Magnesium in PDB 4txz: Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Nonhydrolyzable Gtp

Enzymatic activity of Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Nonhydrolyzable Gtp

All present enzymatic activity of Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Nonhydrolyzable Gtp:
2.7.7.86;

Protein crystallography data

The structure of Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Nonhydrolyzable Gtp, PDB code: 4txz 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) 45.19 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.041, 59.373, 103.498, 90.00, 96.04, 90.00
R / Rfree (%) 22.8 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Nonhydrolyzable Gtp (pdb code 4txz). 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 Nonhydrolyzable Gtp, PDB code: 4txz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4txz

Go back to Magnesium Binding Sites List in 4txz
Magnesium binding site 1 out of 4 in the Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Nonhydrolyzable Gtp


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 Nonhydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:34.1
occ:1.00
 OD1 A:ASP134 2.1 46.7 1.0
OD2 A:ASP194 2.2 44.8 1.0
OD1 A:ASP132 2.3 47.5 1.0
OD2 A:ASP132 2.8 47.6 1.0
CG A:ASP132 2.8 47.0 1.0
CG A:ASP134 3.1 46.1 1.0
O2A A:G2P503 3.2 0.6 1.0
CG A:ASP194 3.3 38.5 1.0
OD2 A:ASP134 3.5 46.3 1.0
CB A:ASP194 3.8 37.4 1.0
CB A:ASP132 4.2 45.7 1.0
NE2 A:HIS192 4.2 41.8 1.0
OD1 A:ASP194 4.3 38.6 1.0
NH2 A:ARG183 4.4 44.6 1.0
PA A:G2P503 4.4 0.7 1.0
MG A:MG502 4.4 68.9 1.0
CB A:ASP134 4.4 45.1 1.0
O1A A:G2P503 4.5 0.8 1.0
O5' A:G2P503 4.8 77.2 1.0
CD2 A:HIS192 4.9 40.0 1.0

Magnesium binding site 2 out of 4 in 4txz

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Magnesium binding site 2 out of 4 in the Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Nonhydrolyzable Gtp


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 Nonhydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:68.9
occ:1.00
 OD2 A:ASP134 2.1 46.3 1.0
O2B A:G2P503 2.1 74.5 1.0
OD2 A:ASP132 2.3 47.6 1.0
O2G A:G2P503 2.8 63.4 1.0
O2A A:G2P503 3.1 0.6 1.0
OG A:SER115 3.1 60.1 1.0
CG A:ASP134 3.3 46.1 1.0
O A:ASP132 3.3 44.3 1.0
CG A:ASP132 3.3 47.0 1.0
N A:SER115 3.5 61.6 1.0
PB A:G2P503 3.6 74.1 1.0
CA A:GLY114 3.8 60.8 1.0
OD1 A:ASP134 3.9 46.7 1.0
PG A:G2P503 4.0 63.1 1.0
C A:ASP132 4.0 44.5 1.0
CB A:ASP132 4.1 45.7 1.0
C A:GLY114 4.1 61.7 1.0
OD1 A:ASP132 4.2 47.5 1.0
CB A:SER115 4.2 62.6 1.0
PA A:G2P503 4.3 0.7 1.0
O3B A:G2P503 4.3 85.9 1.0
C5' A:G2P503 4.3 77.2 1.0
N A:ASP134 4.3 43.8 1.0
O A:GLN113 4.3 56.2 1.0
CB A:ASP134 4.4 45.1 1.0
MG A:MG501 4.4 34.1 1.0
CA A:SER115 4.4 62.9 1.0
O1G A:G2P503 4.5 63.2 1.0
O1B A:G2P503 4.5 74.0 1.0
C3A A:G2P503 4.6 59.3 1.0
CA A:ASP132 4.7 44.7 1.0
N A:ILE133 4.8 44.9 1.0
CA A:ILE133 4.8 44.5 1.0
N A:PHE116 4.8 59.5 1.0
O5' A:G2P503 4.8 77.2 1.0
N A:GLY114 4.9 60.3 1.0
C A:ILE133 4.9 44.4 1.0
CA A:ASP134 5.0 43.8 1.0

Magnesium binding site 3 out of 4 in 4txz

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Magnesium binding site 3 out of 4 in the Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Nonhydrolyzable Gtp


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 Nonhydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:60.4
occ:1.00
 OD2 B:ASP194 2.2 37.5 1.0
OD1 B:ASP134 2.4 47.1 1.0
OD1 B:ASP132 2.7 45.9 1.0
OD2 B:ASP132 3.2 46.0 1.0
CG B:ASP132 3.2 45.6 1.0
CG B:ASP194 3.3 36.6 1.0
CG B:ASP134 3.5 47.7 1.0
O2A B:G2P503 3.8 0.5 1.0
OD2 B:ASP134 3.9 48.8 1.0
CB B:ASP194 3.9 36.1 1.0
NH2 B:ARG183 3.9 44.3 1.0
OD1 B:ASP194 4.4 36.6 1.0
NE2 B:HIS192 4.4 38.4 1.0
MG B:MG502 4.5 65.5 1.0
CB B:ASP132 4.6 45.0 1.0
O1A B:G2P503 4.6 0.2 1.0
PA B:G2P503 4.7 0.3 1.0
CB B:ASP134 4.8 47.5 1.0
O5' B:G2P503 5.0 91.9 1.0

Magnesium binding site 4 out of 4 in 4txz

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Magnesium binding site 4 out of 4 in the Crystal Structure of Vibrio Cholerae Dncv Cyclic Amp-Gmp Synthase in Complex with Nonhydrolyzable Gtp


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 Nonhydrolyzable Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:65.5
occ:1.00
 OD2 B:ASP132 2.0 46.0 1.0
O2A B:G2P503 2.2 0.5 1.0
O2B B:G2P503 2.2 67.3 1.0
OD2 B:ASP134 2.3 48.8 1.0
O2G B:G2P503 2.4 91.8 1.0
OG B:SER115 3.2 53.4 1.0
CG B:ASP132 3.3 45.6 1.0
CG B:ASP134 3.4 47.7 1.0
PB B:G2P503 3.5 66.8 1.0
PA B:G2P503 3.6 0.3 1.0
PG B:G2P503 3.6 91.6 1.0
N B:SER115 3.8 53.9 1.0
O B:ASP132 3.9 46.7 1.0
O3B B:G2P503 3.9 80.1 1.0
OD1 B:ASP134 3.9 47.1 1.0
CB B:ASP132 4.0 45.0 1.0
CA B:GLY114 4.0 52.3 1.0
C5' B:G2P503 4.1 91.9 1.0
C3A B:G2P503 4.1 75.9 1.0
OD1 B:ASP132 4.2 45.9 1.0
O3G B:G2P503 4.2 91.5 1.0
O5' B:G2P503 4.3 91.9 1.0
C B:GLY114 4.4 54.5 1.0
MG B:MG501 4.5 60.4 1.0
C B:ASP132 4.5 45.8 1.0
CB B:SER115 4.5 55.3 1.0
O1A B:G2P503 4.6 0.2 1.0
CB B:ASP134 4.7 47.5 1.0
O1B B:G2P503 4.7 66.5 1.0
CA B:SER115 4.8 56.3 1.0
O B:GLN113 4.8 49.5 1.0
O1G B:G2P503 4.8 91.5 1.0
N B:ASP134 4.9 47.0 1.0
CA B:ASP132 4.9 44.7 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: Mon Dec 14 19:35:19 2020

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