Magnesium in PDB 7n8m: Pptt Pap(Coa) 8978B Complex

Enzymatic activity of Pptt Pap(Coa) 8978B Complex

All present enzymatic activity of Pptt Pap(Coa) 8978B Complex:
2.7.8.7;

Protein crystallography data

The structure of Pptt Pap(Coa) 8978B Complex, PDB code: 7n8m was solved by J.W.Mosior, J.C.Sacchettini, Tb Structural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.79 / 1.57
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.759, 63.709, 79.669, 90, 123.33, 90
R / Rfree (%) 17.2 / 20.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pptt Pap(Coa) 8978B Complex (pdb code 7n8m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Pptt Pap(Coa) 8978B Complex, PDB code: 7n8m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7n8m

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Magnesium binding site 1 out of 7 in the Pptt Pap(Coa) 8978B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pptt Pap(Coa) 8978B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:20.9
occ:0.86
 O2A A:COA301 2.0 24.4 1.0
O A:HOH516 2.1 25.6 1.0
O A:HOH451 2.1 27.1 1.0
ND1 A:HIS93 2.1 24.2 1.0
O A:HOH506 2.2 27.6 1.0
O A:HIS93 2.3 25.6 1.0
CE1 A:HIS93 2.9 23.7 1.0
C A:HIS93 3.3 22.1 1.0
CG A:HIS93 3.3 21.7 1.0
P1A A:COA301 3.4 23.3 1.0
CB A:HIS93 3.8 24.6 1.0
N A:HIS93 3.8 20.0 1.0
CA A:HIS93 3.8 20.3 1.0
O1A A:COA301 3.9 25.0 1.0
NE2 A:HIS93 4.1 25.8 1.0
O A:HOH406 4.1 43.3 1.0
O A:HOH617 4.2 40.7 1.0
OE2 A:GLU51 4.2 30.1 1.0
O A:HOH530 4.3 43.9 1.0
O A:HOH404 4.3 29.4 1.0
O A:HOH460 4.3 23.6 1.0
O A:HOH591 4.3 43.4 1.0
CD2 A:HIS93 4.3 26.0 1.0
O5B A:COA301 4.3 24.4 1.0
O3A A:COA301 4.4 22.3 1.0
C5B A:COA301 4.4 30.2 1.0
N A:CYS94 4.4 22.0 1.0
O A:HOH412 4.5 21.2 1.0
OE1 A:GLU51 4.5 28.1 1.0
CD A:GLU51 4.6 29.4 1.0
CA A:CYS94 4.7 22.6 1.0

Magnesium binding site 2 out of 7 in 7n8m

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Magnesium binding site 2 out of 7 in the Pptt Pap(Coa) 8978B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pptt Pap(Coa) 8978B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:18.7
occ:0.92
 OD1 A:ASP114 2.0 19.8 1.0
O A:HOH419 2.0 21.0 1.0
O3A A:COA301 2.0 22.3 1.0
O A:HOH412 2.1 21.2 1.0
O A:HOH479 2.1 20.3 1.0
O A:HOH460 2.2 23.6 1.0
CG A:ASP114 3.0 18.1 1.0
P1A A:COA301 3.1 23.3 1.0
O1A A:COA301 3.3 25.0 1.0
OD2 A:ASP114 3.4 18.8 1.0
OG1 A:THR92 3.9 18.6 1.0
OE2 A:GLU116 3.9 23.9 1.0
O2A A:COA301 4.0 24.4 1.0
NZ A:LYS161 4.1 20.2 1.0
O A:ALA115 4.2 20.6 1.0
O A:HOH541 4.2 36.4 1.0
O A:HOH563 4.3 55.3 1.0
CB A:ASP114 4.3 16.2 1.0
O5B A:COA301 4.4 24.4 1.0
CG A:GLU157 4.4 16.6 1.0
O A:HOH506 4.4 27.6 1.0
CB A:GLU157 4.5 16.9 1.0
OE1 A:GLU157 4.5 19.7 1.0
O A:HOH530 4.6 43.9 1.0
CE A:LYS161 4.6 18.4 1.0
N A:ALA115 4.8 17.8 1.0
CA A:ASP114 4.8 16.3 1.0
CD A:GLU116 4.9 23.9 1.0
CG A:GLU116 4.9 22.0 1.0
CD A:GLU157 5.0 17.1 1.0

Magnesium binding site 3 out of 7 in 7n8m

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Magnesium binding site 3 out of 7 in the Pptt Pap(Coa) 8978B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pptt Pap(Coa) 8978B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:27.7
occ:1.00
 O A:HOH429 2.0 27.8 1.0
O A:HOH477 2.1 28.9 1.0
O A:HOH475 2.1 27.5 1.0
O A:HOH442 4.1 34.3 1.0
O A:HOH600 4.1 46.0 1.0
OD1 A:ASP119 4.2 29.8 1.0
O A:HOH481 4.2 32.7 1.0
O A:GLY219 4.3 23.1 1.0
OD2 A:ASP119 4.3 26.0 1.0
O A:HOH464 4.4 25.1 1.0
O A:HOH606 4.6 46.5 1.0
CB A:PRO117 4.6 23.1 1.0
CG A:ASP119 4.7 27.0 1.0
O A:HOH589 4.8 40.2 1.0

Magnesium binding site 4 out of 7 in 7n8m

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Magnesium binding site 4 out of 7 in the Pptt Pap(Coa) 8978B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pptt Pap(Coa) 8978B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:19.1
occ:1.00
 OD1 B:ASP114 2.0 18.6 1.0
O1A B:COA301 2.0 19.9 1.0
O B:HOH421 2.1 19.0 1.0
O B:HOH476 2.1 18.2 1.0
O B:HOH483 2.2 21.2 1.0
O B:HOH425 2.2 18.7 1.0
CG B:ASP114 3.0 17.8 1.0
P1A B:COA301 3.1 22.3 1.0
O2A B:COA301 3.3 28.4 1.0
OD2 B:ASP114 3.4 18.3 1.0
OG1 B:THR92 3.9 16.8 1.0
O3A B:COA301 3.9 24.4 1.0
OE2 B:GLU116 4.0 23.2 1.0
NZ B:LYS161 4.0 16.5 1.0
O B:HOH553 4.0 33.4 1.0
O B:ALA115 4.2 18.7 1.0
CB B:ASP114 4.3 17.7 1.0
CG B:GLU157 4.4 17.3 1.0
O5B B:COA301 4.4 23.2 1.0
O B:HOH534 4.4 24.6 1.0
CB B:GLU157 4.4 16.9 1.0
OE1 B:GLU157 4.5 19.6 1.0
O B:HOH403 4.5 57.2 1.0
CE B:LYS161 4.6 17.7 1.0
O B:HOH571 4.7 37.9 1.0
O B:HOH594 4.7 59.5 1.0
N B:ALA115 4.8 17.0 1.0
CA B:ASP114 4.8 14.7 1.0
CD B:GLU116 4.9 23.9 1.0
CD B:GLU157 5.0 17.9 1.0
CG B:GLU116 5.0 21.1 1.0
O B:HIS93 5.0 25.5 1.0

Magnesium binding site 5 out of 7 in 7n8m

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Magnesium binding site 5 out of 7 in the Pptt Pap(Coa) 8978B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pptt Pap(Coa) 8978B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:20.6
occ:0.83
 O3A B:COA301 2.0 24.4 1.0
O B:HOH449 2.1 26.4 1.0
O B:HOH542 2.1 26.9 1.0
ND1 B:HIS93 2.1 22.6 1.0
O B:HOH534 2.2 24.6 1.0
O B:HIS93 2.2 25.5 1.0
CE1 B:HIS93 2.9 21.3 1.0
C B:HIS93 3.2 21.3 1.0
CG B:HIS93 3.3 20.9 1.0
P1A B:COA301 3.3 22.3 1.0
N B:HIS93 3.7 16.8 1.0
CA B:HIS93 3.7 18.1 1.0
CB B:HIS93 3.8 20.9 1.0
O2A B:COA301 3.9 28.4 1.0
O B:HOH635 4.1 41.7 1.0
NE2 B:HIS93 4.1 26.4 1.0
OE2 B:GLU51 4.2 27.6 1.0
O B:HOH414 4.2 40.2 1.0
O B:HOH571 4.3 37.9 1.0
O B:HOH483 4.3 21.2 1.0
CD2 B:HIS93 4.3 23.3 1.0
N B:CYS94 4.3 19.5 1.0
O5B B:COA301 4.3 23.2 1.0
O1A B:COA301 4.3 19.9 1.0
O B:HOH425 4.4 18.7 1.0
O B:HOH413 4.4 31.9 1.0
C5B B:COA301 4.4 24.6 1.0
OE1 B:GLU51 4.5 29.3 1.0
CD B:GLU51 4.6 29.1 1.0
O B:HOH603 4.7 46.3 1.0
CA B:CYS94 4.7 18.1 1.0
C B:THR92 5.0 18.9 1.0
O B:HOH626 5.0 62.1 1.0

Magnesium binding site 6 out of 7 in 7n8m

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Magnesium binding site 6 out of 7 in the Pptt Pap(Coa) 8978B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pptt Pap(Coa) 8978B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:20.6
occ:0.81
 O B:HOH493 2.0 22.6 1.0
O B:HOH453 2.1 24.2 1.0
O B:HOH443 2.1 24.6 1.0
O B:HOH613 3.9 44.3 1.0
O B:HOH622 4.1 39.2 1.0
O B:HOH531 4.1 35.1 1.0
O B:HOH536 4.1 29.6 1.0
OD1 B:ASP119 4.1 23.8 1.0
O B:HOH437 4.2 28.9 1.0
O B:GLY219 4.2 20.5 1.0
OD2 B:ASP119 4.3 23.4 1.0
O B:HOH490 4.6 21.3 1.0
CG B:ASP119 4.6 21.4 1.0
CB B:PRO117 4.7 22.6 1.0
O B:HOH619 4.9 36.6 1.0
CA B:GLY219 5.0 21.9 1.0

Magnesium binding site 7 out of 7 in 7n8m

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Magnesium binding site 7 out of 7 in the Pptt Pap(Coa) 8978B Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pptt Pap(Coa) 8978B Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:22.2
occ:0.49
 O B:HOH521 2.0 36.1 1.0
O B:HOH621 2.2 28.7 0.4
O B:HOH498 2.3 27.3 1.0
O B:HOH578 3.7 31.0 1.0
CG2 B:ILE197 4.3 23.0 1.0
O B:HOH406 4.4 40.5 1.0
O B:HOH491 4.5 32.2 1.0
OD1 B:ASP175 4.6 21.6 1.0
O B:LEU196 4.6 21.4 1.0

Reference:

S.Ottavi, S.M.Scarry, J.Mosior, Y.Ling, J.Roberts, A.Singh, D.Zhang, L.Goullieux, C.Roubert, E.Bacque, H.R.Lagiakos, J.Vendome, F.Moraca, K.Li, A.J.Perkowski, R.Ramesh, M.M.Bowler, W.Tracy, V.A.Feher, J.C.Sacchettini, B.S.Gold, C.F.Nathan, J.Aube. In Vitro and in Vivo Inhibition of the Mycobacterium Tuberculosis Phosphopantetheinyl Transferase Pptt By Amidinoureas. J.Med.Chem. V. 65 1996 2022.
ISSN: ISSN 0022-2623
PubMed: 35044775
DOI: 10.1021/ACS.JMEDCHEM.1C01565
Page generated: Thu Apr 6 17:40:11 2023

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