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Manganese in PDB 2ae7: Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide

Enzymatic activity of Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide

All present enzymatic activity of Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide:
2.4.1.90;

Protein crystallography data

The structure of Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide, PDB code: 2ae7 was solved by V.Ramasamy, B.Ramakrishnan, E.Boeggeman, D.M.Ratner, P.H.Seeberger, P.K.Qasba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 106.982, 195.172, 143.919, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 24.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide (pdb code 2ae7). 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-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide, PDB code: 2ae7:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 2ae7

Go back to Manganese Binding Sites List in 2ae7
Manganese binding site 1 out of 3 in the Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (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-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn400

b:31.3
occ:1.00
 O3B A:UDH399 2.1 30.7 1.0
OD2 A:ASP250 2.1 25.0 1.0
NE2 A:HIS343 2.2 37.2 1.0
NE2 A:HIS340 2.2 28.6 1.0
O1A A:UDH399 2.2 29.6 1.0
O A:HOH482 2.3 23.7 1.0
CG A:ASP250 3.0 26.2 1.0
CD2 A:HIS343 3.1 36.6 1.0
CE1 A:HIS340 3.1 27.9 1.0
CE1 A:HIS343 3.2 38.4 1.0
CD2 A:HIS340 3.3 27.7 1.0
PB A:UDH399 3.3 32.0 1.0
OD1 A:ASP250 3.4 22.6 1.0
PA A:UDH399 3.4 30.2 1.0
O3A A:UDH399 3.6 30.5 1.0
O2B A:UDH399 3.9 34.6 1.0
O3' A:UDH399 3.9 30.5 1.0
O2A A:UDH399 4.3 31.8 1.0
CG A:HIS343 4.3 38.1 1.0
ND1 A:HIS340 4.3 28.8 1.0
NH2 A:ARG187 4.3 34.7 1.0
CB A:ASP250 4.3 24.8 1.0
ND1 A:HIS343 4.3 38.3 1.0
CG A:HIS340 4.4 29.7 1.0
O A:HOH827 4.5 51.2 1.0
NZ A:LYS275 4.5 39.9 1.0
O5' A:UDH399 4.5 31.4 1.0
NH1 A:ARG187 4.6 35.6 1.0
C5B A:UDH399 4.6 29.8 1.0
C3B A:UDH399 4.7 28.4 1.0
O1B A:UDH399 4.7 32.7 1.0
CZ A:ARG187 4.9 33.6 1.0

Manganese binding site 2 out of 3 in 2ae7

Go back to Manganese Binding Sites List in 2ae7
Manganese binding site 2 out of 3 in the Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (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-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:25.5
occ:1.00
 O3B B:UDH401 2.1 28.8 1.0
O1A B:UDH401 2.2 21.7 1.0
NE2 B:HIS343 2.2 24.9 1.0
NE2 B:HIS340 2.3 23.3 1.0
OD2 B:ASP250 2.3 22.6 1.0
O B:HOH484 2.3 25.0 1.0
CG B:ASP250 3.1 19.5 1.0
CD2 B:HIS343 3.1 26.3 1.0
CD2 B:HIS340 3.2 23.9 1.0
CE1 B:HIS340 3.2 23.8 1.0
CE1 B:HIS343 3.3 26.7 1.0
PB B:UDH401 3.3 29.4 1.0
PA B:UDH401 3.4 25.9 1.0
OD1 B:ASP250 3.4 21.0 1.0
O3A B:UDH401 3.6 27.6 1.0
O2B B:UDH401 3.9 31.7 1.0
O3' B:UDH401 3.9 20.6 1.0
NZ B:LYS275 4.1 38.1 1.0
O2A B:UDH401 4.2 28.4 1.0
NH2 B:ARG187 4.3 21.2 1.0
CG B:HIS343 4.3 26.7 1.0
ND1 B:HIS343 4.3 26.2 1.0
NH1 B:ARG187 4.4 21.2 1.0
ND1 B:HIS340 4.4 23.0 1.0
CB B:ASP250 4.4 20.4 1.0
CG B:HIS340 4.4 23.2 1.0
O5' B:UDH401 4.5 24.0 1.0
C5B B:UDH401 4.7 22.4 1.0
C3B B:UDH401 4.7 19.6 1.0
O1B B:UDH401 4.7 28.2 1.0
CZ B:ARG187 4.8 24.1 1.0
O B:HOH723 5.0 46.3 1.0

Manganese binding site 3 out of 3 in 2ae7

Go back to Manganese Binding Sites List in 2ae7
Manganese binding site 3 out of 3 in the Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (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-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn404

b:38.6
occ:1.00
 O3B C:UDH403 2.0 38.2 1.0
OD2 C:ASP250 2.1 32.9 1.0
O C:HOH560 2.1 35.3 1.0
NE2 C:HIS343 2.2 41.1 1.0
O1A C:UDH403 2.3 38.0 1.0
NE2 C:HIS340 2.4 44.0 1.0
CG C:ASP250 3.0 31.8 1.0
CE1 C:HIS343 3.1 41.0 1.0
CD2 C:HIS343 3.2 41.2 1.0
PB C:UDH403 3.3 40.8 1.0
OD1 C:ASP250 3.3 30.7 1.0
CD2 C:HIS340 3.4 44.0 1.0
CE1 C:HIS340 3.4 44.0 1.0
PA C:UDH403 3.4 39.7 1.0
O3A C:UDH403 3.6 40.4 1.0
O2B C:UDH403 3.9 41.5 1.0
O3' C:UDH403 4.0 34.2 1.0
NZ C:LYS275 4.1 45.8 1.0
ND1 C:HIS343 4.2 40.3 1.0
O2A C:UDH403 4.3 43.9 1.0
CG C:HIS343 4.3 41.5 1.0
CB C:ASP250 4.4 30.3 1.0
NH2 C:ARG187 4.4 38.2 1.0
ND1 C:HIS340 4.5 45.2 1.0
O5' C:UDH403 4.5 39.4 1.0
CG C:HIS340 4.5 43.9 1.0
NH1 C:ARG187 4.5 40.9 1.0
C5B C:UDH403 4.6 37.0 1.0
O1B C:UDH403 4.7 37.7 1.0
C3B C:UDH403 4.8 34.4 1.0
CZ C:ARG187 5.0 40.6 1.0

Reference:

V.Ramasamy, B.Ramakrishnan, E.Boeggeman, D.M.Ratner, P.H.Seeberger, P.K.Qasba. Oligosaccharide Preferences of BETA1,4-Galactosyltransferase-I: Crystal Structures of MET340HIS Mutant of Human BETA1,4-Galactosyltransferase-I with A Pentasaccharide and Trisaccharides of the N-Glycan Moiety J.Mol.Biol. V. 353 53 2005.
ISSN: ISSN 0022-2836
PubMed: 16157350
DOI: 10.1016/J.JMB.2005.07.050
Page generated: Sat Oct 5 13:24:06 2024

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