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Manganese in PDB 4eeo: Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl

Enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl

All present enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl:
2.4.1.22; 2.4.1.38; 2.4.1.90;

Protein crystallography data

The structure of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl, PDB code: 4eeo was solved by B.Ramakrishnan, P.K.Qasba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.80 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 107.804, 198.217, 143.732, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 25.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl (pdb code 4eeo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl, PDB code: 4eeo:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4eeo

Go back to Manganese Binding Sites List in 4eeo
Manganese binding site 1 out of 3 in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:48.2
occ:1.00
 O3B A:UDP403 2.0 71.0 1.0
OD2 A:ASP250 2.2 38.6 1.0
NE2 A:HIS343 2.2 47.9 1.0
O1A A:UDP403 2.2 63.5 1.0
NE2 A:HIS340 2.5 34.4 1.0
O A:HOH550 2.8 45.7 1.0
CE1 A:HIS343 3.1 50.7 1.0
CG A:ASP250 3.1 37.8 1.0
PB A:UDP403 3.2 77.3 1.0
CD2 A:HIS343 3.3 51.2 1.0
PA A:UDP403 3.3 67.0 1.0
CE1 A:HIS340 3.4 36.6 1.0
O3A A:UDP403 3.4 71.4 1.0
CD2 A:HIS340 3.5 38.1 1.0
OD1 A:ASP250 3.6 39.8 1.0
O2B A:UDP403 3.9 75.3 1.0
O2A A:UDP403 4.1 64.4 1.0
NH2 A:ARG187 4.2 43.5 1.0
ND1 A:HIS343 4.2 52.3 1.0
CB A:ASP250 4.3 37.5 1.0
O3' A:UDP403 4.3 44.9 1.0
CG A:HIS343 4.3 50.4 1.0
O1B A:UDP403 4.4 74.6 1.0
NH1 A:ARG187 4.4 39.7 1.0
ND1 A:HIS340 4.5 41.3 1.0
CG A:HIS340 4.6 38.9 1.0
O5' A:UDP403 4.6 57.6 1.0
C3' A:UDP403 4.8 40.1 1.0
CZ A:ARG187 4.8 43.4 1.0
NZ A:LYS275 4.9 53.2 1.0
C5' A:UDP403 4.9 48.1 1.0
O A:ILE341 5.0 43.2 1.0

Manganese binding site 2 out of 3 in 4eeo

Go back to Manganese Binding Sites List in 4eeo
Manganese binding site 2 out of 3 in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:42.0
occ:1.00
 O1A B:UDP403 2.1 63.1 1.0
NE2 B:HIS343 2.2 37.5 1.0
NE2 B:HIS340 2.2 37.8 1.0
OD2 B:ASP250 2.3 30.1 1.0
O3B B:UDP403 2.3 79.9 1.0
CE1 B:HIS340 3.0 37.7 1.0
CE1 B:HIS343 3.1 39.4 1.0
O B:HOH533 3.1 53.2 1.0
CG B:ASP250 3.2 26.9 1.0
CD2 B:HIS343 3.3 40.9 1.0
PA B:UDP403 3.3 67.6 1.0
PB B:UDP403 3.3 82.5 1.0
CD2 B:HIS340 3.4 34.8 1.0
O3A B:UDP403 3.5 74.3 1.0
OD1 B:ASP250 3.7 25.8 1.0
O2B B:UDP403 3.9 78.8 1.0
O2A B:UDP403 3.9 69.8 1.0
NH2 B:ARG187 4.1 30.8 1.0
ND1 B:HIS340 4.2 34.3 1.0
ND1 B:HIS343 4.2 41.2 1.0
NZ B:LYS275 4.3 42.0 1.0
O3' B:UDP403 4.3 30.1 1.0
CB B:ASP250 4.3 24.9 1.0
CG B:HIS343 4.4 40.8 1.0
CG B:HIS340 4.4 38.1 1.0
NH1 B:ARG187 4.4 29.1 1.0
O1B B:UDP403 4.6 79.8 1.0
O5' B:UDP403 4.7 56.3 1.0
CZ B:ARG187 4.8 34.1 1.0
C3' B:UDP403 4.9 31.3 1.0

Manganese binding site 3 out of 3 in 4eeo

Go back to Manganese Binding Sites List in 4eeo
Manganese binding site 3 out of 3 in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn404

b:60.4
occ:1.00
 O3B C:UDP403 2.1 89.2 1.0
OD2 C:ASP250 2.1 49.7 1.0
NE2 C:HIS343 2.1 56.8 1.0
NE2 C:HIS340 2.4 61.5 1.0
O C:HOH513 2.5 57.6 1.0
O1A C:UDP403 2.6 85.9 1.0
CE1 C:HIS343 3.0 59.6 1.0
CG C:ASP250 3.1 45.9 1.0
PB C:UDP403 3.1 93.1 1.0
CD2 C:HIS343 3.3 60.8 1.0
O3A C:UDP403 3.3 89.7 1.0
CD2 C:HIS340 3.3 60.3 1.0
CE1 C:HIS340 3.4 63.7 1.0
PA C:UDP403 3.5 86.0 1.0
OD1 C:ASP250 3.5 43.8 1.0
O2B C:UDP403 3.7 91.2 1.0
NH2 C:ARG187 4.1 47.9 1.0
ND1 C:HIS343 4.2 58.2 1.0
O3' C:UDP403 4.3 54.3 1.0
CG C:HIS343 4.3 60.6 1.0
NZ C:LYS275 4.4 68.3 1.0
CB C:ASP250 4.4 43.6 1.0
O2A C:UDP403 4.4 88.9 1.0
O1B C:UDP403 4.4 90.1 1.0
CG C:HIS340 4.5 58.9 1.0
ND1 C:HIS340 4.5 62.7 1.0
NH1 C:ARG187 4.7 56.2 1.0
O5' C:UDP403 4.7 78.9 1.0
C3' C:UDP403 4.9 55.2 1.0
CZ C:ARG187 4.9 52.7 1.0
C5' C:UDP403 5.0 66.9 1.0

Reference:

B.Ramakrishnan, E.Boeggeman, P.K.Qasba. Binding of N-Acetylglucosamine (Glcnac) Beta 1-6-Branched Oligosaccharide Acceptors to Beta 4-Galactosyltransferase I Reveals A New Ligand Binding Mode. J.Biol.Chem. V. 287 28666 2012.
ISSN: ISSN 0021-9258
PubMed: 22740701
DOI: 10.1074/JBC.M112.373514
Page generated: Sat Oct 5 19:18:57 2024

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