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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

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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

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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

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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

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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

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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

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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

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