Magnesium in PDB 6wmn: 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: 6wmn 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) 44.07 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.210, 79.810, 157.790, 90.00, 97.89, 90.00
R / Rfree (%) 21.8 / 23.2

Other elements in 6wmn:

The structure of Human Poly-N-Acetyl-Lactosamine Synthase Structure Demonstrates A Modular Assembly of Catalytic Subsites For Gt-A Glycosyltransferases also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

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 6wmn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 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: 6wmn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6wmn

Go back to Magnesium Binding Sites List in 6wmn
Magnesium binding site 1 out of 4 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:38.4
occ:1.00
 O A:HOH530 2.0 40.4 1.0
O A:HOH501 2.1 39.5 1.0
NE2 A:HIS376 2.1 68.5 1.0
O2A A:UDP402 2.2 42.9 1.0
O2B A:UDP402 2.2 49.8 1.0
OD2 A:ASP247 2.3 52.1 1.0
CD2 A:HIS376 3.0 64.0 1.0
CE1 A:HIS376 3.1 65.0 1.0
CG A:ASP247 3.2 50.2 1.0
OD1 A:ASP247 3.4 52.2 1.0
PA A:UDP402 3.4 45.7 1.0
PB A:UDP402 3.5 50.9 1.0
O3A A:UDP402 3.7 50.3 1.0
O A:HOH528 4.1 45.8 1.0
C5' A:UDP402 4.1 44.5 1.0
ND1 A:HIS376 4.2 66.0 1.0
CG A:HIS376 4.2 64.4 1.0
O5' A:UDP402 4.2 46.8 1.0
O1B A:UDP402 4.3 52.2 1.0
OD2 A:ASP245 4.4 44.5 1.0
O1A A:UDP402 4.6 44.2 1.0
CB A:ASP247 4.6 47.0 1.0
O3B A:UDP402 4.6 52.4 1.0
CB A:SER377 4.8 50.0 1.0

Magnesium binding site 2 out of 4 in 6wmn

Go back to Magnesium Binding Sites List in 6wmn
Magnesium binding site 2 out of 4 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:37.5
occ:1.00
 O B:HOH502 2.1 38.6 1.0
O B:HOH546 2.1 39.0 1.0
NE2 B:HIS376 2.1 67.8 1.0
O1A B:UDP402 2.2 44.0 1.0
O2B B:UDP402 2.2 51.4 1.0
OD2 B:ASP247 2.3 46.1 1.0
CD2 B:HIS376 3.1 62.9 1.0
CE1 B:HIS376 3.1 64.4 1.0
CG B:ASP247 3.2 44.7 1.0
OD1 B:ASP247 3.4 43.9 1.0
PA B:UDP402 3.5 46.5 1.0
PB B:UDP402 3.5 51.1 1.0
O3A B:UDP402 3.8 49.7 1.0
C5' B:UDP402 4.2 45.7 1.0
ND1 B:HIS376 4.2 64.3 1.0
CG B:HIS376 4.2 62.1 1.0
O B:HOH524 4.3 50.8 1.0
O5' B:UDP402 4.3 46.8 1.0
OD2 B:ASP245 4.4 45.9 1.0
O3B B:UDP402 4.5 52.7 1.0
O1B B:UDP402 4.6 50.8 1.0
O2A B:UDP402 4.6 45.2 1.0
CB B:ASP247 4.6 43.1 1.0
CB B:SER377 4.9 43.3 1.0

Magnesium binding site 3 out of 4 in 6wmn

Go back to Magnesium Binding Sites List in 6wmn
Magnesium binding site 3 out of 4 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 3 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
C:Mg401

b:42.5
occ:1.00
 O C:HOH546 2.1 44.0 1.0
O C:HOH501 2.1 39.3 1.0
O2A C:UDP402 2.2 44.0 1.0
O2B C:UDP402 2.2 47.6 1.0
NE2 C:HIS376 2.2 41.0 1.0
OD2 C:ASP247 2.4 46.2 1.0
CD2 C:HIS376 3.1 39.3 1.0
CE1 C:HIS376 3.3 42.0 1.0
CG C:ASP247 3.3 43.7 1.0
PA C:UDP402 3.4 45.9 1.0
OD1 C:ASP247 3.5 43.1 1.0
PB C:UDP402 3.5 47.1 1.0
O3A C:UDP402 3.7 46.8 1.0
C5' C:UDP402 4.2 42.0 1.0
O5' C:UDP402 4.2 44.3 1.0
O1B C:UDP402 4.3 48.2 1.0
CG C:HIS376 4.3 39.5 1.0
ND1 C:HIS376 4.3 41.4 1.0
OD2 C:ASP245 4.4 38.1 1.0
O1A C:UDP402 4.6 44.4 1.0
O3B C:UDP402 4.7 47.5 1.0
CB C:ASP247 4.7 41.2 1.0
CB C:SER377 4.8 37.8 1.0

Magnesium binding site 4 out of 4 in 6wmn

Go back to Magnesium Binding Sites List in 6wmn
Magnesium binding site 4 out of 4 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 4 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
D:Mg401

b:39.9
occ:1.00
 O D:HOH529 2.1 40.3 1.0
NE2 D:HIS376 2.1 82.2 1.0
O1A D:UDP402 2.2 45.8 1.0
O2B D:UDP402 2.2 52.3 1.0
O D:HOH502 2.2 39.7 1.0
OD2 D:ASP247 2.3 55.3 1.0
CD2 D:HIS376 3.1 79.6 1.0
CE1 D:HIS376 3.1 80.9 1.0
CG D:ASP247 3.2 55.0 1.0
PA D:UDP402 3.5 48.9 1.0
OD1 D:ASP247 3.5 55.1 1.0
PB D:UDP402 3.5 54.3 1.0
O3A D:UDP402 3.8 51.1 1.0
O D:HOH535 4.1 67.0 1.0
ND1 D:HIS376 4.2 82.9 1.0
O3B D:UDP402 4.2 58.2 1.0
C5' D:UDP402 4.2 46.8 1.0
CG D:HIS376 4.3 80.4 1.0
O5' D:UDP402 4.3 48.3 1.0
OD2 D:ASP245 4.5 52.5 1.0
O2A D:UDP402 4.5 50.0 1.0
CB D:ASP247 4.6 53.9 1.0
O1B D:UDP402 4.7 55.6 1.0
CB D:SER377 4.7 61.1 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 Dec 15 01:35:59 2020

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