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Cobalt in PDB 5nrd: A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (A-3GALT) Supports A Conserved Reaction Mechanism For Retaining Glycosyltransferases - Alpha-3GALT in Complex with CO2+, Udp-Gal and Lactose - A3GALT-CO2+-Udp-Gal-Lat-2

Enzymatic activity of A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (A-3GALT) Supports A Conserved Reaction Mechanism For Retaining Glycosyltransferases - Alpha-3GALT in Complex with CO2+, Udp-Gal and Lactose - A3GALT-CO2+-Udp-Gal-Lat-2

All present enzymatic activity of A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (A-3GALT) Supports A Conserved Reaction Mechanism For Retaining Glycosyltransferases - Alpha-3GALT in Complex with CO2+, Udp-Gal and Lactose - A3GALT-CO2+-Udp-Gal-Lat-2:
2.4.1.87;

Protein crystallography data

The structure of A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (A-3GALT) Supports A Conserved Reaction Mechanism For Retaining Glycosyltransferases - Alpha-3GALT in Complex with CO2+, Udp-Gal and Lactose - A3GALT-CO2+-Udp-Gal-Lat-2, PDB code: 5nrd was solved by D.Albesa-Jove, A.Marina, M.A.Sainz-Polo, M.E.Guerin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.32 / 2.12
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.414, 65.694, 83.014, 90.00, 102.89, 90.00
R / Rfree (%) 21.2 / 24.9

Cobalt Binding Sites:

The binding sites of Cobalt atom in the A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (A-3GALT) Supports A Conserved Reaction Mechanism For Retaining Glycosyltransferases - Alpha-3GALT in Complex with CO2+, Udp-Gal and Lactose - A3GALT-CO2+-Udp-Gal-Lat-2 (pdb code 5nrd). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (A-3GALT) Supports A Conserved Reaction Mechanism For Retaining Glycosyltransferases - Alpha-3GALT in Complex with CO2+, Udp-Gal and Lactose - A3GALT-CO2+-Udp-Gal-Lat-2, PDB code: 5nrd:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 5nrd

Go back to Cobalt Binding Sites List in 5nrd
Cobalt binding site 1 out of 2 in the A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (A-3GALT) Supports A Conserved Reaction Mechanism For Retaining Glycosyltransferases - Alpha-3GALT in Complex with CO2+, Udp-Gal and Lactose - A3GALT-CO2+-Udp-Gal-Lat-2


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (A-3GALT) Supports A Conserved Reaction Mechanism For Retaining Glycosyltransferases - Alpha-3GALT in Complex with CO2+, Udp-Gal and Lactose - A3GALT-CO2+-Udp-Gal-Lat-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:50.3
occ:0.74
 O A:HOH546 2.2 62.5 1.0
O1A A:GDU403 2.3 45.4 0.7
OD1 A:ASP227 2.4 52.7 1.0
O1B A:GDU403 2.4 50.4 0.7
OD2 A:ASP225 2.4 41.7 1.0
OD2 A:ASP227 2.7 53.5 1.0
CG A:ASP227 2.9 50.5 1.0
HB3 A:ASP225 2.9 47.0 1.0
NZ A:LYS359 3.1 70.0 1.0
CG A:ASP225 3.3 44.6 1.0
HO3' A:GDU403 3.3 52.5 0.7
CB A:ASP225 3.4 39.2 1.0
PA A:GDU403 3.5 53.1 0.7
HB2 A:ASP225 3.5 47.0 1.0
PB A:GDU403 3.5 48.3 0.7
O2' A:GDU403 3.6 47.7 0.7
O3D A:GDU403 3.6 43.7 0.7
H5'1 A:GDU403 3.6 56.4 0.7
O3A A:GDU403 3.7 45.8 0.7
O A:HOH507 3.9 49.4 1.0
H3' A:GDU403 4.0 58.4 0.7
HB2 A:ALA282 4.0 30.4 1.0
HO2A A:GDU403 4.1 57.3 0.7
O2B A:GDU403 4.3 60.4 0.7
HO3A A:GDU403 4.3 50.5 0.7
H A:ASP227 4.3 34.9 1.0
CB A:ASP227 4.4 41.7 1.0
OD1 A:ASP225 4.4 38.9 1.0
C5D A:GDU403 4.5 47.0 0.7
H3D A:GDU403 4.5 57.6 0.7
HB1 A:ALA282 4.5 30.4 1.0
O2A A:GDU403 4.5 55.6 0.7
O5D A:GDU403 4.5 49.9 0.7
HE2 A:HIS280 4.6 40.0 1.0
CE A:LYS359 4.6 74.7 1.0
C3D A:GDU403 4.6 48.0 0.7
C3' A:GDU403 4.7 48.6 0.7
C2' A:GDU403 4.7 49.2 0.7
CB A:ALA282 4.7 25.4 1.0
O A:ASP227 4.7 36.9 1.0
HB3 A:ASP227 4.8 50.0 1.0
O3' A:GDU403 4.8 42.1 0.7
HB2 A:ASP227 4.8 50.0 1.0
O3B A:GDU403 4.9 58.8 0.7
CA A:ASP225 4.9 30.5 1.0
HG2 A:GLN228 4.9 42.2 1.0
HA A:ALA282 4.9 36.1 1.0
C4D A:GDU403 4.9 44.9 0.7

Cobalt binding site 2 out of 2 in 5nrd

Go back to Cobalt Binding Sites List in 5nrd
Cobalt binding site 2 out of 2 in the A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (A-3GALT) Supports A Conserved Reaction Mechanism For Retaining Glycosyltransferases - Alpha-3GALT in Complex with CO2+, Udp-Gal and Lactose - A3GALT-CO2+-Udp-Gal-Lat-2


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (A-3GALT) Supports A Conserved Reaction Mechanism For Retaining Glycosyltransferases - Alpha-3GALT in Complex with CO2+, Udp-Gal and Lactose - A3GALT-CO2+-Udp-Gal-Lat-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co401

b:58.8
occ:0.74
 O B:HOH514 2.1 45.2 1.0
O1A B:GDU402 2.3 47.6 0.7
O1B B:GDU402 2.4 51.2 0.7
OD2 B:ASP227 2.4 55.5 1.0
O B:HOH577 2.8 55.0 1.0
OD1 B:ASP227 2.8 46.7 1.0
CG B:ASP227 2.9 46.0 1.0
PB B:GDU402 3.3 47.6 0.7
PA B:GDU402 3.4 47.6 0.7
O3A B:GDU402 3.5 42.9 0.7
O B:HOH526 3.5 56.5 1.0
O3B B:GDU402 3.7 58.1 0.7
HO3' B:GDU402 3.9 54.5 0.7
O B:HOH585 3.9 58.0 1.0
OD2 B:ASP225 3.9 47.1 1.0
O2A B:GDU402 4.1 50.0 0.7
H5'1 B:GDU402 4.2 53.0 0.7
HB3 B:ASP225 4.2 48.2 1.0
CB B:ASP227 4.3 46.1 1.0
HB2 B:ASP227 4.4 55.3 1.0
O3D B:GDU402 4.5 45.4 0.7
HOA2 B:GDU402 4.6 60.1 0.7
O2B B:GDU402 4.7 55.4 0.7
O5D B:GDU402 4.7 44.4 0.7
HB3 B:ASP227 4.7 55.3 1.0
H3D B:GDU402 4.8 60.0 0.7
CG B:ASP225 4.8 45.3 1.0
O B:ASP227 4.8 42.4 1.0
CB B:ASP225 4.9 40.2 1.0
H3' B:GDU402 4.9 56.4 0.7
C1' B:GDU402 4.9 50.6 0.7
H B:ASP227 4.9 44.1 1.0
O2' B:GDU402 4.9 44.6 0.7
C5D B:GDU402 5.0 44.1 0.7
HB2 B:ASP225 5.0 48.2 1.0

Reference:

D.Albesa-Jove, M.A.Sainz-Polo, A.Marina, M.E.Guerin. Structural Snapshots of Alpha-1,3-Galactosyltransferase with Native Substrates: Insight Into the Catalytic Mechanism of Retaining Glycosyltransferases. Angew. Chem. Int. Ed. Engl. V. 56 14853 2017.
ISSN: ESSN 1521-3773
PubMed: 28960760
DOI: 10.1002/ANIE.201707922
Page generated: Sun Dec 13 10:48:21 2020

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