Atomistry » Magnesium » PDB 6gog-6gtp » 6gs8
Atomistry »
  Magnesium »
    PDB 6gog-6gtp »
      6gs8 »

Magnesium in PDB 6gs8: Crystal Structure of Smba in Complex with C-Di-Gmp

Protein crystallography data

The structure of Crystal Structure of Smba in Complex with C-Di-Gmp, PDB code: 6gs8 was solved by B.N.Dubey, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 127.910, 87.420, 130.270, 90.00, 119.48, 90.00
R / Rfree (%) 20.9 / 26

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Smba in Complex with C-Di-Gmp (pdb code 6gs8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Smba in Complex with C-Di-Gmp, PDB code: 6gs8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6gs8

Go back to Magnesium Binding Sites List in 6gs8
Magnesium binding site 1 out of 6 in the Crystal Structure of Smba 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 Crystal Structure of Smba in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:39.6
occ:1.00
 O A:ASN153 2.3 56.3 1.0
O A:LEU151 2.3 50.4 1.0
O A:VAL156 2.6 51.0 1.0
O A:HOH501 3.4 52.4 1.0
C A:ASN153 3.5 55.2 1.0
C A:LEU151 3.6 52.5 1.0
C A:VAL156 3.8 50.1 1.0
C A:ALA152 4.0 52.3 1.0
O A:ALA152 4.0 53.4 1.0
CE1 A:PHE183 4.0 54.8 1.0
CZ A:PHE183 4.1 56.0 1.0
CA A:ASP154 4.2 57.5 1.0
N A:ASN153 4.3 50.8 1.0
N A:VAL156 4.3 54.5 1.0
CA A:ALA152 4.3 53.6 1.0
N A:ASP154 4.3 56.6 1.0
O A:ASP154 4.3 50.8 1.0
CA A:VAL156 4.4 50.5 1.0
CB A:VAL156 4.4 49.6 1.0
N A:ALA152 4.4 52.4 1.0
C A:ASP154 4.4 53.4 1.0
CA A:ASN153 4.5 52.8 1.0
CA A:LEU151 4.7 52.5 1.0
N A:THR157 4.9 52.3 1.0
CG1 A:VAL156 4.9 47.7 1.0
OD1 A:ASP154 5.0 58.8 1.0

Magnesium binding site 2 out of 6 in 6gs8

Go back to Magnesium Binding Sites List in 6gs8
Magnesium binding site 2 out of 6 in the Crystal Structure of Smba 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 Crystal Structure of Smba in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:62.6
occ:1.00
 O B:ASN153 2.1 68.9 1.0
O B:LEU151 2.2 68.8 1.0
O B:HOH602 2.6 60.0 1.0
O B:VAL156 2.7 66.8 1.0
C B:ASN153 3.3 75.5 1.0
C B:LEU151 3.4 68.6 1.0
C B:ALA152 3.7 78.0 1.0
O B:ALA152 3.8 82.2 1.0
C B:VAL156 3.8 65.2 1.0
N B:ASN153 4.0 76.9 1.0
CE1 B:PHE183 4.1 67.9 1.0
N B:ASP154 4.1 79.6 1.0
CA B:ALA152 4.1 77.8 1.0
N B:ALA152 4.2 75.9 1.0
CA B:ASP154 4.2 81.1 1.0
N B:VAL156 4.2 65.7 1.0
CZ B:PHE183 4.2 69.4 1.0
CB B:VAL156 4.2 66.9 1.0
CA B:VAL156 4.3 64.9 1.0
CA B:ASN153 4.3 76.0 1.0
O B:ASP154 4.3 75.2 1.0
C B:ASP154 4.4 77.2 1.0
CA B:LEU151 4.6 65.4 1.0
CG1 B:VAL156 4.9 67.9 1.0
N B:THR157 5.0 62.0 1.0

Magnesium binding site 3 out of 6 in 6gs8

Go back to Magnesium Binding Sites List in 6gs8
Magnesium binding site 3 out of 6 in the Crystal Structure of Smba 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 Crystal Structure of Smba in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:52.3
occ:1.00
 O C:ASN153 2.1 64.3 1.0
O C:LEU151 2.2 59.5 1.0
O C:VAL156 2.8 69.8 1.0
C C:ASN153 3.3 68.3 1.0
O C:HOH615 3.4 58.4 1.0
C C:LEU151 3.4 62.1 1.0
C C:ALA152 3.6 69.3 1.0
O C:ALA152 3.7 69.3 1.0
C C:VAL156 3.9 61.6 1.0
N C:ASN153 4.0 64.7 1.0
CA C:ALA152 4.0 71.6 1.0
CE1 C:PHE183 4.1 58.7 1.0
N C:ALA152 4.1 66.3 1.0
N C:ASP154 4.1 71.7 1.0
CZ C:PHE183 4.2 61.3 1.0
CA C:ASP154 4.2 73.3 1.0
CA C:ASN153 4.3 65.7 1.0
N C:VAL156 4.3 60.8 1.0
CB C:VAL156 4.3 56.0 1.0
CA C:VAL156 4.4 58.5 1.0
C C:ASP154 4.4 67.7 1.0
O C:ASP154 4.4 69.2 1.0
CA C:LEU151 4.6 63.3 1.0
CG1 C:VAL156 4.9 53.7 1.0

Magnesium binding site 4 out of 6 in 6gs8

Go back to Magnesium Binding Sites List in 6gs8
Magnesium binding site 4 out of 6 in the Crystal Structure of Smba 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 Crystal Structure of Smba in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:66.3
occ:1.00
 O D:HOH606 1.6 79.3 1.0
O D:ASN153 2.1 72.6 1.0
O D:LEU151 2.2 73.4 1.0
O D:VAL156 2.7 57.0 1.0
C D:ASN153 3.3 70.6 1.0
C D:LEU151 3.4 68.2 1.0
C D:ALA152 3.7 64.7 1.0
O D:ALA152 3.8 65.0 1.0
C D:VAL156 3.8 58.2 1.0
N D:ASN153 4.0 66.0 1.0
CE1 D:PHE183 4.1 56.2 1.0
CA D:ALA152 4.1 67.9 1.0
N D:ASP154 4.1 72.6 1.0
CZ D:PHE183 4.2 56.4 1.0
N D:ALA152 4.2 68.3 1.0
CA D:ASP154 4.2 74.4 1.0
N D:VAL156 4.2 61.0 1.0
CB D:VAL156 4.3 63.5 1.0
CA D:ASN153 4.3 70.5 1.0
CA D:VAL156 4.3 60.4 1.0
O D:ASP154 4.4 70.2 1.0
C D:ASP154 4.4 69.8 1.0
CA D:LEU151 4.6 67.9 1.0
CG1 D:VAL156 4.9 63.6 1.0

Magnesium binding site 5 out of 6 in 6gs8

Go back to Magnesium Binding Sites List in 6gs8
Magnesium binding site 5 out of 6 in the Crystal Structure of Smba 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 Crystal Structure of Smba in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg503

b:46.0
occ:1.00
 O E:LEU151 2.2 58.5 1.0
O E:ASN153 2.2 49.4 1.0
O E:VAL156 2.7 52.8 1.0
C E:ASN153 3.4 52.4 1.0
C E:LEU151 3.4 55.9 1.0
O E:HOH601 3.5 45.6 1.0
C E:ALA152 3.7 57.8 1.0
O E:ALA152 3.7 60.7 1.0
C E:VAL156 3.8 49.6 1.0
CE1 E:PHE183 3.9 59.2 1.0
CZ E:PHE183 4.0 58.2 1.0
N E:ASN153 4.0 55.4 1.0
CA E:ALA152 4.1 58.2 1.0
N E:ALA152 4.2 57.8 1.0
N E:ASP154 4.2 53.7 1.0
CA E:ASP154 4.3 56.4 1.0
CB E:VAL156 4.3 51.6 1.0
N E:VAL156 4.3 50.0 1.0
CA E:VAL156 4.3 50.9 1.0
CA E:ASN153 4.3 53.6 1.0
O E:ASP154 4.4 55.7 1.0
C E:ASP154 4.4 55.1 1.0
CA E:LEU151 4.6 53.4 1.0
CG1 E:VAL156 4.8 50.4 1.0
N E:THR157 5.0 49.6 1.0

Magnesium binding site 6 out of 6 in 6gs8

Go back to Magnesium Binding Sites List in 6gs8
Magnesium binding site 6 out of 6 in the Crystal Structure of Smba 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 Crystal Structure of Smba in Complex with C-Di-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg503

b:83.3
occ:1.00
 O F:HOH601 2.1 49.0 1.0
O F:ASN153 2.1 90.7 1.0
O F:VAL156 2.2 82.9 1.0
O F:LEU151 2.2 98.6 1.0
C F:VAL156 3.3 75.8 1.0
C F:ASN153 3.3 93.0 1.0
C F:LEU151 3.4 96.3 1.0
CB F:VAL156 3.7 79.0 1.0
CA F:VAL156 3.8 77.0 1.0
N F:VAL156 3.8 78.2 1.0
CE1 F:PHE183 3.9 78.9 1.0
C F:ALA152 4.0 99.8 1.0
O F:ALA152 4.1 99.9 1.0
N F:ASN153 4.1 96.3 1.0
CZ F:PHE183 4.1 78.7 1.0
N F:ASP154 4.2 98.0 1.0
O F:ASP154 4.3 85.1 1.0
N F:ALA152 4.3 0.2 1.0
C F:ASP154 4.3 88.7 1.0
CA F:ASP154 4.3 97.6 1.0
CA F:ASN153 4.3 93.0 1.0
CG1 F:VAL156 4.3 82.0 1.0
CA F:ALA152 4.4 0.8 1.0
CA F:LEU151 4.4 94.9 1.0
N F:THR157 4.4 73.1 1.0
C F:LEU155 4.8 80.4 1.0
O F:LEU150 4.8 0.7 1.0
N F:LEU155 4.9 81.5 1.0
CD1 F:PHE183 4.9 76.0 1.0
CA F:THR157 5.0 75.4 1.0
CG2 F:VAL156 5.0 78.1 1.0

Reference:

V.Shyp, B.N.Dubey, R.Bohm, J.Nesper, S.Hiller, U.Jenal, T.Schirmer. Reciprocal Regulation of Bacterial Growth and Development By Competitive Binding of Two Second Messengers to A (Central) Metabolic Switch To Be Published.
Page generated: Tue Oct 1 01:24:14 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy