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Manganese in PDB 5ndf: Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation

Enzymatic activity of Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation

All present enzymatic activity of Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation:
2.4.1.41;

Protein crystallography data

The structure of Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation, PDB code: 5ndf was solved by R.Hurtado-Guerrero, M.De Las Rivas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 124.08 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.980, 123.111, 248.152, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation (pdb code 5ndf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation, PDB code: 5ndf:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5ndf

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Manganese binding site 1 out of 6 in the Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:33.3
occ:1.00
 O2A A:UDP602 2.0 39.0 1.0
O3B A:UDP602 2.0 30.9 1.0
NE2 A:HIS359 2.2 32.0 1.0
NE2 A:HIS226 2.2 22.9 1.0
OD2 A:ASP224 2.3 26.7 1.0
O A:HOH768 2.5 31.3 1.0
CE1 A:HIS226 3.1 27.6 1.0
PB A:UDP602 3.1 42.0 1.0
CE1 A:HIS359 3.2 34.5 1.0
CD2 A:HIS359 3.2 34.1 1.0
CD2 A:HIS226 3.3 25.0 1.0
PA A:UDP602 3.3 37.2 1.0
CG A:ASP224 3.4 35.5 1.0
O1B A:UDP602 3.4 42.8 1.0
O3A A:UDP602 3.7 38.8 1.0
CB A:ASP224 3.9 32.4 1.0
C5' A:UDP602 4.1 40.7 1.0
O5' A:UDP602 4.1 39.0 1.0
O A:HOH813 4.2 41.2 1.0
ND1 A:HIS359 4.3 32.2 1.0
ND1 A:HIS226 4.3 27.9 1.0
C2 A:EDO605 4.4 53.2 1.0
CG A:HIS359 4.4 30.4 1.0
O A:VAL360 4.4 35.2 1.0
CG A:HIS226 4.4 23.6 1.0
O2B A:UDP602 4.4 39.6 1.0
OD1 A:ASP224 4.5 32.0 1.0
O1A A:UDP602 4.5 43.4 1.0
O A:HOH796 4.6 32.6 1.0
C3' A:UDP602 4.7 39.1 1.0
C4' A:UDP602 4.9 38.4 1.0
NH2 A:ARG362 4.9 51.3 1.0
C1 A:EDO605 5.0 46.9 1.0

Manganese binding site 2 out of 6 in 5ndf

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Manganese binding site 2 out of 6 in the Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:43.0
occ:1.00
 O2A B:UDP602 2.1 44.7 1.0
OD2 B:ASP224 2.2 39.7 1.0
NE2 B:HIS359 2.2 43.8 1.0
O2B B:UDP602 2.2 39.7 1.0
NE2 B:HIS226 2.3 32.7 1.0
CE1 B:HIS359 3.1 44.0 1.0
CD2 B:HIS359 3.2 39.3 1.0
CE1 B:HIS226 3.2 37.6 1.0
PB B:UDP602 3.2 44.8 1.0
CG B:ASP224 3.3 40.6 1.0
PA B:UDP602 3.3 51.2 1.0
CD2 B:HIS226 3.3 34.2 1.0
O3B B:UDP602 3.5 43.8 1.0
O3A B:UDP602 3.6 46.9 1.0
CB B:ASP224 3.8 38.8 1.0
ND1 B:HIS359 4.3 43.4 1.0
C5' B:UDP602 4.3 46.9 1.0
O5' B:UDP602 4.3 47.0 1.0
CG B:HIS359 4.3 42.7 1.0
OD1 B:ASP224 4.4 38.4 1.0
ND1 B:HIS226 4.4 36.5 1.0
O1A B:UDP602 4.5 54.2 1.0
CG B:HIS226 4.5 35.3 1.0
O B:VAL360 4.5 37.7 1.0
O1B B:UDP602 4.5 45.1 1.0
C3' B:UDP602 4.8 49.9 1.0
NH2 B:ARG362 5.0 52.8 1.0
C4' B:UDP602 5.0 48.6 1.0

Manganese binding site 3 out of 6 in 5ndf

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Manganese binding site 3 out of 6 in the Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn601

b:36.5
occ:1.00
 O2A C:UDP602 2.0 46.4 1.0
OD2 C:ASP224 2.1 40.9 1.0
NE2 C:HIS359 2.2 27.7 1.0
NE2 C:HIS226 2.3 44.5 1.0
O1B C:UDP602 2.3 46.7 1.0
O C:HOH744 2.4 39.5 1.0
CE1 C:HIS359 3.1 31.5 1.0
CD2 C:HIS359 3.1 31.7 1.0
CE1 C:HIS226 3.2 42.5 1.0
PB C:UDP602 3.2 45.4 1.0
CG C:ASP224 3.2 38.1 1.0
CD2 C:HIS226 3.3 39.8 1.0
PA C:UDP602 3.3 45.6 1.0
O3A C:UDP602 3.5 49.1 1.0
O3B C:UDP602 3.6 45.4 1.0
CB C:ASP224 3.8 35.9 1.0
ND1 C:HIS359 4.2 33.5 1.0
O5' C:UDP602 4.3 38.5 1.0
C5' C:UDP602 4.3 40.8 1.0
CG C:HIS359 4.3 29.0 1.0
OD1 C:ASP224 4.3 33.5 1.0
ND1 C:HIS226 4.4 37.2 1.0
CG C:HIS226 4.4 38.6 1.0
O1A C:UDP602 4.5 47.3 1.0
O C:VAL360 4.5 37.7 1.0
O C:HOH820 4.5 48.9 1.0
O2B C:UDP602 4.6 43.5 1.0
C3' C:UDP602 4.8 50.0 1.0
C4' C:UDP602 5.0 44.6 1.0

Manganese binding site 4 out of 6 in 5ndf

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Manganese binding site 4 out of 6 in the Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn601

b:36.1
occ:1.00
 O1A D:UDP602 2.0 39.3 1.0
O3B D:UDP602 2.1 39.5 1.0
NE2 D:HIS359 2.2 34.3 1.0
OD2 D:ASP224 2.2 37.3 1.0
NE2 D:HIS226 2.3 28.1 1.0
CE1 D:HIS359 3.1 29.5 1.0
CD2 D:HIS359 3.2 30.7 1.0
CE1 D:HIS226 3.2 28.7 1.0
PB D:UDP602 3.2 40.9 1.0
CD2 D:HIS226 3.3 27.2 1.0
CG D:ASP224 3.3 32.8 1.0
PA D:UDP602 3.3 43.6 1.0
O3A D:UDP602 3.6 46.6 1.0
O1B D:UDP602 3.6 50.4 1.0
CB D:ASP224 3.8 33.5 1.0
C5' D:UDP602 4.2 41.6 1.0
ND1 D:HIS359 4.3 32.6 1.0
CG D:HIS359 4.3 31.7 1.0
O5' D:UDP602 4.3 37.5 1.0
ND1 D:HIS226 4.3 28.4 1.0
OD1 D:ASP224 4.4 40.4 1.0
CG D:HIS226 4.4 27.8 1.0
O D:VAL360 4.4 34.7 1.0
O2A D:UDP602 4.5 45.9 1.0
O2B D:UDP602 4.5 49.5 1.0
C3' D:UDP602 4.7 41.6 1.0
C4' D:UDP602 4.9 41.3 1.0
O D:HOH855 4.9 48.1 1.0
NH2 D:ARG362 5.0 67.2 1.0

Manganese binding site 5 out of 6 in 5ndf

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Manganese binding site 5 out of 6 in the Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn601

b:40.3
occ:1.00
 NE2 E:HIS359 2.1 40.5 1.0
O2A E:UDP602 2.2 51.0 1.0
OD2 E:ASP224 2.2 39.4 1.0
O3B E:UDP602 2.2 52.9 1.0
NE2 E:HIS226 2.3 34.0 1.0
O E:HOH728 2.7 40.8 1.0
CE1 E:HIS359 3.1 47.5 1.0
CD2 E:HIS359 3.1 45.7 1.0
PB E:UDP602 3.2 48.7 1.0
CE1 E:HIS226 3.2 42.1 1.0
CD2 E:HIS226 3.3 35.5 1.0
O1B E:UDP602 3.4 47.8 1.0
CG E:ASP224 3.4 40.8 1.0
PA E:UDP602 3.4 45.7 1.0
O3A E:UDP602 3.6 43.4 1.0
CB E:ASP224 3.9 37.0 1.0
ND1 E:HIS359 4.2 41.8 1.0
CG E:HIS359 4.3 38.9 1.0
O E:HOH802 4.3 51.0 1.0
C5' E:UDP602 4.3 46.9 1.0
O5' E:UDP602 4.3 42.9 1.0
ND1 E:HIS226 4.4 38.9 1.0
O E:VAL360 4.4 41.9 1.0
CG E:HIS226 4.4 33.3 1.0
OD1 E:ASP224 4.4 39.9 1.0
O1A E:UDP602 4.6 46.9 1.0
O2B E:UDP602 4.6 50.2 1.0
O E:HOH756 4.9 44.0 1.0
C3' E:UDP602 4.9 48.4 1.0

Manganese binding site 6 out of 6 in 5ndf

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Manganese binding site 6 out of 6 in the Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Small-Molecule Inhibition of Ppgalnac-Ts Selectively Reduces Mucin- Type O-Glycosylation within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn601

b:50.0
occ:1.00
 O2A F:UDP602 1.9 63.5 1.0
O3B F:UDP602 2.1 57.6 1.0
OD2 F:ASP224 2.1 48.9 1.0
NE2 F:HIS359 2.1 33.6 1.0
NE2 F:HIS226 2.4 40.7 1.0
PB F:UDP602 3.1 63.2 1.0
CE1 F:HIS359 3.1 34.2 1.0
CD2 F:HIS359 3.1 37.8 1.0
PA F:UDP602 3.2 60.3 1.0
CG F:ASP224 3.2 54.0 1.0
CE1 F:HIS226 3.3 40.3 1.0
CD2 F:HIS226 3.4 43.4 1.0
O3A F:UDP602 3.5 53.3 1.0
O1B F:UDP602 3.6 59.7 1.0
CB F:ASP224 3.8 52.8 1.0
O F:HOH773 3.9 40.1 1.0
C5' F:UDP602 4.2 61.4 1.0
O5' F:UDP602 4.2 55.8 1.0
ND1 F:HIS359 4.2 35.5 1.0
OD1 F:ASP224 4.2 61.8 1.0
CG F:HIS359 4.3 33.9 1.0
O1A F:UDP602 4.3 61.6 1.0
O2B F:UDP602 4.4 68.1 1.0
ND1 F:HIS226 4.5 39.0 1.0
CG F:HIS226 4.5 43.4 1.0
O F:VAL360 4.6 49.4 1.0
C3' F:UDP602 4.9 64.3 1.0

Reference:

F.Liu, K.Xu, Z.Xu, M.De Las Rivas, C.Wang, X.Li, J.Lu, Y.Zhou, I.Delso, P.Merino, R.Hurtado-Guerrero, Y.Zhang, F.Wu. The Small Molecule Luteolin Inhibits N-Acetyl-Alpha-Galactosaminyltransferases and Reduces Mucin-Type O-Glycosylation of Amyloid Precursor Protein. J. Biol. Chem. V. 292 21304 2017.
ISSN: ESSN 1083-351X
PubMed: 29061849
DOI: 10.1074/JBC.M117.814202
Page generated: Sun Oct 6 02:01:31 2024

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