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

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

All present enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Gal-BETA1,4-Glc-Beta:
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-Gal-BETA1,4-Glc-Beta, PDB code: 4eea 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) 40.50 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 107.322, 196.204, 143.594, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24

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-Gal-BETA1,4-Glc-Beta (pdb code 4eea). 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-Gal-BETA1,4-Glc-Beta, PDB code: 4eea:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4eea

Go back to Manganese Binding Sites List in 4eea
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-Gal-BETA1,4-Glc-Beta


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-Gal-BETA1,4-Glc-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:53.1
occ:1.00
 O2B A:UDP404 1.8 89.0 1.0
OD2 A:ASP250 2.2 34.4 1.0
NE2 A:HIS343 2.3 41.3 1.0
O3B A:UDP404 2.4 89.6 1.0
PB A:UDP404 2.4 93.7 1.0
NE2 A:HIS340 2.4 37.5 1.0
O1A A:UDP404 2.4 71.3 1.0
CG A:ASP250 3.1 31.8 1.0
CD2 A:HIS343 3.2 42.4 1.0
O3A A:UDP404 3.3 83.7 1.0
CE1 A:HIS343 3.3 46.0 1.0
CE1 A:HIS340 3.4 38.3 1.0
CD2 A:HIS340 3.4 37.2 1.0
PA A:UDP404 3.4 76.6 1.0
OD1 A:ASP250 3.6 28.2 1.0
O1B A:UDP404 3.7 94.0 1.0
NH2 A:ARG187 4.1 35.8 1.0
O3' A:UDP404 4.2 38.3 1.0
O2A A:UDP404 4.2 74.7 1.0
CB A:ASP250 4.3 28.1 1.0
NH1 A:ARG187 4.4 35.3 1.0
ND1 A:HIS343 4.4 48.5 1.0
CG A:HIS343 4.4 45.1 1.0
ND1 A:HIS340 4.5 38.8 1.0
CG A:HIS340 4.5 33.8 1.0
O5' A:UDP404 4.7 64.6 1.0
CZ A:ARG187 4.7 37.8 1.0
O A:ILE341 4.9 36.9 1.0
C3' A:UDP404 4.9 35.7 1.0
O A:HOH691 4.9 42.4 1.0

Manganese binding site 2 out of 3 in 4eea

Go back to Manganese Binding Sites List in 4eea
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-Gal-BETA1,4-Glc-Beta


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-Gal-BETA1,4-Glc-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn405

b:40.4
occ:1.00
 NE2 B:HIS340 2.3 26.5 1.0
OD2 B:ASP250 2.3 30.8 1.0
NE2 B:HIS343 2.3 35.1 1.0
O1A B:UDP404 2.4 66.1 1.0
O3B B:UDP404 2.4 95.8 1.0
CG B:ASP250 3.1 24.7 1.0
CD2 B:HIS343 3.2 34.6 1.0
CD2 B:HIS340 3.2 27.8 1.0
CE1 B:HIS340 3.3 30.3 1.0
O3A B:UDP404 3.3 86.9 1.0
PB B:UDP404 3.3 98.6 1.0
CE1 B:HIS343 3.3 35.7 1.0
O B:HOH535 3.4 36.0 1.0
PA B:UDP404 3.4 76.6 1.0
OD1 B:ASP250 3.5 25.2 1.0
O2B B:UDP404 3.9 97.1 1.0
NH2 B:ARG187 4.1 24.0 1.0
O2A B:UDP404 4.2 76.9 1.0
CB B:ASP250 4.3 21.0 1.0
O B:HOH615 4.3 55.0 1.0
O3' B:UDP404 4.3 29.4 1.0
ND1 B:HIS340 4.4 26.5 1.0
CG B:HIS340 4.4 28.0 1.0
ND1 B:HIS343 4.4 36.5 1.0
CG B:HIS343 4.4 36.9 1.0
NH1 B:ARG187 4.4 22.2 1.0
NZ B:LYS275 4.6 49.1 1.0
O1B B:UDP404 4.6 95.6 1.0
CZ B:ARG187 4.7 31.1 1.0
O5' B:UDP404 4.8 59.6 1.0
O B:ILE341 4.9 27.9 1.0
O B:HOH589 5.0 36.6 1.0

Manganese binding site 3 out of 3 in 4eea

Go back to Manganese Binding Sites List in 4eea
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-Gal-BETA1,4-Glc-Beta


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-Gal-BETA1,4-Glc-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn405

b:63.1
occ:1.00
 OD2 C:ASP250 2.3 45.4 1.0
NE2 C:HIS343 2.3 60.0 1.0
O1A C:UDP404 2.3 0.0 1.0
O3B C:UDP404 2.4 0.5 1.0
NE2 C:HIS340 2.5 54.5 1.0
O C:HOH587 2.9 53.0 1.0
CG C:ASP250 3.2 41.2 1.0
CD2 C:HIS343 3.2 58.0 1.0
PA C:UDP404 3.3 0.8 1.0
CE1 C:HIS343 3.3 58.1 1.0
CD2 C:HIS340 3.4 53.0 1.0
PB C:UDP404 3.4 0.2 1.0
O2A C:UDP404 3.5 0.2 1.0
OD1 C:ASP250 3.6 43.8 1.0
O3A C:UDP404 3.6 0.8 1.0
CE1 C:HIS340 3.6 55.8 1.0
O2B C:UDP404 4.1 0.4 1.0
NH2 C:ARG187 4.2 43.4 1.0
O3' C:UDP404 4.3 42.9 1.0
CG C:HIS343 4.4 59.3 1.0
ND1 C:HIS343 4.4 59.7 1.0
NZ C:LYS275 4.4 64.9 1.0
CB C:ASP250 4.5 36.7 1.0
CG C:HIS340 4.6 51.4 1.0
NH1 C:ARG187 4.6 48.2 1.0
O1B C:UDP404 4.7 0.0 1.0
ND1 C:HIS340 4.7 53.0 1.0
O5' C:UDP404 4.7 91.2 1.0
CZ C:ARG187 4.9 51.3 1.0
O C:ILE341 4.9 50.9 1.0
C3' C:UDP404 5.0 46.0 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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