Magnesium in PDB 2z4t: Crystal Structure of Vibrionaceae Photobacterium Sp. Jt-Ish-224 2,6- Sialyltransferase in A Ternary Complex with Donor Product Cmp and Accepter Substrate Lactose

The structure of Crystal Structure of Vibrionaceae Photobacterium Sp. Jt-Ish-224 2,6- Sialyltransferase in A Ternary Complex with Donor Product Cmp and Accepter Substrate Lactose, PDB code: 2z4t was solved by Y.Kakuta, N.Okino, H.Kajiwara, M.Ichikawa, Y.Takakura, M.Ito, T.Yamamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.31 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.292, 90.292, 204.330, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 24.3

The binding sites of Magnesium atom in the Crystal Structure of Vibrionaceae Photobacterium Sp. Jt-Ish-224 2,6- Sialyltransferase in A Ternary Complex with Donor Product Cmp and Accepter Substrate Lactose (pdb code 2z4t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Vibrionaceae Photobacterium Sp. Jt-Ish-224 2,6- Sialyltransferase in A Ternary Complex with Donor Product Cmp and Accepter Substrate Lactose, PDB code: 2z4t:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Vibrionaceae Photobacterium Sp. Jt-Ish-224 2,6- Sialyltransferase in A Ternary Complex with Donor Product Cmp and Accepter Substrate Lactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Vibrionaceae Photobacterium Sp. Jt-Ish-224 2,6- Sialyltransferase in A Ternary Complex with Donor Product Cmp and Accepter Substrate Lactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5000 b:39.8 occ:1.00 O A:TYR349 2.5 51.1 1.0 O A:LEU354 2.7 43.3 1.0 OD1 A:ASN356 2.7 36.3 1.0 O A:SER352 2.8 49.7 1.0 OD2 A:ASP399 2.9 43.3 1.0 C A:TYR349 3.5 50.7 1.0 C A:SER352 3.5 49.8 1.0 CG A:ASN356 3.6 37.3 1.0 ND2 A:ASN356 3.7 35.3 1.0 N A:SER352 3.7 50.5 1.0 CB A:SER352 3.8 49.7 1.0 CA A:SER352 3.8 50.0 1.0 C A:LEU354 3.9 43.4 1.0 CG A:ASP399 4.1 41.4 1.0 N A:LEU354 4.2 46.0 1.0 OG A:SER352 4.3 49.0 1.0 CA A:TYR349 4.3 49.3 1.0 N A:ASN350 4.3 51.8 1.0 C A:ASN353 4.5 47.8 1.0 CA A:LEU354 4.6 44.6 1.0 N A:ASN353 4.6 49.6 1.0 O A:GLU348 4.6 48.7 1.0 CB A:ASP399 4.8 39.9 1.0 CA A:ASN350 4.8 52.8 1.0 C A:PRO355 4.9 40.1 1.0 O A:ASN353 4.9 47.6 1.0 N A:PRO355 4.9 42.1 1.0 C A:SER351 4.9 51.3 1.0 C A:ASN350 4.9 53.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Vibrionaceae Photobacterium Sp. Jt-Ish-224 2,6- Sialyltransferase in A Ternary Complex with Donor Product Cmp and Accepter Substrate Lactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Vibrionaceae Photobacterium Sp. Jt-Ish-224 2,6- Sialyltransferase in A Ternary Complex with Donor Product Cmp and Accepter Substrate Lactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5001 b:36.0 occ:1.00 O A:ALA124 2.7 37.4 1.0 OG1 A:THR128 2.7 36.8 1.0 N A:ARG153 2.9 40.8 1.0 N A:GLY152 2.9 38.8 1.0 O A:ASP122 3.2 38.5 1.0 C A:HIS123 3.4 38.5 1.0 CA A:GLY152 3.5 39.6 1.0 CB A:THR128 3.5 36.8 1.0 CB A:ARG153 3.6 42.1 1.0 O A:HIS123 3.6 39.5 1.0 C A:GLY152 3.6 39.8 1.0 N A:ALA124 3.7 37.9 1.0 CG A:ARG153 3.7 44.6 1.0 CA A:ARG153 3.7 41.9 1.0 C A:ALA124 3.8 37.6 1.0 CG2 A:THR128 3.8 36.0 1.0 CA A:HIS123 3.8 38.3 1.0 C A:ASP122 3.8 38.5 1.0 OD2 A:ASP122 3.9 38.9 1.0 C A:TRP151 3.9 38.0 1.0 N A:HIS123 4.1 38.5 1.0 CA A:TRP151 4.1 37.6 1.0 CB A:TRP151 4.2 37.4 1.0 CA A:ALA124 4.3 37.5 1.0 N A:ILE154 4.4 42.7 1.0 CG A:ASP122 4.4 38.7 1.0 C A:ARG153 4.5 42.3 1.0 CG A:TRP151 4.6 38.2 1.0 CB A:ASP122 4.7 38.6 1.0 CD1 A:TRP151 4.8 39.0 1.0 O A:GLY152 4.8 39.4 1.0 N A:SER125 4.8 37.2 1.0 CA A:ASP122 4.9 38.5 1.0 CA A:THR128 5.0 36.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Vibrionaceae Photobacterium Sp. Jt-Ish-224 2,6- Sialyltransferase in A Ternary Complex with Donor Product Cmp and Accepter Substrate Lactose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Vibrionaceae Photobacterium Sp. Jt-Ish-224 2,6- Sialyltransferase in A Ternary Complex with Donor Product Cmp and Accepter Substrate Lactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5002 b:54.7 occ:1.00 OE1 A:GLU301 2.5 47.0 1.0 OG A:SER303 2.8 45.1 1.0 N A:SER303 2.8 41.9 1.0 CB A:SER303 3.2 42.6 1.0 CB A:GLU301 3.3 41.9 1.0 N A:PRO302 3.3 41.7 1.0 C A:GLU301 3.3 41.9 1.0 CA A:GLU301 3.4 42.1 1.0 CD A:PRO302 3.4 41.5 1.0 CA A:SER303 3.5 42.4 1.0 CD A:GLU301 3.6 47.5 1.0 C A:PRO302 3.8 41.6 1.0 O A:GLU301 3.9 41.9 1.0 CD A:ARG244 4.0 40.4 1.0 O A:HOH5281 4.0 60.5 1.0 CG A:GLU301 4.0 44.5 1.0 CA A:PRO302 4.0 41.8 1.0 NH1 A:ARG244 4.2 40.0 1.0 N A:LEU304 4.3 42.0 1.0 CG A:PRO302 4.4 41.7 1.0 C A:SER303 4.4 42.1 1.0 CB A:PRO302 4.4 41.5 1.0 CG A:ARG244 4.4 40.8 1.0 OE2 A:GLU301 4.7 48.8 1.0 NE A:ARG244 4.9 40.9 1.0 N A:GLU301 4.9 42.0 1.0 O A:PRO302 5.0 41.4 1.0 CB A:ARG244 5.0 40.6 1.0 CZ A:ARG244 5.0 39.6 1.0

Y.Kakuta, N.Okino, H.Kajiwara, M.Ichikawa, Y.Takakura, M.Ito, T.Yamamoto. Crystal Structure of Vibrionaceae Photobacterium Sp. Jt-Ish-224 ALPHA2,6-Sialyltransferase in A Ternary Complex with Donor Product Cmp and Acceptor Substrate Lactose: Catalytic Mechanism and Substrate Recognition Glycobiology V. 18 66 2008.
ISSN: ISSN 0959-6658
PubMed: 17962295
DOI: 10.1093/GLYCOB/CWM119