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Magnesium in PDB 6zxm: Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp

Protein crystallography data

The structure of Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp, PDB code: 6zxm 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 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 122.603, 72.917, 125.729, 90, 118.2, 90
R / Rfree (%) 22.5 / 29.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp (pdb code 6zxm). 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 in Complex with C-Di-Gmp, PDB code: 6zxm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6zxm

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Magnesium binding site 1 out of 6 in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp


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 in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:123.6
occ:1.00
 OD1 A:ASP13 2.1 124.6 1.0
OE2 A:GLU12 2.1 120.2 1.0
OD2 A:ASP56 2.1 120.7 1.0
CG A:ASP13 3.0 127.3 1.0
CG A:ASP56 3.3 117.4 1.0
CD A:GLU12 3.3 113.3 1.0
OD2 A:ASP13 3.3 133.1 1.0
O A:GLU58 3.7 115.8 1.0
OD1 A:ASP56 4.0 113.8 1.0
OE1 A:GLU12 4.0 110.6 1.0
NE2 A:GLN17 4.3 108.8 1.0
N A:ASP13 4.3 115.9 1.0
CB A:ASP56 4.4 117.4 1.0
N A:SER14 4.4 109.6 1.0
OE1 A:GLN17 4.4 103.7 1.0
CB A:ASP13 4.4 124.0 1.0
CG A:GLU12 4.4 111.5 1.0
CD A:GLN17 4.6 105.7 1.0
CB A:SER14 4.6 108.6 1.0
NZ A:LYS108 4.7 112.6 1.0
CA A:ASP13 4.8 118.2 1.0
C A:GLU58 4.9 118.6 1.0
CB A:GLU58 4.9 123.5 1.0

Magnesium binding site 2 out of 6 in 6zxm

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Magnesium binding site 2 out of 6 in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp


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 in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:135.6
occ:1.00
 OD2 B:ASP56 2.1 134.0 1.0
OE2 B:GLU12 2.1 133.6 1.0
OD1 B:ASP13 2.1 133.8 1.0
O F:GLY87 2.9 144.7 1.0
CG B:ASP13 3.1 134.1 1.0
CG B:ASP56 3.2 133.5 1.0
CD B:GLU12 3.3 129.7 1.0
OD2 B:ASP13 3.4 137.0 1.0
O B:GLU58 3.6 151.6 1.0
OD1 B:ASP56 3.9 132.8 1.0
C F:GLY87 4.0 142.4 1.0
OE1 B:GLU12 4.0 124.3 1.0
NE2 B:GLN17 4.3 133.3 1.0
N B:ASP13 4.3 127.9 1.0
CB B:ASP56 4.4 130.8 1.0
N B:SER14 4.4 126.7 1.0
CG B:GLU12 4.4 129.0 1.0
CB B:ASP13 4.4 132.7 1.0
OE1 B:GLN17 4.5 128.0 1.0
CG B:GLU58 4.6 142.8 1.0
NZ B:LYS108 4.6 113.4 1.0
CB B:SER14 4.6 130.2 1.0
CA F:GLY87 4.7 142.6 1.0
CD B:GLN17 4.7 129.9 1.0
C B:GLU58 4.7 154.3 1.0
CA B:ASP13 4.8 129.5 1.0
N F:HIS88 4.9 137.8 1.0
CA F:HIS88 5.0 136.0 1.0

Magnesium binding site 3 out of 6 in 6zxm

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Magnesium binding site 3 out of 6 in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp


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 in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:114.3
occ:1.00
 OD1 C:ASP13 2.1 113.5 1.0
OE2 C:GLU12 2.1 111.5 1.0
OD2 C:ASP56 2.1 115.6 1.0
CG C:ASP13 3.0 116.4 1.0
CG C:ASP56 3.3 112.9 1.0
OD2 C:ASP13 3.3 121.1 1.0
CD C:GLU12 3.3 106.4 1.0
O C:GLU58 3.6 137.1 1.0
OD1 C:ASP56 3.9 111.1 1.0
OE1 C:GLU12 3.9 104.9 1.0
NZ C:LYS108 4.1 113.2 1.0
N C:ASP13 4.3 106.8 1.0
CB C:ASP13 4.4 115.3 1.0
CB C:ASP56 4.4 111.0 1.0
N C:SER14 4.4 106.0 1.0
OE1 C:GLN17 4.4 101.3 1.0
CG C:GLU12 4.5 103.5 1.0
NE2 C:GLN17 4.5 103.9 1.0
CG C:GLU58 4.6 135.0 1.0
CB C:SER14 4.7 103.7 1.0
CD C:GLN17 4.8 101.8 1.0
CA C:ASP13 4.8 110.5 1.0
C C:GLU58 4.8 137.4 1.0

Magnesium binding site 4 out of 6 in 6zxm

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Magnesium binding site 4 out of 6 in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp


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 in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:157.5
occ:1.00
 OD2 D:ASP56 2.1 161.3 1.0
OD1 D:ASP13 2.1 162.1 1.0
OE2 D:GLU12 2.1 156.8 1.0
N D:ASP13 2.6 159.0 1.0
CG D:ASP13 2.8 164.9 1.0
CG D:ASP56 3.0 161.6 1.0
CD D:GLU12 3.2 154.1 1.0
CB D:ASP56 3.3 159.0 1.0
CB D:ASP13 3.4 166.2 1.0
C D:GLU12 3.4 157.3 1.0
CA D:GLU12 3.4 153.3 1.0
CA D:ASP13 3.5 163.7 1.0
OD2 D:ASP13 3.8 166.2 1.0
O D:GLU58 3.8 164.0 1.0
CG D:GLU12 3.9 154.1 1.0
OE1 D:GLU12 4.1 152.8 1.0
OD1 D:ASP56 4.1 162.6 1.0
CB D:GLU12 4.2 153.2 1.0
CD1 D:LEU59 4.2 173.8 1.0
N D:SER14 4.3 162.5 1.0
CD2 D:LEU59 4.3 165.9 1.0
C D:ASP13 4.5 164.4 1.0
N D:GLU12 4.6 149.4 1.0
O D:GLU12 4.7 157.9 1.0
CA D:ASP56 4.8 155.3 1.0
C D:GLU58 4.8 166.3 1.0
CG D:LEU59 4.9 172.2 1.0

Magnesium binding site 5 out of 6 in 6zxm

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Magnesium binding site 5 out of 6 in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp


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 in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:153.7
occ:1.00
 OD2 E:ASP56 2.1 156.8 1.0
OD1 E:ASP13 2.1 153.0 1.0
OE2 E:GLU12 2.1 146.5 1.0
CG E:ASP13 3.0 154.3 1.0
CG E:ASP56 3.2 157.6 1.0
CD E:GLU12 3.3 143.1 1.0
OD2 E:ASP13 3.3 156.0 1.0
O E:GLU58 3.5 170.6 1.0
OD1 E:ASP56 3.9 157.0 1.0
OE1 E:GLU12 3.9 141.1 1.0
NZ E:LYS108 4.2 142.7 1.0
N E:ASP13 4.3 148.7 1.0
CB E:ASP56 4.3 156.2 1.0
CB E:ASP13 4.4 153.8 1.0
CG E:GLU12 4.4 142.4 1.0
N E:SER14 4.5 150.8 1.0
CG E:GLU58 4.6 164.5 1.0
C E:GLU58 4.8 169.7 1.0
CA E:ASP13 4.8 151.2 1.0
CB E:SER14 4.8 151.0 1.0

Magnesium binding site 6 out of 6 in 6zxm

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Magnesium binding site 6 out of 6 in the Diguanylate Cyclase Dgcr in Complex with C-Di-Gmp


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 in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg303

b:148.2
occ:1.00
 OE2 F:GLU12 2.1 144.8 1.0
OD2 F:ASP56 2.1 146.2 1.0
OD1 F:ASP13 2.1 144.3 1.0
CG F:ASP13 3.1 143.1 1.0
CG F:ASP56 3.2 145.0 1.0
CD F:GLU12 3.3 141.6 1.0
OD2 F:ASP13 3.4 145.6 1.0
NE2 F:GLN17 3.5 144.9 1.0
O F:GLU58 3.7 159.6 1.0
OD1 F:ASP56 3.9 145.5 1.0
OE1 F:GLU12 3.9 140.9 1.0
NZ F:LYS108 4.1 130.6 1.0
N F:ASP13 4.3 135.5 1.0
CB F:ASP56 4.4 141.2 1.0
OD1 B:ASN63 4.4 174.2 1.0
N F:SER14 4.4 136.4 1.0
CG F:GLU12 4.4 139.7 1.0
CB F:ASP13 4.5 141.5 1.0
CB B:ASN63 4.5 173.4 1.0
CD F:GLN17 4.6 144.9 1.0
CB F:SER14 4.7 140.2 1.0
CG F:GLU58 4.7 156.8 1.0
CG B:ASN63 4.7 172.3 1.0
CA F:ASP13 4.8 138.1 1.0
C F:GLU58 4.9 158.7 1.0
OE1 F:GLN17 4.9 143.0 1.0

Reference:

R.D.Teixeira, T.Schirmer. Dgcr Structure in Activated State To Be Published.
Page generated: Wed Oct 2 03:15:09 2024

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