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Manganese in PDB 4eeg: Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Gal-Beta

Enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Gal-Beta

All present enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Gal-Beta:
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 Glcnac-BETA1,6-Gal-Beta, PDB code: 4eeg 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) 47.05 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 107.365, 195.456, 143.733, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24.4

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 Glcnac-BETA1,6-Gal-Beta (pdb code 4eeg). 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 Glcnac-BETA1,6-Gal-Beta, PDB code: 4eeg:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4eeg

Go back to Manganese Binding Sites List in 4eeg
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 Glcnac-BETA1,6-Gal-Beta


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 Glcnac-BETA1,6-Gal-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:50.6
occ:1.00
 O3B A:UDP403 2.1 87.3 1.0
OD2 A:ASP250 2.2 33.7 1.0
NE2 A:HIS343 2.3 50.2 1.0
O1A A:UDP403 2.3 71.6 1.0
NE2 A:HIS340 2.5 39.1 1.0
O A:HOH555 2.8 50.5 1.0
PB A:UDP403 3.1 88.7 1.0
O3A A:UDP403 3.2 79.8 1.0
CG A:ASP250 3.2 34.8 1.0
CE1 A:HIS343 3.2 52.3 1.0
CD2 A:HIS343 3.3 49.9 1.0
PA A:UDP403 3.3 73.0 1.0
CD2 A:HIS340 3.4 43.2 1.0
CE1 A:HIS340 3.5 44.7 1.0
O2B A:UDP403 3.6 88.4 1.0
OD1 A:ASP250 3.6 36.7 1.0
O2A A:UDP403 4.1 71.9 1.0
O3' A:UDP403 4.2 41.5 1.0
NH2 A:ARG187 4.2 42.2 1.0
NH1 A:ARG187 4.3 39.2 1.0
CB A:ASP250 4.3 32.2 1.0
ND1 A:HIS343 4.4 53.2 1.0
O1B A:UDP403 4.4 87.8 1.0
CG A:HIS343 4.4 52.6 1.0
CG A:HIS340 4.6 43.5 1.0
ND1 A:HIS340 4.6 43.1 1.0
O A:HOH584 4.7 48.7 1.0
O5' A:UDP403 4.7 62.3 1.0
CZ A:ARG187 4.8 39.6 1.0
C3' A:UDP403 4.8 34.3 1.0
O A:ILE341 5.0 45.5 1.0

Manganese binding site 2 out of 3 in 4eeg

Go back to Manganese Binding Sites List in 4eeg
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 Glcnac-BETA1,6-Gal-Beta


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 Glcnac-BETA1,6-Gal-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:40.8
occ:1.00
 NE2 B:HIS340 2.1 34.3 1.0
O1A B:UDP403 2.2 68.9 1.0
NE2 B:HIS343 2.2 39.6 1.0
OD2 B:ASP250 2.4 27.9 1.0
O3B B:UDP403 2.6 87.1 1.0
CE1 B:HIS340 2.9 31.9 1.0
O3A B:UDP403 3.2 80.3 1.0
CG B:ASP250 3.2 28.6 1.0
CE1 B:HIS343 3.2 38.5 1.0
CD2 B:HIS343 3.2 41.0 1.0
CD2 B:HIS340 3.2 32.0 1.0
PA B:UDP403 3.3 73.4 1.0
PB B:UDP403 3.3 89.0 1.0
OD1 B:ASP250 3.6 29.0 1.0
O B:HOH537 3.7 31.9 1.0
O2B B:UDP403 3.8 86.1 1.0
O2A B:UDP403 4.0 74.0 1.0
ND1 B:HIS340 4.1 29.3 1.0
NH2 B:ARG187 4.1 24.2 1.0
O B:HOH612 4.1 52.8 1.0
CG B:HIS340 4.3 30.6 1.0
CB B:ASP250 4.3 25.9 1.0
ND1 B:HIS343 4.3 42.5 1.0
O3' B:UDP403 4.4 30.0 1.0
NH1 B:ARG187 4.4 22.4 1.0
CG B:HIS343 4.4 41.0 1.0
NZ B:LYS275 4.6 38.0 1.0
O1B B:UDP403 4.7 86.2 1.0
O5' B:UDP403 4.7 59.1 1.0
CZ B:ARG187 4.7 30.0 1.0
O B:ILE341 4.9 28.2 1.0
C3' B:UDP403 5.0 29.3 1.0

Manganese binding site 3 out of 3 in 4eeg

Go back to Manganese Binding Sites List in 4eeg
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 Glcnac-BETA1,6-Gal-Beta


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 Glcnac-BETA1,6-Gal-Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn404

b:61.4
occ:1.00
 OD2 C:ASP250 2.1 48.8 1.0
O3B C:UDP403 2.2 97.7 1.0
NE2 C:HIS343 2.2 55.0 1.0
O1A C:UDP403 2.3 89.3 1.0
NE2 C:HIS340 2.4 58.9 1.0
O C:HOH542 3.1 49.9 1.0
CG C:ASP250 3.1 42.7 1.0
CE1 C:HIS343 3.1 55.7 1.0
CD2 C:HIS343 3.2 55.4 1.0
CD2 C:HIS340 3.3 56.4 1.0
PB C:UDP403 3.3 99.3 1.0
CE1 C:HIS340 3.4 59.0 1.0
PA C:UDP403 3.4 87.2 1.0
OD1 C:ASP250 3.6 41.4 1.0
O3A C:UDP403 3.7 93.5 1.0
O2B C:UDP403 3.8 99.1 1.0
O C:HOH605 3.8 54.4 1.0
O2A C:UDP403 3.9 88.7 1.0
NH2 C:ARG187 4.0 48.8 1.0
O3' C:UDP403 4.2 41.0 1.0
ND1 C:HIS343 4.3 54.3 1.0
CB C:ASP250 4.3 39.6 1.0
CG C:HIS343 4.4 56.6 1.0
NZ C:LYS275 4.4 62.0 1.0
NH1 C:ARG187 4.5 50.1 1.0
ND1 C:HIS340 4.5 59.6 1.0
CG C:HIS340 4.5 54.9 1.0
O1B C:UDP403 4.6 98.6 1.0
CZ C:ARG187 4.7 51.2 1.0
O5' C:UDP403 4.8 78.2 1.0
O C:ILE341 4.9 54.6 1.0
C3' C:UDP403 4.9 47.4 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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