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Manganese in PDB 4ee4: Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Tetrasaccharide From Lacto-N- Neohexose

Enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Tetrasaccharide From Lacto-N- Neohexose

All present enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Tetrasaccharide From Lacto-N- Neohexose:
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 Tetrasaccharide From Lacto-N- Neohexose, PDB code: 4ee4 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) 36.82 / 1.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 107.364, 195.969, 143.776, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.2

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 Tetrasaccharide From Lacto-N- Neohexose (pdb code 4ee4). 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 Tetrasaccharide From Lacto-N- Neohexose, PDB code: 4ee4:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4ee4

Go back to Manganese Binding Sites List in 4ee4
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 Tetrasaccharide From Lacto-N- Neohexose


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 Tetrasaccharide From Lacto-N- Neohexose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn406

b:59.6
occ:1.00
 NE2 A:HIS343 2.3 46.3 1.0
O2A A:UDP405 2.3 89.3 1.0
NE2 A:HIS340 2.4 35.8 1.0
OD2 A:ASP250 2.4 34.4 1.0
O A:HOH728 3.0 39.3 1.0
O3B A:UDP405 3.1 0.4 1.0
O1A A:UDP405 3.2 91.8 1.0
CG A:ASP250 3.2 34.3 1.0
CE1 A:HIS343 3.3 48.1 1.0
PA A:UDP405 3.3 92.1 1.0
CD2 A:HIS343 3.3 43.9 1.0
CD2 A:HIS340 3.3 37.7 1.0
CE1 A:HIS340 3.4 40.3 1.0
OD1 A:ASP250 3.6 31.5 1.0
O3A A:UDP405 4.1 99.8 1.0
PB A:UDP405 4.1 0.4 1.0
NH2 A:ARG187 4.2 42.0 1.0
O3' A:UDP405 4.3 44.2 1.0
CB A:ASP250 4.4 29.9 1.0
ND1 A:HIS343 4.4 50.7 1.0
CG A:HIS343 4.5 47.5 1.0
NH1 A:ARG187 4.5 37.3 1.0
ND1 A:HIS340 4.5 38.5 1.0
CG A:HIS340 4.5 36.4 1.0
O A:HOH702 4.6 46.5 1.0
O5' A:UDP405 4.7 75.3 1.0
O2B A:UDP405 4.8 0.1 1.0
CZ A:ARG187 4.8 41.4 1.0
C3' A:UDP405 4.9 39.7 1.0

Manganese binding site 2 out of 3 in 4ee4

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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 Tetrasaccharide From Lacto-N- Neohexose


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 Tetrasaccharide From Lacto-N- Neohexose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn406

b:45.8
occ:1.00
 NE2 B:HIS340 2.3 31.1 1.0
O2A B:UDP405 2.3 73.7 1.0
OD2 B:ASP250 2.4 29.4 1.0
NE2 B:HIS343 2.4 35.0 1.0
O3B B:UDP405 2.7 97.7 1.0
CG B:ASP250 3.2 24.8 1.0
CE1 B:HIS340 3.2 31.1 1.0
O1A B:UDP405 3.2 81.1 1.0
PA B:UDP405 3.2 81.8 1.0
CD2 B:HIS340 3.3 28.2 1.0
CD2 B:HIS343 3.3 34.8 1.0
O B:HOH746 3.4 36.4 1.0
CE1 B:HIS343 3.4 37.0 1.0
OD1 B:ASP250 3.5 26.1 1.0
O3A B:UDP405 3.7 89.9 1.0
PB B:UDP405 3.7 0.1 1.0
NH2 B:ARG187 4.1 25.9 1.0
O B:HOH584 4.3 58.6 1.0
CB B:ASP250 4.3 22.1 1.0
ND1 B:HIS340 4.4 28.6 1.0
O3' B:UDP405 4.4 32.6 1.0
CG B:HIS340 4.4 29.2 1.0
NH1 B:ARG187 4.5 25.6 1.0
CG B:HIS343 4.5 36.9 1.0
ND1 B:HIS343 4.5 39.2 1.0
O1B B:UDP405 4.6 0.8 1.0
O B:HOH761 4.7 41.0 1.0
CZ B:ARG187 4.7 33.6 1.0
O5' B:UDP405 4.7 60.0 1.0
O2B B:UDP405 4.8 98.8 1.0
O B:ILE341 4.9 30.4 1.0

Manganese binding site 3 out of 3 in 4ee4

Go back to Manganese Binding Sites List in 4ee4
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 Tetrasaccharide From Lacto-N- Neohexose


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 Tetrasaccharide From Lacto-N- Neohexose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn406

b:64.2
occ:1.00
 O3B C:UDP405 2.2 0.1 1.0
NE2 C:HIS343 2.3 49.7 1.0
OD2 C:ASP250 2.4 45.7 1.0
NE2 C:HIS340 2.5 50.4 1.0
O1A C:UDP405 3.0 0.9 1.0
O C:HOH602 3.1 52.2 1.0
O3A C:UDP405 3.2 0.3 1.0
PB C:UDP405 3.2 0.9 1.0
CD2 C:HIS343 3.2 44.4 1.0
CG C:ASP250 3.3 41.1 1.0
CE1 C:HIS343 3.3 48.5 1.0
CD2 C:HIS340 3.3 50.4 1.0
OD1 C:ASP250 3.5 41.4 1.0
CE1 C:HIS340 3.6 52.5 1.0
PA C:UDP405 3.7 0.2 1.0
O2B C:UDP405 4.0 0.6 1.0
NH2 C:ARG187 4.1 43.5 1.0
O3' C:UDP405 4.3 45.4 1.0
ND1 C:HIS343 4.4 51.6 1.0
CG C:HIS343 4.4 53.1 1.0
O1B C:UDP405 4.4 0.7 1.0
CB C:ASP250 4.5 37.4 1.0
O C:HOH607 4.5 68.2 1.0
CG C:HIS340 4.5 49.5 1.0
O2A C:UDP405 4.6 0.8 1.0
NH1 C:ARG187 4.6 43.6 1.0
ND1 C:HIS340 4.7 50.5 1.0
CZ C:ARG187 4.8 51.1 1.0
O C:ILE341 4.9 46.6 1.0
O5' C:UDP405 5.0 92.4 1.0
C3' C:UDP405 5.0 49.2 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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