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Magnesium in PDB 6zxb: Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State

Protein crystallography data

The structure of Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State, PDB code: 6zxb was solved by R.D.Teixeira, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.676, 39.344, 146.222, 90, 108.77, 90
R / Rfree (%) 22.7 / 25.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State (pdb code 6zxb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State, PDB code: 6zxb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6zxb

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Magnesium binding site 1 out of 6 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:92.2
occ:1.00
 OE2 A:GLU12 2.1 89.4 1.0
OD2 A:ASP56 2.1 90.2 1.0
OD1 A:ASP13 2.1 96.0 1.0
CG A:ASP13 3.2 98.7 1.0
CG A:ASP56 3.2 86.3 1.0
CD A:GLU12 3.2 87.6 1.0
OG A:SER14 3.4 100.2 1.0
O A:GLU58 3.5 104.4 1.0
OD2 A:ASP13 3.7 101.4 1.0
OD1 A:ASP56 3.7 89.2 1.0
OE1 A:GLU12 3.8 84.2 1.0
N A:SER14 4.2 95.3 1.0
N A:ASP13 4.4 92.9 1.0
NZ A:LYS108 4.4 91.1 1.0
CB A:SER14 4.4 96.0 1.0
CG A:GLU12 4.5 84.9 1.0
CB A:ASP56 4.5 83.4 1.0
CB A:ASP13 4.5 98.9 1.0
C A:GLU58 4.7 104.9 1.0
CA A:ASP13 4.8 95.7 1.0
CA A:SER14 5.0 94.3 1.0

Magnesium binding site 2 out of 6 in 6zxb

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Magnesium binding site 2 out of 6 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:41.2
occ:1.00
 O A:HOH406 2.1 30.9 1.0
OE2 A:GLU218 2.1 37.4 1.0
O A:HOH424 2.1 39.3 1.0
OE2 A:GLU217 2.1 35.5 1.0
OD2 A:ASP174 2.1 34.2 1.0
CG A:ASP174 3.1 32.8 1.0
CD A:GLU218 3.2 36.6 1.0
CD A:GLU217 3.3 33.4 1.0
OD1 A:ASP174 3.5 32.9 1.0
CG A:GLU218 3.8 35.6 1.0
MG A:MG304 4.0 32.1 1.0
CG A:GLU217 4.1 32.8 1.0
O2G A:GH3301 4.1 33.5 1.0
OE1 A:GLU217 4.2 32.1 1.0
OE1 A:GLU218 4.2 38.2 1.0
O1A A:GH3301 4.3 41.0 1.0
O A:HOH411 4.4 54.2 1.0
O3A A:GH3301 4.5 36.9 1.0
CB A:ASP174 4.5 32.6 1.0
O A:HOH428 4.7 49.3 1.0
O A:GLU217 5.0 31.7 1.0

Magnesium binding site 3 out of 6 in 6zxb

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Magnesium binding site 3 out of 6 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:32.1
occ:1.00
 O2G A:GH3301 1.9 33.5 1.0
O2B A:GH3301 2.0 35.0 1.0
O A:ILE175 2.1 30.9 1.0
OE1 A:GLU217 2.1 32.1 1.0
OD1 A:ASP174 2.1 32.9 1.0
OE2 A:GLU217 2.6 35.5 1.0
CD A:GLU217 2.6 33.4 1.0
PB A:GH3301 3.0 35.7 1.0
PG A:GH3301 3.1 34.6 1.0
C A:ILE175 3.2 30.1 1.0
CG A:ASP174 3.3 32.8 1.0
O A:HOH406 3.3 30.9 1.0
O3B A:GH3301 3.4 35.6 1.0
O3A A:GH3301 3.4 36.9 1.0
O3G A:GH3301 3.5 34.8 1.0
NZ A:LYS289 3.6 36.6 1.0
N A:ILE175 3.7 29.8 1.0
OD2 A:ASP174 3.8 34.2 1.0
MG A:MG303 4.0 41.2 1.0
CA A:ILE175 4.0 29.4 1.0
CG A:GLU217 4.1 32.8 1.0
C A:ASP174 4.2 30.9 1.0
N A:ASP176 4.2 30.6 1.0
O1G A:GH3301 4.3 35.3 1.0
N A:LYS177 4.4 33.4 1.0
N A:PHE178 4.4 32.1 1.0
O1B A:GH3301 4.4 37.4 1.0
CB A:PHE178 4.4 31.2 1.0
CB A:ASP174 4.5 32.6 1.0
CA A:ASP176 4.5 31.4 1.0
CE A:LYS289 4.5 36.5 1.0
CB A:ILE175 4.6 28.9 1.0
C A:ASP176 4.6 31.8 1.0
O A:ASP174 4.7 31.1 1.0
CA A:ASP174 4.8 31.2 1.0
CB A:GLU217 4.9 32.2 1.0
O A:GLU217 4.9 31.7 1.0
PA A:GH3301 4.9 40.7 1.0

Magnesium binding site 4 out of 6 in 6zxb

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Magnesium binding site 4 out of 6 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:100.4
occ:1.00
 OE2 B:GLU12 2.1 94.8 1.0
OD2 B:ASP56 2.1 103.4 1.0
OD1 B:ASP13 2.1 101.7 1.0
CG B:ASP13 3.2 104.8 1.0
CD B:GLU12 3.2 89.4 1.0
CG B:ASP56 3.2 105.0 1.0
O B:GLU58 3.6 125.9 1.0
OD2 B:ASP13 3.7 107.0 1.0
OD1 B:ASP56 3.7 108.0 1.0
OE1 B:GLU12 3.7 87.9 1.0
N B:SER14 4.2 96.2 1.0
N B:ASP13 4.3 97.9 1.0
NZ B:LYS108 4.4 95.2 1.0
CB B:SER14 4.5 100.1 1.0
CG B:GLU12 4.5 90.0 1.0
CB B:ASP56 4.5 101.0 1.0
CB B:ASP13 4.5 104.7 1.0
OG B:SER14 4.8 104.6 1.0
C B:GLU58 4.8 126.3 1.0
CA B:ASP13 4.8 101.0 1.0
CA B:SER14 5.0 98.2 1.0

Magnesium binding site 5 out of 6 in 6zxb

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Magnesium binding site 5 out of 6 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:52.5
occ:1.00
 OE2 B:GLU217 2.1 49.4 1.0
OE1 B:GLU218 2.1 60.2 1.0
OD2 B:ASP174 2.2 42.2 1.0
CD B:GLU218 2.6 56.4 1.0
O1A B:GH3301 3.0 85.0 1.0
OE2 B:GLU218 3.0 64.8 1.0
CG B:ASP174 3.2 38.5 1.0
CD B:GLU217 3.3 43.7 1.0
CG B:GLU218 3.5 47.9 1.0
OD1 B:ASP174 3.6 40.5 1.0
MG B:MG304 3.9 44.5 1.0
OE1 B:GLU217 4.1 41.7 1.0
PA B:GH3301 4.1 86.1 1.0
O3A B:GH3301 4.3 65.2 1.0
CG B:GLU217 4.4 41.5 1.0
CB B:ASP174 4.5 36.7 1.0
O5' B:GH3301 4.5 77.5 1.0
O2G B:GH3301 4.6 48.6 1.0
CB B:GLU218 5.0 41.8 1.0

Magnesium binding site 6 out of 6 in 6zxb

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Magnesium binding site 6 out of 6 in the Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Diguanylate Cyclase Dgcr (I-Site Mutant) in Native State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:44.5
occ:1.00
 O2G B:GH3301 1.9 48.6 1.0
O2B B:GH3301 1.9 52.5 1.0
OE1 B:GLU217 2.1 41.7 1.0
OD1 B:ASP174 2.1 40.5 1.0
O B:ILE175 2.2 37.9 1.0
CD B:GLU217 2.8 43.7 1.0
PB B:GH3301 2.9 56.8 1.0
OE2 B:GLU217 3.1 49.4 1.0
O3A B:GH3301 3.1 65.2 1.0
PG B:GH3301 3.2 52.1 1.0
CG B:ASP174 3.2 38.5 1.0
O3B B:GH3301 3.4 55.1 1.0
C B:ILE175 3.4 35.2 1.0
OD2 B:ASP174 3.6 42.2 1.0
NZ B:LYS289 3.7 46.4 1.0
N B:ILE175 3.9 33.2 1.0
MG B:MG303 3.9 52.5 1.0
O3G B:GH3301 3.9 53.7 1.0
O5' B:GH3301 4.0 77.5 1.0
PA B:GH3301 4.1 86.1 1.0
CA B:ILE175 4.2 33.8 1.0
CG B:GLU217 4.2 41.5 1.0
O1G B:GH3301 4.3 52.1 1.0
C B:ASP174 4.3 33.7 1.0
O1B B:GH3301 4.3 60.4 1.0
O1A B:GH3301 4.3 85.0 1.0
N B:LYS177 4.4 39.0 1.0
N B:ASP176 4.4 35.8 1.0
CB B:ASP174 4.5 36.7 1.0
N B:PHE178 4.5 39.6 1.0
CE B:LYS289 4.5 46.4 1.0
CB B:PHE178 4.6 39.6 1.0
CA B:ASP176 4.7 36.9 1.0
C B:ASP176 4.7 37.4 1.0
O B:ASP174 4.8 34.3 1.0
CB B:ILE175 4.8 33.3 1.0
CA B:ASP174 4.9 34.1 1.0
O B:GLU217 4.9 35.9 1.0

Reference:

R.D.Teixeira, T.Schirmer. Dgcr Structure in Native State To Be Published.
Page generated: Wed Oct 2 03:14:05 2024

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