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

Go back to Magnesium Binding Sites List in 6zxm
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

Go back to Magnesium Binding Sites List in 6zxm
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

Go back to Magnesium Binding Sites List in 6zxm
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

Go back to Magnesium Binding Sites List in 6zxm
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

Go back to Magnesium Binding Sites List in 6zxm
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

Go back to Magnesium Binding Sites List in 6zxm
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: Sat Apr 3 16:43:50 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy