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Magnesium in PDB 6wmm: 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: 6wmm 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) 35.86 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.730, 110.920, 147.400, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 19.8

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 6wmm). 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: 6wmm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6wmm

Go back to Magnesium Binding Sites List in 6wmm
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:31.5
occ:1.00
 O2B A:UDP402 2.0 33.6 1.0
O A:HOH644 2.1 31.3 1.0
O1A A:UDP402 2.1 32.9 1.0
O A:HOH513 2.1 27.8 1.0
NE2 A:HIS376 2.3 32.7 1.0
OD2 A:ASP247 2.3 28.3 1.0
PB A:UDP402 3.1 40.6 1.0
CD2 A:HIS376 3.3 30.8 1.0
CG A:ASP247 3.3 24.7 1.0
PA A:UDP402 3.3 35.0 1.0
CE1 A:HIS376 3.3 34.3 1.0
O3A A:UDP402 3.4 37.5 1.0
OD1 A:ASP247 3.5 25.5 1.0
O A:HOH504 3.5 44.1 1.0
O3B A:UDP402 3.7 40.9 1.0
O A:HOH549 4.2 38.4 1.0
C5' A:UDP402 4.3 29.6 1.0
O5' A:UDP402 4.3 32.8 1.0
O A:HOH542 4.3 42.1 1.0
O2A A:UDP402 4.4 33.5 1.0
ND1 A:HIS376 4.4 33.4 1.0
CG A:HIS376 4.4 31.2 1.0
O1B A:UDP402 4.5 42.9 1.0
OD2 A:ASP245 4.5 25.7 1.0
O A:HOH584 4.6 51.0 1.0
CB A:ASP247 4.7 23.3 1.0
O A:HOH510 4.9 55.4 1.0
CB A:SER377 5.0 30.1 1.0

Magnesium binding site 2 out of 2 in 6wmm

Go back to Magnesium Binding Sites List in 6wmm
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:26.6
occ:1.00
 O2B B:UDP402 2.0 30.6 1.0
O B:HOH654 2.1 25.5 1.0
O B:HOH516 2.1 21.6 1.0
O2A B:UDP402 2.1 32.2 1.0
NE2 B:HIS376 2.3 21.8 1.0
OD2 B:ASP247 2.3 25.6 1.0
CG B:ASP247 3.2 22.0 1.0
CD2 B:HIS376 3.2 23.9 1.0
CE1 B:HIS376 3.2 22.4 1.0
PB B:UDP402 3.3 39.0 1.0
OD1 B:ASP247 3.4 23.8 1.0
PA B:UDP402 3.4 32.6 1.0
O B:HOH506 3.5 37.9 1.0
O3A B:UDP402 3.6 32.7 1.0
O1B B:UDP402 4.0 40.7 1.0
O B:HOH501 4.2 60.1 1.0
O B:HOH621 4.2 38.6 1.0
O B:HOH646 4.3 37.3 1.0
O5' B:UDP402 4.3 30.7 1.0
C5' B:UDP402 4.3 29.0 1.0
ND1 B:HIS376 4.4 24.6 1.0
CG B:HIS376 4.4 22.5 1.0
O B:HOH610 4.5 48.1 1.0
O1A B:UDP402 4.5 30.2 1.0
OD2 B:ASP245 4.5 24.6 1.0
O3B B:UDP402 4.6 39.4 1.0
CB B:ASP247 4.6 19.3 1.0
CB B:SER377 5.0 22.2 1.0

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 23:01:51 2024

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