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Manganese in PDB 3ee5: Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,3-Gal-Beta- Naphthalenemethanol

Enzymatic activity of Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,3-Gal-Beta- Naphthalenemethanol

All present enzymatic activity of Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,3-Gal-Beta- Naphthalenemethanol:
2.4.1.38;

Protein crystallography data

The structure of Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,3-Gal-Beta- Naphthalenemethanol, PDB code: 3ee5 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) 46.33 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 107.127, 195.742, 143.801, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24

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 Glcnac-BETA1,3-Gal-Beta- Naphthalenemethanol (pdb code 3ee5). 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 Glcnac-BETA1,3-Gal-Beta- Naphthalenemethanol, PDB code: 3ee5:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 3ee5

Go back to Manganese Binding Sites List in 3ee5
Manganese binding site 1 out of 3 in the Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,3-Gal-Beta- Naphthalenemethanol


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 Glcnac-BETA1,3-Gal-Beta- Naphthalenemethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn611

b:38.5
occ:1.00
 O1A A:UDH399 2.1 39.0 1.0
O3B A:UDH399 2.1 36.8 1.0
O A:HOH3012 2.2 31.6 1.0
OD2 A:ASP250 2.2 29.7 1.0
NE2 A:HIS343 2.3 42.7 1.0
NE2 A:HIS340 2.3 31.1 1.0
CG A:ASP250 3.0 30.5 1.0
CD2 A:HIS343 3.2 42.5 1.0
CE1 A:HIS340 3.3 33.2 1.0
CD2 A:HIS340 3.3 33.8 1.0
PA A:UDH399 3.3 38.6 1.0
CE1 A:HIS343 3.4 42.2 1.0
OD1 A:ASP250 3.4 27.9 1.0
PB A:UDH399 3.4 38.5 1.0
O3A A:UDH399 3.7 37.5 1.0
O5' A:UDH399 3.9 39.9 1.0
O2B A:UDH399 3.9 39.5 1.0
O3' A:UDH399 4.0 34.3 1.0
CB A:ASP250 4.3 29.2 1.0
NH2 A:ARG187 4.3 33.0 1.0
CG A:HIS343 4.4 43.5 1.0
ND1 A:HIS340 4.4 33.6 1.0
ND1 A:HIS343 4.4 44.3 1.0
O2A A:UDH399 4.5 39.5 1.0
CG A:HIS340 4.5 34.5 1.0
NH1 A:ARG187 4.5 32.2 1.0
NZ A:LYS275 4.5 43.5 1.0
O A:HOH3068 4.6 52.2 1.0
C5B A:UDH399 4.7 30.9 1.0
C3B A:UDH399 4.7 31.1 1.0
O1B A:UDH399 4.8 37.9 1.0
CZ A:ARG187 4.9 32.8 1.0

Manganese binding site 2 out of 3 in 3ee5

Go back to Manganese Binding Sites List in 3ee5
Manganese binding site 2 out of 3 in the Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,3-Gal-Beta- Naphthalenemethanol


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 Glcnac-BETA1,3-Gal-Beta- Naphthalenemethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn400

b:30.5
occ:1.00
 O1A B:UDH1399 2.1 29.2 1.0
O3B B:UDH1399 2.2 37.7 1.0
NE2 B:HIS343 2.2 30.5 1.0
NE2 B:HIS340 2.3 32.2 1.0
OD2 B:ASP250 2.3 25.1 1.0
O B:HOH3155 2.4 29.3 1.0
CG B:ASP250 3.1 25.4 1.0
CD2 B:HIS343 3.1 31.9 1.0
CE1 B:HIS343 3.2 32.0 1.0
CE1 B:HIS340 3.2 30.8 1.0
CD2 B:HIS340 3.3 30.1 1.0
PB B:UDH1399 3.4 35.7 1.0
OD1 B:ASP250 3.4 22.3 1.0
PA B:UDH1399 3.4 31.5 1.0
O3A B:UDH1399 3.7 33.7 1.0
O2B B:UDH1399 3.8 36.1 1.0
O3' B:UDH1399 4.0 26.4 1.0
O5' B:UDH1399 4.0 33.9 1.0
NZ B:LYS275 4.1 38.9 1.0
NH2 B:ARG187 4.2 24.7 1.0
NH1 B:ARG187 4.3 25.5 1.0
ND1 B:HIS343 4.3 32.2 1.0
CG B:HIS343 4.3 30.7 1.0
ND1 B:HIS340 4.4 31.8 1.0
CB B:ASP250 4.4 23.7 1.0
CG B:HIS340 4.4 29.9 1.0
O2A B:UDH1399 4.4 33.9 1.0
C3B B:UDH1399 4.8 25.1 1.0
CZ B:ARG187 4.8 28.3 1.0
O1B B:UDH1399 4.8 35.2 1.0
O B:HOH3289 4.9 43.0 1.0
C5B B:UDH1399 4.9 27.4 1.0

Manganese binding site 3 out of 3 in 3ee5

Go back to Manganese Binding Sites List in 3ee5
Manganese binding site 3 out of 3 in the Crystal Structure of Human M340H-BETA1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,3-Gal-Beta- Naphthalenemethanol


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 Glcnac-BETA1,3-Gal-Beta- Naphthalenemethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn400

b:48.3
occ:1.00
 O3B C:UDH2399 2.0 44.2 1.0
O1A C:UDH2399 2.1 53.7 1.0
O C:HOH3275 2.2 38.6 1.0
OD2 C:ASP250 2.2 38.5 1.0
NE2 C:HIS343 2.3 46.2 1.0
NE2 C:HIS340 2.4 53.9 1.0
CG C:ASP250 3.1 36.5 1.0
CE1 C:HIS343 3.2 46.2 1.0
CE1 C:HIS340 3.3 54.0 1.0
CD2 C:HIS343 3.3 47.0 1.0
OD1 C:ASP250 3.3 36.2 1.0
PB C:UDH2399 3.3 45.4 1.0
PA C:UDH2399 3.3 46.4 1.0
CD2 C:HIS340 3.4 53.5 1.0
O3A C:UDH2399 3.6 48.9 1.0
O2B C:UDH2399 3.9 48.3 1.0
O5' C:UDH2399 4.0 49.3 1.0
O3' C:UDH2399 4.1 37.5 1.0
NZ C:LYS275 4.1 56.4 1.0
NH2 C:ARG187 4.3 46.3 1.0
ND1 C:HIS340 4.4 54.3 1.0
ND1 C:HIS343 4.4 46.5 1.0
CB C:ASP250 4.4 35.9 1.0
O2A C:UDH2399 4.4 52.8 1.0
CG C:HIS343 4.4 46.5 1.0
CG C:HIS340 4.5 53.4 1.0
NH1 C:ARG187 4.6 48.8 1.0
O C:HOH3199 4.7 60.0 1.0
O1B C:UDH2399 4.7 45.0 1.0
C3B C:UDH2399 4.9 41.5 1.0
C5B C:UDH2399 4.9 45.0 1.0
CZ C:ARG187 4.9 46.1 1.0

Reference:

J.R.Brown, F.Yang, A.Sinha, B.Ramakrishnan, Y.Tor, P.K.Qasba, J.D.Esko. Deoxygenated Disaccharide Analogs As Specific Inhibitors of {Beta}1-4-Galactosyltransferase 1 and Selectin-Mediated Tumor Metastasis J.Biol.Chem. V. 284 4952 2009.
ISSN: ISSN 0021-9258
PubMed: 19106107
DOI: 10.1074/JBC.M805782200
Page generated: Sat Oct 5 16:12:58 2024

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