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Magnesium in PDB 6wmo: Human Poly-N-Acetyl-Lactosamine Synthase Structure Demonstrates A Modular Assembly of Catalytic Subsites For Gt-A Glycosyltransferases

Enzymatic activity of Human Poly-N-Acetyl-Lactosamine Synthase Structure Demonstrates A Modular Assembly of Catalytic Subsites For Gt-A Glycosyltransferases

All present enzymatic activity of Human Poly-N-Acetyl-Lactosamine Synthase Structure Demonstrates A Modular Assembly of Catalytic Subsites For Gt-A Glycosyltransferases:
2.4.1.149;

Protein crystallography data

The structure of Human Poly-N-Acetyl-Lactosamine Synthase Structure Demonstrates A Modular Assembly of Catalytic Subsites For Gt-A Glycosyltransferases, PDB code: 6wmo was solved by R.Kadirvelraj, Z.A.Wood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.85 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.190, 109.280, 147.550, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Poly-N-Acetyl-Lactosamine Synthase Structure Demonstrates A Modular Assembly of Catalytic Subsites For Gt-A Glycosyltransferases (pdb code 6wmo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Poly-N-Acetyl-Lactosamine Synthase Structure Demonstrates A Modular Assembly of Catalytic Subsites For Gt-A Glycosyltransferases, PDB code: 6wmo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6wmo

Go back to Magnesium Binding Sites List in 6wmo
Magnesium binding site 1 out of 2 in the Human Poly-N-Acetyl-Lactosamine Synthase Structure Demonstrates A Modular Assembly of Catalytic Subsites For Gt-A Glycosyltransferases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Poly-N-Acetyl-Lactosamine Synthase Structure Demonstrates A Modular Assembly of Catalytic Subsites For Gt-A Glycosyltransferases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:38.9
occ:1.00
 O A:HOH511 2.0 41.5 1.0
O A:HOH573 2.1 46.8 1.0
O2B A:UDP402 2.1 36.0 1.0
O1A A:UDP402 2.1 38.0 1.0
NE2 A:HIS376 2.3 39.8 1.0
OD2 A:ASP247 2.5 47.9 1.0
CD2 A:HIS376 3.2 39.9 1.0
PB A:UDP402 3.2 42.0 1.0
CE1 A:HIS376 3.3 46.0 1.0
PA A:UDP402 3.4 42.2 1.0
CG A:ASP247 3.5 46.3 1.0
O3A A:UDP402 3.6 42.6 1.0
O3B A:UDP402 3.7 50.0 1.0
OD1 A:ASP247 3.7 42.6 1.0
O A:HOH517 4.1 40.8 1.0
O5' A:UDP402 4.2 38.2 1.0
C5' A:UDP402 4.3 29.6 1.0
CG A:HIS376 4.4 37.9 1.0
ND1 A:HIS376 4.4 43.1 1.0
O2A A:UDP402 4.5 42.7 1.0
O1B A:UDP402 4.6 45.9 1.0
OD2 A:ASP245 4.6 39.8 1.0
CB A:SER377 4.8 39.0 1.0
CB A:ASP247 4.9 38.5 1.0

Magnesium binding site 2 out of 2 in 6wmo

Go back to Magnesium Binding Sites List in 6wmo
Magnesium binding site 2 out of 2 in the Human Poly-N-Acetyl-Lactosamine Synthase Structure Demonstrates A Modular Assembly of Catalytic Subsites For Gt-A Glycosyltransferases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Poly-N-Acetyl-Lactosamine Synthase Structure Demonstrates A Modular Assembly of Catalytic Subsites For Gt-A Glycosyltransferases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:41.7
occ:1.00
 O2B B:UDP402 1.9 39.4 1.0
O1 B:EDO412 2.0 49.3 0.9
O B:HOH502 2.1 35.6 1.0
NE2 B:HIS376 2.2 42.3 1.0
O2A B:UDP402 2.2 48.4 1.0
O2 B:EDO412 2.3 50.1 0.9
C2 B:EDO412 2.9 48.5 0.9
C1 B:EDO412 3.0 47.0 0.9
PB B:UDP402 3.0 40.5 1.0
CE1 B:HIS376 3.1 47.0 1.0
CD2 B:HIS376 3.2 40.3 1.0
PA B:UDP402 3.3 40.7 1.0
O3A B:UDP402 3.4 44.1 1.0
O1B B:UDP402 3.4 42.6 1.0
OD2 B:ASP247 3.9 46.3 1.0
O2 B:EDO414 4.0 60.3 0.9
O B:HOH508 4.1 46.3 1.0
OD1 B:ASP247 4.1 41.3 1.0
C5' B:UDP402 4.1 34.8 1.0
O5' B:UDP402 4.1 39.0 1.0
OD2 B:ASP245 4.2 42.0 1.0
ND1 B:HIS376 4.3 44.4 1.0
CG B:HIS376 4.4 46.5 1.0
O3B B:UDP402 4.4 41.3 1.0
CG B:ASP247 4.4 43.8 1.0
O1A B:UDP402 4.5 40.0 1.0
CB B:SER377 4.9 47.5 1.0
C2 B:EDO414 5.0 51.4 0.9

Reference:

R.Kadirvelraj, J.Y.Yang, H.W.Kim, J.H.Sanders, K.W.Moremen, Z.A.Wood. Comparison of Human Poly-N-Acetyl-Lactosamine Synthase Structure with Gt-A Fold Glycosyltransferases Supports A Modular Assembly of Catalytic Subsites. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33229435
DOI: 10.1074/JBC.RA120.015305
Page generated: Tue Oct 1 23:02:14 2024

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