Atomistry » Magnesium » PDB 6zup-7a1x » 6zxm
Atomistry »
  Magnesium »
    PDB 6zup-7a1x »
      6zxm »

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: Wed Oct 2 03:15:09 2024

Last articles

Cl in 3NVS
Cl in 3NW8
Cl in 3NVR
Cl in 3NVU
Cl in 3NU5
Cl in 3NUQ
Cl in 3NUX
Cl in 3NV8
Cl in 3NUE
Cl in 3NTG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy