Atomistry » Magnesium » PDB 6whm-6wpf » 6wmn
Atomistry »
  Magnesium »
    PDB 6whm-6wpf »
      6wmn »

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 Oct 1 23:02:15 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy