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

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

All present enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Man-Alpha-Methyl:
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-Man-Alpha-Methyl, PDB code: 4eem 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) 47.10 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 107.351, 196.386, 143.755, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.6

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-Man-Alpha-Methyl (pdb code 4eem). 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-Man-Alpha-Methyl, PDB code: 4eem:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4eem

Go back to Manganese Binding Sites List in 4eem
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-Man-Alpha-Methyl


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-Man-Alpha-Methyl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:45.5
occ:1.00
 O3B A:UDP403 1.9 71.1 1.0
OD2 A:ASP250 2.2 28.6 1.0
NE2 A:HIS343 2.3 43.3 1.0
O1A A:UDP403 2.3 58.1 1.0
NE2 A:HIS340 2.4 27.9 1.0
O A:HOH549 2.6 45.2 1.0
PB A:UDP403 3.1 75.8 1.0
CG A:ASP250 3.2 30.3 1.0
CE1 A:HIS343 3.2 45.7 1.0
CD2 A:HIS343 3.3 44.7 1.0
CE1 A:HIS340 3.3 28.3 1.0
CD2 A:HIS340 3.3 32.1 1.0
O3A A:UDP403 3.4 67.0 1.0
PA A:UDP403 3.4 61.8 1.0
OD1 A:ASP250 3.6 28.4 1.0
O2B A:UDP403 3.8 74.2 1.0
O2A A:UDP403 4.2 63.1 1.0
NH2 A:ARG187 4.3 34.6 1.0
O3' A:UDP403 4.3 37.9 1.0
O1B A:UDP403 4.3 74.0 1.0
CB A:ASP250 4.3 28.7 1.0
ND1 A:HIS343 4.3 47.7 1.0
CG A:HIS343 4.4 44.6 1.0
NH1 A:ARG187 4.4 31.1 1.0
ND1 A:HIS340 4.4 31.9 1.0
CG A:HIS340 4.5 33.5 1.0
O5' A:UDP403 4.7 51.7 1.0
NZ A:LYS275 4.7 50.4 1.0
C3' A:UDP403 4.8 30.5 1.0
CZ A:ARG187 4.9 33.9 1.0
O A:HOH594 5.0 47.1 1.0

Manganese binding site 2 out of 3 in 4eem

Go back to Manganese Binding Sites List in 4eem
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-Man-Alpha-Methyl


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-Man-Alpha-Methyl within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:35.1
occ:1.00
 O1A B:UDP403 2.2 56.4 1.0
NE2 B:HIS340 2.2 27.3 1.0
NE2 B:HIS343 2.3 32.3 1.0
OD2 B:ASP250 2.4 28.7 1.0
O3B B:UDP403 2.5 78.9 1.0
CE1 B:HIS340 3.1 28.5 1.0
CG B:ASP250 3.2 25.2 1.0
CE1 B:HIS343 3.2 32.2 1.0
CD2 B:HIS340 3.3 26.7 1.0
PA B:UDP403 3.3 63.4 1.0
CD2 B:HIS343 3.3 31.2 1.0
O B:HOH552 3.5 35.2 1.0
O3A B:UDP403 3.5 72.1 1.0
PB B:UDP403 3.5 83.5 1.0
OD1 B:ASP250 3.5 23.8 1.0
O2A B:UDP403 4.1 69.3 1.0
O B:HOH627 4.1 45.6 1.0
NH2 B:ARG187 4.1 21.2 1.0
O2B B:UDP403 4.2 81.4 1.0
O3' B:UDP403 4.3 27.5 1.0
ND1 B:HIS340 4.3 27.7 1.0
NZ B:LYS275 4.3 37.4 1.0
CB B:ASP250 4.3 22.4 1.0
ND1 B:HIS343 4.3 34.2 1.0
NH1 B:ARG187 4.3 17.7 1.0
CG B:HIS340 4.4 29.6 1.0
CG B:HIS343 4.5 32.5 1.0
O5' B:UDP403 4.7 53.0 1.0
CZ B:ARG187 4.7 24.1 1.0
O1B B:UDP403 4.7 78.7 1.0
C3' B:UDP403 4.9 26.1 1.0

Manganese binding site 3 out of 3 in 4eem

Go back to Manganese Binding Sites List in 4eem
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-Man-Alpha-Methyl


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-Man-Alpha-Methyl within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn404

b:52.1
occ:1.00
 O3B C:UDP403 2.1 84.0 1.0
OD2 C:ASP250 2.2 44.7 1.0
NE2 C:HIS343 2.2 50.4 1.0
O1A C:UDP403 2.4 79.4 1.0
NE2 C:HIS340 2.5 51.8 1.0
O C:HOH542 2.6 48.4 1.0
CE1 C:HIS343 3.0 51.7 1.0
CG C:ASP250 3.1 38.6 1.0
PB C:UDP403 3.2 87.2 1.0
CD2 C:HIS343 3.3 51.5 1.0
CD2 C:HIS340 3.3 50.2 1.0
PA C:UDP403 3.5 77.2 1.0
OD1 C:ASP250 3.5 39.4 1.0
O3A C:UDP403 3.5 82.6 1.0
CE1 C:HIS340 3.6 51.7 1.0
O2B C:UDP403 3.7 86.6 1.0
NH2 C:ARG187 4.0 39.9 1.0
NZ C:LYS275 4.1 57.2 1.0
O3' C:UDP403 4.1 39.9 1.0
O2A C:UDP403 4.2 80.9 1.0
ND1 C:HIS343 4.2 47.8 1.0
CG C:HIS343 4.3 49.3 1.0
CB C:ASP250 4.4 36.4 1.0
O1B C:UDP403 4.5 84.3 1.0
CG C:HIS340 4.5 50.1 1.0
NH1 C:ARG187 4.6 43.2 1.0
ND1 C:HIS340 4.6 53.7 1.0
O5' C:UDP403 4.8 71.1 1.0
CZ C:ARG187 4.8 44.7 1.0
C3' C:UDP403 4.9 42.8 1.0
O C:HOH572 5.0 53.9 1.0
O C:ILE341 5.0 49.5 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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