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Manganese in PDB 2agd: Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase- I(M340H-B4GAL-T1) in Complex with Glcnac-BETA1,4-Man-ALPHA1,3-Man- Beta-or

Enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase- I(M340H-B4GAL-T1) in Complex with Glcnac-BETA1,4-Man-ALPHA1,3-Man- Beta-or

All present enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase- I(M340H-B4GAL-T1) in Complex with Glcnac-BETA1,4-Man-ALPHA1,3-Man- Beta-or:
2.4.1.90;

Protein crystallography data

The structure of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase- I(M340H-B4GAL-T1) in Complex with Glcnac-BETA1,4-Man-ALPHA1,3-Man- Beta-or, PDB code: 2agd 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 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 107.464, 194.784, 143.700, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase- I(M340H-B4GAL-T1) in Complex with Glcnac-BETA1,4-Man-ALPHA1,3-Man- Beta-or (pdb code 2agd). 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- I(M340H-B4GAL-T1) in Complex with Glcnac-BETA1,4-Man-ALPHA1,3-Man- Beta-or, PDB code: 2agd:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 2agd

Go back to Manganese Binding Sites List in 2agd
Manganese binding site 1 out of 3 in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase- I(M340H-B4GAL-T1) in Complex with Glcnac-BETA1,4-Man-ALPHA1,3-Man- Beta-or


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- I(M340H-B4GAL-T1) in Complex with Glcnac-BETA1,4-Man-ALPHA1,3-Man- Beta-or within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn400

b:27.7
occ:1.00
 O3B A:UDH399 2.1 26.4 1.0
O1A A:UDH399 2.2 27.3 1.0
OD2 A:ASP250 2.2 21.8 1.0
NE2 A:HIS343 2.3 31.2 1.0
NE2 A:HIS340 2.3 24.2 1.0
O A:HOH468 2.3 22.5 1.0
CG A:ASP250 3.1 24.9 1.0
CD2 A:HIS343 3.1 32.1 1.0
CE1 A:HIS340 3.2 25.1 1.0
CD2 A:HIS340 3.3 25.1 1.0
PB A:UDH399 3.3 27.1 1.0
CE1 A:HIS343 3.3 33.4 1.0
PA A:UDH399 3.4 25.6 1.0
OD1 A:ASP250 3.4 22.2 1.0
O3A A:UDH399 3.6 25.7 1.0
O2B A:UDH399 3.9 29.5 1.0
O3' A:UDH399 4.0 23.0 1.0
NH2 A:ARG187 4.3 27.2 1.0
O2A A:UDH399 4.3 27.5 1.0
CG A:HIS343 4.3 33.4 1.0
NZ A:LYS275 4.3 38.8 1.0
ND1 A:HIS340 4.4 26.0 1.0
NH1 A:ARG187 4.4 24.4 1.0
CB A:ASP250 4.4 23.3 1.0
ND1 A:HIS343 4.4 32.9 1.0
CG A:HIS340 4.4 26.6 1.0
O5' A:UDH399 4.5 24.8 1.0
C5B A:UDH399 4.6 23.9 1.0
C3B A:UDH399 4.7 24.2 1.0
O1B A:UDH399 4.7 27.0 1.0
O A:HOH913 4.8 45.5 1.0
CZ A:ARG187 4.8 28.1 1.0

Manganese binding site 2 out of 3 in 2agd

Go back to Manganese Binding Sites List in 2agd
Manganese binding site 2 out of 3 in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase- I(M340H-B4GAL-T1) in Complex with Glcnac-BETA1,4-Man-ALPHA1,3-Man- Beta-or


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- I(M340H-B4GAL-T1) in Complex with Glcnac-BETA1,4-Man-ALPHA1,3-Man- Beta-or within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:20.5
occ:1.00
 O1A B:UDH401 2.1 17.1 1.0
O3B B:UDH401 2.1 20.0 1.0
OD2 B:ASP250 2.2 17.7 1.0
NE2 B:HIS340 2.3 19.6 1.0
O B:HOH453 2.3 18.5 1.0
NE2 B:HIS343 2.3 23.8 1.0
CG B:ASP250 3.1 15.9 1.0
CD2 B:HIS343 3.2 23.3 1.0
CE1 B:HIS340 3.2 21.5 1.0
CD2 B:HIS340 3.3 19.6 1.0
PB B:UDH401 3.4 23.5 1.0
CE1 B:HIS343 3.4 23.4 1.0
PA B:UDH401 3.4 20.2 1.0
OD1 B:ASP250 3.4 17.3 1.0
O3A B:UDH401 3.6 21.4 1.0
O2B B:UDH401 3.9 26.2 1.0
O3' B:UDH401 4.0 17.5 1.0
NZ B:LYS275 4.1 32.3 1.0
O2A B:UDH401 4.2 22.2 1.0
NH2 B:ARG187 4.3 19.2 1.0
ND1 B:HIS340 4.3 18.7 1.0
CG B:HIS343 4.4 24.6 1.0
NH1 B:ARG187 4.4 18.2 1.0
CG B:HIS340 4.4 20.1 1.0
CB B:ASP250 4.4 16.3 1.0
ND1 B:HIS343 4.4 22.6 1.0
O5' B:UDH401 4.5 19.5 1.0
C5B B:UDH401 4.6 18.8 1.0
C3B B:UDH401 4.7 17.9 1.0
O1B B:UDH401 4.7 21.3 1.0
CZ B:ARG187 4.8 20.4 1.0

Manganese binding site 3 out of 3 in 2agd

Go back to Manganese Binding Sites List in 2agd
Manganese binding site 3 out of 3 in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase- I(M340H-B4GAL-T1) in Complex with Glcnac-BETA1,4-Man-ALPHA1,3-Man- Beta-or


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- I(M340H-B4GAL-T1) in Complex with Glcnac-BETA1,4-Man-ALPHA1,3-Man- Beta-or within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn404

b:31.0
occ:1.00
 O3B C:UDH403 2.1 30.1 1.0
OD2 C:ASP250 2.2 26.9 1.0
O1A C:UDH403 2.2 30.8 1.0
O C:HOH519 2.3 28.7 1.0
NE2 C:HIS340 2.3 33.7 1.0
NE2 C:HIS343 2.3 31.0 1.0
CG C:ASP250 3.1 26.6 1.0
CD2 C:HIS340 3.3 35.1 1.0
CD2 C:HIS343 3.3 29.7 1.0
CE1 C:HIS340 3.3 35.5 1.0
CE1 C:HIS343 3.3 31.3 1.0
PB C:UDH403 3.3 30.1 1.0
PA C:UDH403 3.4 31.2 1.0
OD1 C:ASP250 3.4 27.4 1.0
O3A C:UDH403 3.6 31.4 1.0
O2B C:UDH403 3.8 34.8 1.0
NZ C:LYS275 4.0 40.7 1.0
O3' C:UDH403 4.0 28.6 1.0
O2A C:UDH403 4.2 31.9 1.0
NH2 C:ARG187 4.4 32.5 1.0
CB C:ASP250 4.4 26.0 1.0
ND1 C:HIS340 4.4 34.5 1.0
CG C:HIS340 4.4 34.2 1.0
ND1 C:HIS343 4.4 31.7 1.0
CG C:HIS343 4.5 31.8 1.0
O5' C:UDH403 4.5 30.0 1.0
NH1 C:ARG187 4.5 34.1 1.0
C5B C:UDH403 4.6 30.1 1.0
O1B C:UDH403 4.7 28.1 1.0
C3B C:UDH403 4.7 28.7 1.0
O C:HOH502 4.9 55.7 1.0
CZ C:ARG187 5.0 35.0 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 13:25:54 2024

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