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Manganese in PDB 4ee3: Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Pentasaccharide

Enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Pentasaccharide

All present enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Pentasaccharide:
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 Pentasaccharide, PDB code: 4ee3 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) 36.31 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 107.612, 195.158, 143.695, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 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 Pentasaccharide (pdb code 4ee3). 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 Pentasaccharide, PDB code: 4ee3:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4ee3

Go back to Manganese Binding Sites List in 4ee3
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 Pentasaccharide


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 Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn407

b:31.4
occ:1.00
 O3B A:UDH406 1.9 28.4 1.0
O1A A:UDH406 2.1 28.1 1.0
OD2 A:ASP250 2.2 27.0 1.0
NE2 A:HIS343 2.2 33.9 1.0
O A:HOH522 2.3 26.9 1.0
NE2 A:HIS340 2.3 23.0 1.0
CG A:ASP250 3.1 29.9 1.0
CE1 A:HIS343 3.1 36.9 1.0
PB A:UDH406 3.2 30.3 1.0
CE1 A:HIS340 3.2 22.7 1.0
PA A:UDH406 3.3 30.1 1.0
CD2 A:HIS343 3.3 33.8 1.0
CD2 A:HIS340 3.4 24.8 1.0
OD1 A:ASP250 3.5 26.6 1.0
O3A A:UDH406 3.5 28.7 1.0
O2B A:UDH406 3.9 32.6 1.0
O3' A:UDH406 3.9 27.3 1.0
O A:HOH678 4.1 44.8 1.0
O2A A:UDH406 4.1 33.2 1.0
ND1 A:HIS343 4.3 36.2 1.0
NH2 A:ARG187 4.3 30.4 1.0
CB A:ASP250 4.3 25.0 1.0
CG A:HIS343 4.4 36.1 1.0
ND1 A:HIS340 4.4 23.7 1.0
O5' A:UDH406 4.5 25.9 1.0
C3B A:UDH406 4.5 24.3 1.0
CG A:HIS340 4.5 28.3 1.0
NH1 A:ARG187 4.5 27.8 1.0
O1B A:UDH406 4.5 32.6 1.0
C5B A:UDH406 4.6 24.9 1.0
NZ A:LYS275 4.6 39.2 1.0
OD2 A:ASP248 4.9 32.0 1.0
CZ A:ARG187 4.9 28.6 1.0

Manganese binding site 2 out of 3 in 4ee3

Go back to Manganese Binding Sites List in 4ee3
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 Pentasaccharide


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 Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn407

b:25.1
occ:1.00
 O1A B:UDH406 2.0 17.9 1.0
NE2 B:HIS343 2.1 29.5 1.0
NE2 B:HIS340 2.2 21.4 1.0
O3B B:UDH406 2.2 28.2 1.0
OD2 B:ASP250 2.3 19.4 1.0
O B:HOH559 2.3 22.8 1.0
CE1 B:HIS340 3.0 23.4 1.0
CD2 B:HIS343 3.1 25.9 1.0
CE1 B:HIS343 3.1 27.4 1.0
CG B:ASP250 3.2 18.4 1.0
PA B:UDH406 3.3 19.3 1.0
PB B:UDH406 3.3 23.7 1.0
CD2 B:HIS340 3.4 21.4 1.0
O3A B:UDH406 3.6 21.1 1.0
OD1 B:ASP250 3.6 17.7 1.0
O2B B:UDH406 3.9 28.8 1.0
O3' B:UDH406 4.0 20.9 1.0
O B:HOH570 4.0 47.9 1.0
NZ B:LYS275 4.1 37.2 1.0
O2A B:UDH406 4.2 19.3 1.0
ND1 B:HIS340 4.2 19.7 1.0
NH2 B:ARG187 4.2 18.2 1.0
ND1 B:HIS343 4.2 23.5 1.0
CG B:HIS343 4.3 28.3 1.0
NH1 B:ARG187 4.3 18.0 1.0
CG B:HIS340 4.4 23.5 1.0
CB B:ASP250 4.5 17.9 1.0
O5' B:UDH406 4.6 14.1 1.0
O1B B:UDH406 4.6 28.5 1.0
C3B B:UDH406 4.6 19.2 1.0
C5B B:UDH406 4.8 15.6 1.0
CZ B:ARG187 4.8 24.4 1.0
O B:HOH589 4.8 41.7 1.0

Manganese binding site 3 out of 3 in 4ee3

Go back to Manganese Binding Sites List in 4ee3
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 Pentasaccharide


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 Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn407

b:36.8
occ:1.00
 O3B C:UDH406 1.9 28.7 1.0
OD2 C:ASP250 2.1 31.6 1.0
O1A C:UDH406 2.2 35.7 1.0
NE2 C:HIS343 2.2 42.4 1.0
NE2 C:HIS340 2.3 44.4 1.0
O C:HOH524 2.4 28.9 1.0
CG C:ASP250 3.1 28.9 1.0
CE1 C:HIS343 3.1 36.5 1.0
PB C:UDH406 3.2 31.5 1.0
CE1 C:HIS340 3.2 44.1 1.0
CD2 C:HIS340 3.3 42.8 1.0
CD2 C:HIS343 3.3 39.6 1.0
PA C:UDH406 3.4 31.0 1.0
OD1 C:ASP250 3.4 30.8 1.0
O3A C:UDH406 3.6 33.2 1.0
O2B C:UDH406 3.9 37.3 1.0
NZ C:LYS275 4.0 50.9 1.0
O3' C:UDH406 4.1 26.0 1.0
O2A C:UDH406 4.2 36.7 1.0
ND1 C:HIS343 4.3 32.1 1.0
CB C:ASP250 4.3 26.1 1.0
NH2 C:ARG187 4.3 37.1 1.0
ND1 C:HIS340 4.4 43.5 1.0
CG C:HIS343 4.4 36.0 1.0
O1B C:UDH406 4.4 25.0 1.0
CG C:HIS340 4.4 41.6 1.0
O5' C:UDH406 4.6 35.0 1.0
C3B C:UDH406 4.6 30.2 1.0
NH1 C:ARG187 4.7 37.1 1.0
C5B C:UDH406 4.8 33.8 1.0
O C:ILE341 5.0 39.6 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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