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Magnesium in PDB 9g85: Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp

Enzymatic activity of Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp

All present enzymatic activity of Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp:
2.7.7.65;

Protein crystallography data

The structure of Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp, PDB code: 9g85 was solved by C.Jaboulay, C.Dugelay, M.Guzzo, L.Terradot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.70 / 2.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 133.001, 133.001, 510.767, 90, 90, 120
R / Rfree (%) 20.1 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp (pdb code 9g85). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp, PDB code: 9g85:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 9g85

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Magnesium binding site 1 out of 8 in the Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:70.2
occ:1.00
 O A:MET55 2.4 87.5 1.0
OD1 A:ASP10 2.5 74.5 1.0
OD2 A:ASP53 2.6 69.3 1.0
OD2 A:ASP10 3.2 74.0 1.0
CG A:ASP10 3.2 79.9 1.0
C A:MET55 3.6 83.3 1.0
CG A:ASP53 3.7 84.4 1.0
OD1 A:ASP9 4.1 86.9 1.0
OD1 A:ASP53 4.1 94.5 1.0
CB A:MET55 4.2 97.9 1.0
CA A:MET55 4.4 83.3 1.0
N A:MET56 4.6 73.1 1.0
CB A:ASP10 4.7 73.5 1.0
CG A:ASP9 4.8 88.6 1.0
CA A:MET56 4.8 76.5 1.0
N A:MET55 4.9 68.6 1.0
OD2 A:ASP9 4.9 85.7 1.0
CB A:ASP53 4.9 75.7 1.0
NZ A:LYS105 4.9 110.5 1.0
N A:ASP10 5.0 82.6 1.0

Magnesium binding site 2 out of 8 in 9g85

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Magnesium binding site 2 out of 8 in the Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:65.4
occ:1.00
 O3B A:G4P502 1.9 95.7 1.0
OD2 A:ASP327 2.0 110.4 1.0
OE1 A:GLU370 2.2 91.9 1.0
O A:ILE328 2.2 65.3 1.0
CD A:GLU370 2.7 77.6 1.0
O2A A:G4P502 2.9 104.4 1.0
OE2 A:GLU370 2.9 74.1 1.0
CG A:ASP327 3.0 91.7 1.0
PB A:G4P502 3.2 104.1 1.0
C A:ILE328 3.4 66.1 1.0
OD1 A:ASP327 3.4 99.1 1.0
O1A A:G4P502 3.4 88.8 1.0
PA A:G4P502 3.5 68.4 1.0
N A:ILE328 3.7 55.2 1.0
O3A A:G4P502 3.7 86.8 1.0
NZ A:LYS442 3.8 82.1 1.0
CG A:GLU370 3.8 63.6 1.0
O2B A:G4P502 3.9 79.7 1.0
CA A:ILE328 4.1 58.6 1.0
C A:ASP327 4.2 65.6 1.0
CB A:ASP327 4.2 69.5 1.0
O1B A:G4P502 4.3 101.6 1.0
N A:ASP329 4.4 71.8 1.0
CA A:ASP327 4.6 73.5 1.0
CB A:ILE328 4.6 55.9 1.0
CA A:ASP329 4.7 64.9 1.0
CE A:LYS442 4.7 89.5 1.0
O A:ASP327 4.8 68.2 1.0
CB A:GLU370 4.8 64.0 1.0
O A:GLU370 4.9 66.5 1.0
CB A:PHE331 4.9 65.1 1.0
N A:PHE330 4.9 70.3 1.0

Magnesium binding site 3 out of 8 in 9g85

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Magnesium binding site 3 out of 8 in the Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:81.5
occ:1.00
 OD2 B:ASP53 2.3 97.5 1.0
OD1 B:ASP10 2.7 88.0 1.0
O B:MET55 2.7 109.1 1.0
CG B:ASP53 3.4 100.8 1.0
CG B:ASP10 3.5 93.1 1.0
OD2 B:ASP10 3.6 92.8 1.0
OD1 B:ASP53 3.8 111.8 1.0
OD1 B:ASP9 3.8 111.3 1.0
C B:MET55 3.9 103.0 1.0
NZ B:LYS105 4.1 105.3 1.0
CB B:MET55 4.3 110.5 1.0
OD2 B:ASP9 4.5 78.9 1.0
CG B:ASP9 4.5 101.4 1.0
CA B:MET55 4.6 101.5 1.0
CB B:ASP53 4.6 86.0 1.0
CD1 B:ILE11 4.8 78.6 1.0
N B:MET55 4.9 91.8 1.0
CB B:ASP10 5.0 86.1 1.0
ND2 B:ASN14 5.0 90.3 1.0
N B:MET56 5.0 94.8 1.0
N B:ASP10 5.0 79.5 1.0

Magnesium binding site 4 out of 8 in 9g85

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Magnesium binding site 4 out of 8 in the Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:81.2
occ:1.00
 O3A B:G4P503 1.9 93.9 1.0
O B:ILE328 2.2 76.5 1.0
OD1 B:ASP327 2.7 91.1 1.0
PB B:G4P503 3.1 105.2 1.0
PA B:G4P503 3.1 68.9 1.0
O2A B:G4P503 3.2 72.7 1.0
NZ B:LYS442 3.2 97.4 1.0
O2B B:G4P503 3.3 128.2 1.0
C B:ILE328 3.3 72.7 1.0
OE1 B:GLU370 3.4 96.9 1.0
O1B B:G4P503 3.6 83.3 1.0
N B:PHE330 3.7 72.3 1.0
CA B:ASP329 3.8 89.6 1.0
CG B:ASP327 3.9 107.8 1.0
CD B:GLU370 3.9 80.2 1.0
O5' B:G4P503 3.9 88.4 1.0
N B:ASP329 4.0 76.2 1.0
C B:ASP329 4.1 79.6 1.0
OE2 B:GLU370 4.1 87.9 1.0
O1A B:G4P503 4.2 100.3 1.0
CE B:LYS442 4.3 103.9 1.0
O3B B:G4P503 4.3 71.7 1.0
N B:PHE331 4.3 72.6 1.0
OD2 B:ASP327 4.5 115.6 1.0
CA B:ILE328 4.5 66.8 1.0
N B:ILE328 4.5 61.8 1.0
NH1 B:ARG446 4.6 93.7 0.8
CA B:PHE330 4.7 93.5 1.0
OD1 B:ASP329 4.9 86.9 1.0
CG B:GLU370 4.9 69.8 1.0
CB B:PHE331 4.9 72.3 1.0
C B:ASP327 4.9 62.0 1.0

Magnesium binding site 5 out of 8 in 9g85

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Magnesium binding site 5 out of 8 in the Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:73.9
occ:1.00
 O C:MET55 2.0 92.5 1.0
OD2 C:ASP53 2.2 102.0 1.0
OD1 C:ASP10 2.8 92.7 1.0
C C:MET55 3.2 101.3 1.0
CG C:ASP53 3.2 102.8 1.0
CB C:MET55 3.6 105.8 1.0
CG C:ASP10 3.6 97.9 1.0
OD2 C:ASP10 3.7 96.5 1.0
OD1 C:ASP53 3.7 98.5 1.0
CA C:MET55 3.8 88.6 1.0
N C:MET55 4.2 91.0 1.0
OD1 C:ASP9 4.2 100.5 1.0
N C:MET56 4.3 102.7 1.0
CB C:ASP53 4.5 85.2 1.0
CA C:MET56 4.7 90.4 1.0
CG C:MET56 4.7 98.9 1.0
NZ C:LYS105 4.8 100.1 1.0
OD2 C:ASP9 4.8 102.1 1.0
CG C:ASP9 4.8 98.4 1.0
CG C:MET55 5.0 124.6 1.0

Magnesium binding site 6 out of 8 in 9g85

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Magnesium binding site 6 out of 8 in the Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg506

b:82.4
occ:1.00
 OD1 C:ASP327 2.0 97.6 1.0
O1A C:G4P505 2.0 102.3 1.0
O C:ILE328 2.1 86.4 1.0
O1B C:G4P505 2.1 105.3 1.0
OE1 C:GLU370 2.8 99.2 1.0
CG C:ASP327 3.1 92.6 1.0
PA C:G4P505 3.2 90.5 1.0
C C:ILE328 3.3 84.6 1.0
CD C:GLU370 3.3 92.0 1.0
PB C:G4P505 3.4 114.6 1.0
O3A C:G4P505 3.5 68.4 1.0
OE2 C:GLU370 3.5 84.0 1.0
OD2 C:ASP327 3.7 98.7 1.0
N C:ILE328 4.0 71.0 1.0
N C:ASP329 4.1 84.8 1.0
CA C:ASP329 4.1 94.2 1.0
O2A C:G4P505 4.2 67.6 1.0
CA C:ILE328 4.2 78.5 1.0
O5' C:G4P505 4.3 102.5 1.0
O2B C:G4P505 4.3 88.9 1.0
CB C:ASP327 4.3 76.2 1.0
O3B C:G4P505 4.3 115.3 1.0
C C:ASP327 4.4 78.5 1.0
N C:PHE330 4.4 96.1 1.0
CG C:GLU370 4.5 88.0 1.0
C C:ASP329 4.6 94.5 1.0
O C:ASP327 4.8 79.5 1.0
OD1 C:ASP329 4.8 95.8 1.0
CA C:ASP327 4.8 81.3 1.0
N C:PHE331 4.9 83.8 1.0
CB C:ILE328 5.0 73.9 1.0

Magnesium binding site 7 out of 8 in 9g85

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Magnesium binding site 7 out of 8 in the Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:92.4
occ:1.00
 OD2 D:ASP53 2.0 93.1 1.0
O D:MET55 2.3 75.2 1.0
OD1 D:ASP10 2.4 78.9 1.0
CG D:ASP53 3.2 89.2 1.0
CG D:ASP10 3.3 74.4 1.0
OD2 D:ASP10 3.5 74.0 1.0
C D:MET55 3.6 75.5 1.0
OD1 D:ASP53 3.7 97.4 1.0
OD1 D:ASP9 3.8 85.0 1.0
NZ D:LYS105 4.3 79.2 1.0
CB D:MET55 4.3 73.2 1.0
CB D:ASP53 4.4 71.5 1.0
CA D:MET55 4.4 82.0 1.0
CG D:ASP9 4.5 79.9 1.0
OD2 D:ASP9 4.5 90.1 1.0
N D:MET56 4.5 75.1 1.0
N D:MET55 4.7 68.5 1.0
CB D:ASP10 4.7 56.1 1.0
N D:ASP10 4.8 60.1 1.0
CA D:MET56 4.8 62.3 1.0
CG D:MET56 4.9 67.2 1.0

Magnesium binding site 8 out of 8 in 9g85

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Magnesium binding site 8 out of 8 in the Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg504

b:82.5
occ:1.00
 O3B D:G4P503 2.0 122.3 1.0
O1A D:G4P503 2.0 98.8 1.0
OD1 D:ASP327 2.0 94.7 1.0
O D:ILE328 2.2 82.7 1.0
OE1 D:GLU370 2.4 96.0 1.0
CD D:GLU370 2.8 90.3 1.0
PB D:G4P503 3.0 116.7 1.0
OE2 D:GLU370 3.0 94.4 1.0
O3A D:G4P503 3.1 106.9 1.0
PA D:G4P503 3.1 97.5 1.0
CG D:ASP327 3.1 93.0 1.0
C D:ILE328 3.4 80.7 1.0
OD2 D:ASP327 3.6 97.7 1.0
O2B D:G4P503 3.6 90.2 1.0
NZ D:LYS442 3.6 88.4 1.0
N D:ILE328 3.9 64.2 1.0
CG D:GLU370 4.0 75.0 1.0
O5' D:G4P503 4.1 82.2 1.0
O2A D:G4P503 4.2 67.9 1.0
CA D:ILE328 4.2 71.2 1.0
O1B D:G4P503 4.3 107.3 1.0
C5' D:G4P503 4.3 73.4 1.0
C D:ASP327 4.4 73.1 1.0
CB D:ASP327 4.4 78.4 1.0
N D:ASP329 4.4 77.4 1.0
CE D:LYS442 4.5 96.5 1.0
CA D:ASP329 4.6 76.5 1.0
CB D:ILE328 4.8 67.2 1.0
N D:PHE330 4.8 80.4 1.0
CA D:ASP327 4.8 74.1 1.0
CB D:PHE331 4.8 63.5 1.0
N D:PHE331 4.9 72.0 1.0
O D:ASP327 4.9 72.9 1.0
C D:ASP329 5.0 81.7 1.0

Reference:

C.Jaboulay, C.Dugelay, M.Guzzo, L.Terradot. Structure of Response Regulator Pled in Complex with C-Digmp and Ppgpp To Be Published.
Page generated: Sat Aug 23 05:40:31 2025

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