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Manganese in PDB 6rcx: Mycobacterial 4'-Phosphopantetheinyl Transferase Pptab in Complex with the Acp Domain of Ppsc.

Enzymatic activity of Mycobacterial 4'-Phosphopantetheinyl Transferase Pptab in Complex with the Acp Domain of Ppsc.

All present enzymatic activity of Mycobacterial 4'-Phosphopantetheinyl Transferase Pptab in Complex with the Acp Domain of Ppsc.:
2.3.1.41;

Protein crystallography data

The structure of Mycobacterial 4'-Phosphopantetheinyl Transferase Pptab in Complex with the Acp Domain of Ppsc., PDB code: 6rcx was solved by M.C.Nguyen, L.Mourey, J.D.Pedelacq, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.15 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.142, 63.167, 108.459, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.4

Other elements in 6rcx:

The structure of Mycobacterial 4'-Phosphopantetheinyl Transferase Pptab in Complex with the Acp Domain of Ppsc. also contains other interesting chemical elements:

Arsenic (As) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Mycobacterial 4'-Phosphopantetheinyl Transferase Pptab in Complex with the Acp Domain of Ppsc. (pdb code 6rcx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Mycobacterial 4'-Phosphopantetheinyl Transferase Pptab in Complex with the Acp Domain of Ppsc., PDB code: 6rcx:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 6rcx

Go back to Manganese Binding Sites List in 6rcx
Manganese binding site 1 out of 3 in the Mycobacterial 4'-Phosphopantetheinyl Transferase Pptab in Complex with the Acp Domain of Ppsc.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Mycobacterial 4'-Phosphopantetheinyl Transferase Pptab in Complex with the Acp Domain of Ppsc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:31.9
occ:0.46
 O A:HOH403 2.0 38.0 1.0
OD2 A:ASP111 2.1 46.0 1.0
OE1 A:GLU153 2.2 67.1 1.0
O A:HOH428 2.2 35.0 1.0
OE2 A:GLU113 2.3 37.0 1.0
CG A:ASP111 2.8 41.6 1.0
OD1 A:ASP111 2.8 43.3 1.0
CD A:GLU153 3.1 63.6 1.0
CD A:GLU113 3.2 37.7 1.0
OE2 A:GLU153 3.4 69.8 1.0
CG A:GLU113 3.4 36.0 1.0
O A:ALA112 3.8 35.6 1.0
O A:HOH455 3.8 31.6 1.0
O3A A:COA301 3.9 36.2 1.0
CE2 A:PHE149 4.0 38.9 1.0
O2A A:COA301 4.0 26.2 1.0
CB A:ASP111 4.3 29.6 1.0
OE1 A:GLU113 4.3 37.3 1.0
CG A:GLU153 4.4 53.9 1.0
O A:HOH423 4.5 41.9 1.0
CZ A:PHE149 4.5 37.8 1.0
C A:ALA112 4.6 29.7 1.0
CB A:GLU153 4.6 44.6 1.0
P1A A:COA301 4.7 30.2 1.0
O5A A:COA301 4.7 64.6 1.0
CD2 A:PHE149 4.7 34.3 1.0
O A:HOH454 4.8 47.0 1.0
N A:ALA112 4.8 25.8 1.0
CB A:GLU113 4.8 34.5 1.0
P2A A:COA301 5.0 56.7 1.0
O A:HOH461 5.0 25.0 1.0

Manganese binding site 2 out of 3 in 6rcx

Go back to Manganese Binding Sites List in 6rcx
Manganese binding site 2 out of 3 in the Mycobacterial 4'-Phosphopantetheinyl Transferase Pptab in Complex with the Acp Domain of Ppsc.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Mycobacterial 4'-Phosphopantetheinyl Transferase Pptab in Complex with the Acp Domain of Ppsc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:24.2
occ:0.73
 O A:HOH434 1.8 31.1 1.0
O1A A:COA301 2.0 27.9 1.0
O A:HOH461 2.1 25.0 1.0
ND1 A:HIS90 2.1 29.1 1.0
O A:HOH401 2.1 25.3 1.0
O A:HIS90 2.1 32.7 1.0
CE1 A:HIS90 2.8 31.0 1.0
C A:HIS90 3.1 31.9 1.0
CG A:HIS90 3.3 27.2 1.0
P1A A:COA301 3.5 30.2 1.0
O4A A:COA301 3.5 58.9 1.0
N A:HIS90 3.7 25.1 1.0
CA A:HIS90 3.7 26.5 1.0
CB A:HIS90 3.9 26.9 1.0
NE2 A:HIS90 4.0 30.7 1.0
O3A A:COA301 4.0 36.2 1.0
O A:HOH405 4.1 48.4 1.0
OE1 A:GLU48 4.2 39.8 1.0
P2A A:COA301 4.2 56.7 1.0
O B:HOH2306 4.2 49.7 1.0
N A:THR91 4.2 32.1 1.0
CD2 A:HIS90 4.3 30.7 1.0
O2A A:COA301 4.3 26.2 1.0
O A:HOH423 4.3 41.9 1.0
OE2 A:GLU48 4.4 41.6 1.0
O5A A:COA301 4.4 64.6 1.0
CD A:GLU48 4.5 39.1 1.0
C5B A:COA301 4.5 25.7 1.0
O5B A:COA301 4.5 29.6 1.0
O A:HOH428 4.5 35.0 1.0
CA A:THR91 4.6 29.8 1.0
CB B:ASP2104 4.7 40.3 1.0
C A:THR89 5.0 27.8 1.0

Manganese binding site 3 out of 3 in 6rcx

Go back to Manganese Binding Sites List in 6rcx
Manganese binding site 3 out of 3 in the Mycobacterial 4'-Phosphopantetheinyl Transferase Pptab in Complex with the Acp Domain of Ppsc.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Mycobacterial 4'-Phosphopantetheinyl Transferase Pptab in Complex with the Acp Domain of Ppsc. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn304

b:0.9
occ:1.00
 OE1 A:GLU170 3.2 87.5 1.0
CZ2 A:TRP166 3.5 55.6 1.0
CA A:GLY168 3.8 37.2 1.0
N A:PHE169 3.8 35.6 1.0
OE2 A:GLU170 3.9 92.5 1.0
CB B:VAL2125 3.9 0.8 1.0
CD A:GLU170 4.0 87.4 1.0
N B:ALA2126 4.0 99.2 1.0
CD2 A:PHE169 4.2 45.3 1.0
C B:VAL2125 4.3 97.7 1.0
CE2 A:TRP166 4.3 54.1 1.0
C A:GLY168 4.4 34.5 1.0
NE1 A:TRP166 4.4 55.1 1.0
CH2 A:TRP166 4.4 58.2 1.0
CA B:VAL2125 4.5 97.5 1.0
CG2 B:VAL2125 4.5 0.1 1.0
N B:VAL2125 4.6 94.6 1.0
CB B:ALA2126 4.7 99.9 1.0
CA B:ALA2126 4.8 97.3 1.0
CG1 B:VAL2125 4.8 0.1 1.0
CB A:PHE169 4.9 40.1 1.0
CA A:PHE169 4.9 39.8 1.0
CE2 A:PHE169 4.9 43.6 1.0
O B:VAL2125 4.9 96.5 1.0
CG A:PHE169 5.0 42.0 1.0

Reference:

M.C.Nguyen, O.Saurel, C.Carivenc, S.Gavalda, S.Saitta, M.P.Tran, A.Milon, C.Chalut, C.Guilhot, L.Mourey, J.D.Pedelacq. Conformational Flexibility of Coenzyme A and Its Impact on the Post-Translational Modification of Acyl Carrier Proteins By 4'-Phosphopantetheinyl Transferases. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32128972
DOI: 10.1111/FEBS.15273
Page generated: Tue Dec 15 05:00:26 2020

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