.0
OD1 A:ASP134 2.1 23.4 1.0
O A:HOH679 2.1 28.1 1.0
OD2 A:ASP132 2.2 23.5 1.0
OD1 A:ASP132 2.2 29.1 1.0
O A:HOH678 2.2 27.2 1.0
CG A:ASP132 2.4 29.5 1.0
CG A:ASP194 3.0 29.4 1.0
CG A:ASP134 3.1 35.6 1.0
CB A:ASP194 3.6 21.3 1.0
OD2 A:ASP134 3.6 28.6 1.0
O37 A:38V503 3.6 24.8 1.0
MG A:MG502 3.8 28.0 1.0
CB A:ASP132 3.9 23.5 1.0
NE2 A:HIS192 4.0 30.9 1.0
OD1 A:ASP194 4.0 29.4 1.0
NH2 A:ARG183 4.0 30.9 1.0
C48 A:38V503 4.1 25.7 1.0
O49 A:38V503 4.1 28.0 1.0
CD2 A:HIS192 4.2 28.4 1.0
O A:HOH681 4.2 30.9 1.0
CB A:ASP134 4.4 26.2 1.0
O15 A:38V503 4.5 40.7 1.0
O A:ILE133 4.7 25.1 1.0
C12 A:38V503 4.7 24.6 1.0
CA A:ASP134 4.8 23.1 1.0
CA A:ASP132 4.8 24.9 1.0
CA A:ASP194 4.8 26.4 1.0
N A:ASP194 4.9 22.3 1.0
P36 A:38V503 4.9 29.1 1.0
C11 A:38V503 4.9 24.0 1.0
O46 A:38V503 4.9 27.0 1.0
C A:ILE133 4.9 22.4 1.0
N A:ASP134 4.9 21.2 1.0
O A:HOH680 5.0 30.0 1.0

Magnesium binding site 2 out of 4 in 4ty0

Go back to Magnesium Binding Sites List in 4ty0
Magnesium binding site 2 out of 4 in the Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:28.0
occ:1.00
 O37 A:38V503 2.0 24.8 1.0
O A:HOH680 2.1 30.0 1.0
O46 A:38V503 2.1 27.0 1.0
OD2 A:ASP132 2.1 23.5 1.0
O42 A:38V503 2.1 24.3 1.0
OD2 A:ASP134 2.2 28.6 1.0
CG A:ASP132 3.1 29.5 1.0
CG A:ASP134 3.2 35.6 1.0
P36 A:38V503 3.2 29.1 1.0
P40 A:38V503 3.2 26.5 1.0
P44 A:38V503 3.3 28.8 1.0
OD1 A:ASP134 3.5 23.4 1.0
O43 A:38V503 3.5 27.0 1.0
O A:HOH679 3.7 28.1 1.0
O38 A:38V503 3.7 29.3 1.0
O A:HOH681 3.7 30.9 1.0
CB A:ASP132 3.8 23.5 1.0
MG A:MG501 3.8 24.4 1.0
C39 A:38V503 3.8 29.3 1.0
O45 A:38V503 4.0 23.9 1.0
OG A:SER115 4.0 27.4 1.0
OD1 A:ASP132 4.1 29.1 1.0
O A:HOH696 4.1 21.7 1.0
N A:SER115 4.3 28.7 1.0
O A:ASP132 4.4 27.7 1.0
O47 A:38V503 4.4 26.2 1.0
O35 A:38V503 4.5 27.5 1.0
CB A:ASP134 4.5 26.2 1.0
O41 A:38V503 4.5 26.5 1.0
CA A:GLY114 4.6 30.1 1.0
O A:HOH678 4.6 27.2 1.0
C A:ASP132 4.8 27.4 1.0
CA A:ASP132 4.9 24.9 1.0
CB A:SER115 4.9 27.8 1.0
C A:GLY114 5.0 24.2 1.0

Magnesium binding site 3 out of 4 in 4ty0

Go back to Magnesium Binding Sites List in 4ty0
Magnesium binding site 3 out of 4 in the Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:24.3
occ:1.00
 OD1 B:ASP134 2.0 25.5 1.0
O B:HOH682 2.1 27.0 1.0
OD2 B:ASP194 2.1 27.8 1.0
OD1 B:ASP132 2.1 25.7 1.0
OD2 B:ASP132 2.1 23.8 1.0
O B:HOH681 2.2 23.9 1.0
CG B:ASP132 2.4 25.2 1.0
CG B:ASP134 3.0 29.3 1.0
CG B:ASP194 3.1 30.1 1.0
OD2 B:ASP134 3.4 28.1 1.0
CB B:ASP194 3.6 20.1 1.0
O37 B:38V503 3.7 24.4 1.0
MG B:MG502 3.7 25.3 1.0
CB B:ASP132 3.9 20.1 1.0
NE2 B:HIS192 4.0 33.7 1.0
C48 B:38V503 4.1 32.1 1.0
OD1 B:ASP194 4.1 31.1 1.0
O B:HOH771 4.2 34.2 1.0
O49 B:38V503 4.2 27.3 1.0
CD2 B:HIS192 4.2 28.1 1.0
NH2 B:ARG183 4.3 27.5 1.0
CB B:ASP134 4.3 23.5 1.0
O15 B:38V503 4.6 49.1 1.0
O B:HOH790 4.6 45.1 1.0
O B:ILE133 4.7 26.6 1.0
C12 B:38V503 4.7 32.6 1.0
CA B:ASP134 4.8 22.2 1.0
CA B:ASP132 4.8 23.5 1.0
O46 B:38V503 4.8 24.2 1.0
C B:ILE133 4.8 23.2 1.0
O B:HOH683 4.9 24.1 1.0
N B:ASP134 4.9 19.5 1.0
CA B:ASP194 4.9 20.3 1.0
C11 B:38V503 4.9 33.9 1.0
N B:ASP194 4.9 22.8 1.0
P36 B:38V503 4.9 28.1 1.0
C B:ASP132 4.9 25.2 1.0

Magnesium binding site 4 out of 4 in 4ty0

Go back to Magnesium Binding Sites List in 4ty0
Magnesium binding site 4 out of 4 in the Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Linear Intermediate 5' Pppa(3',5')Pg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:25.3
occ:1.00
 O46 B:38V503 2.1 24.2 1.0
O B:HOH683 2.1 24.1 1.0
OD2 B:ASP132 2.1 23.8 1.0
OD2 B:ASP134 2.1 28.1 1.0
O42 B:38V503 2.1 22.7 1.0
O37 B:38V503 2.1 24.4 1.0
CG B:ASP132 3.1 25.2 1.0
CG B:ASP134 3.2 29.3 1.0
P44 B:38V503 3.3 26.5 1.0
P40 B:38V503 3.3 24.6 1.0
P36 B:38V503 3.3 28.1 1.0
O43 B:38V503 3.5 25.1 1.0
OD1 B:ASP134 3.6 25.5 1.0
MG B:MG501 3.7 24.3 1.0
CB B:ASP132 3.8 20.1 1.0
O38 B:38V503 3.8 27.4 1.0
O B:HOH682 3.8 27.0 1.0
C39 B:38V503 3.9 25.6 1.0
OG B:SER115 3.9 25.4 1.0
O45 B:38V503 3.9 25.7 1.0
O B:HOH771 3.9 34.2 1.0
OD1 B:ASP132 4.0 25.7 1.0
O B:HOH694 4.1 22.4 1.0
N B:SER115 4.2 23.8 1.0
O B:ASP132 4.3 24.1 1.0
O47 B:38V503 4.5 21.8 1.0
CB B:ASP134 4.5 23.5 1.0
O B:HOH681 4.5 23.9 1.0
O41 B:38V503 4.6 25.0 1.0
CA B:GLY114 4.6 31.3 1.0
O35 B:38V503 4.6 27.4 1.0
C B:ASP132 4.7 25.2 1.0
CB B:SER115 4.8 27.1 1.0
CA B:ASP132 4.9 23.5 1.0
C B:GLY114 5.0 27.9 1.0
C34 B:38V503 5.0 26.6 1.0

Reference:

P.J.Kranzusch, A.S.Lee, S.C.Wilson, M.S.Solovykh, R.E.Vance, J.M.Berger, J.A.Doudna. Structure-Guided Reprogramming of Human Cgas Dinucleotide Linkage Specificity. Cell V. 158 1011 2014.
ISSN: ISSN 1097-4172
PubMed: 25131990
DOI: 10.1016/J.CELL.2014.07.028
Page generated: Tue Aug 12 00:16:30 2025

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