Zinc in PDB 2wvk: Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein

All present enzymatic activity of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein:
2.4.1.217;

The structure of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein, PDB code: 2wvk was solved by S.Goncalves, N.Borges, A.M.Esteves, B.Victor, C.M.Soares, H.Santos, P.M.Matias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.91 / 2.97
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	113.456, 113.456, 195.982, 90.00, 90.00, 90.00
R / Rfree (%)	19.779 / 26.636

The binding sites of Zinc atom in the Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein (pdb code 2wvk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein, PDB code: 2wvk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1393 b:90.1 occ:1.00 OE2 A:GLU19 2.1 74.7 1.0 ND1 A:HIS8 2.2 72.2 1.0 O A:HOH2043 2.5 53.4 1.0 OE1 A:GLU19 2.6 72.3 1.0 CD A:GLU19 2.6 73.0 1.0 CE1 A:HIS8 3.0 70.8 1.0 CG A:HIS8 3.1 70.4 1.0 OD1 A:ASN7 3.4 72.7 1.0 CB A:HIS8 3.4 70.4 1.0 NE2 A:HIS8 4.0 71.0 1.0 CG A:GLU19 4.1 71.2 1.0 CD2 A:HIS8 4.1 71.0 1.0 N A:HIS8 4.1 70.5 1.0 CG A:ASN7 4.2 72.0 1.0 CB A:ASN7 4.4 70.8 1.0 CA A:HIS8 4.4 70.4 1.0 C A:ASN7 4.8 70.5 1.0 CB A:GLU19 4.9 70.1 1.0

Zinc binding site 2 out of 5 in the Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1394 b:92.6 occ:1.00 OE1 A:GLU251 2.0 76.3 1.0 ND1 A:HIS309 2.1 72.5 1.0 NE2 A:HIS311 2.2 70.7 1.0 O A:HOH2044 2.6 66.9 1.0 CE1 A:HIS309 2.9 74.7 1.0 CD A:GLU251 3.0 73.2 1.0 CE1 A:HIS311 3.0 70.1 1.0 CG A:HIS309 3.1 72.6 1.0 CD2 A:HIS311 3.2 72.3 1.0 CG A:GLU251 3.4 71.9 1.0 CB A:HIS309 3.6 67.7 1.0 OE2 A:GLU251 4.0 73.9 1.0 NE2 A:HIS309 4.1 73.3 1.0 ND1 A:HIS311 4.1 77.5 1.0 CD2 A:HIS309 4.2 75.2 1.0 CG A:HIS311 4.2 75.3 1.0 CE2 A:TYR179 4.2 70.7 1.0 CB A:GLU251 4.4 71.8 1.0 CA A:HIS309 4.6 70.8 1.0 O A:HOH2027 4.8 67.5 1.0 OH A:TYR179 4.8 71.2 1.0 CZ A:TYR179 4.8 71.3 1.0 CB A:ASP167 4.8 70.6 1.0 OD2 A:ASP167 4.9 72.2 1.0 CD2 A:TYR179 4.9 70.5 1.0

Zinc binding site 3 out of 5 in the Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1392 b:90.8 occ:1.00 OE2 B:GLU19 1.9 71.9 1.0 OD1 B:ASP242 2.1 70.8 1.0 NE2 B:HIS8 2.2 70.0 1.0 OD2 B:ASP242 2.5 75.5 1.0 O B:HOH2029 2.5 69.1 1.0 CG B:ASP242 2.6 71.0 1.0 CD2 B:HIS8 2.9 70.5 1.0 CD B:GLU19 3.1 71.8 1.0 CE1 B:HIS8 3.3 67.5 1.0 O B:HOH2020 3.5 62.3 1.0 CG B:GLU19 3.8 70.4 1.0 OE1 B:GLU19 4.0 73.2 1.0 NZ B:LYS245 4.0 70.9 1.0 CB B:ASP242 4.1 68.2 1.0 CG B:HIS8 4.2 71.8 1.0 ND1 B:HIS8 4.3 68.8 1.0 N B:VAL243 4.6 70.3 1.0 C B:ASP242 4.6 68.8 1.0 CB B:GLU19 4.7 70.8 1.0 CA B:ASP242 4.8 70.0 1.0 CA B:VAL243 4.9 73.9 1.0

Zinc binding site 4 out of 5 in the Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1393 b:94.9 occ:1.00 OE1 B:GLU251 2.1 76.1 1.0 ND1 B:HIS309 2.2 77.8 1.0 NE2 B:HIS311 2.3 71.5 1.0 CE1 B:HIS309 3.0 74.2 1.0 CD B:GLU251 3.0 73.6 1.0 CD2 B:HIS311 3.1 74.3 1.0 CG B:HIS309 3.2 75.2 1.0 CE1 B:HIS311 3.3 74.0 1.0 OE2 B:GLU251 3.4 75.4 1.0 CB B:HIS309 3.5 67.1 1.0 CE1 B:TYR179 4.1 72.2 1.0 NE2 B:HIS309 4.1 74.1 1.0 CD2 B:HIS309 4.2 74.5 1.0 CG B:HIS311 4.3 77.5 1.0 CG B:GLU251 4.3 71.4 1.0 ND1 B:HIS311 4.3 78.3 1.0 OH B:TYR179 4.5 75.4 1.0 CB B:GLU251 4.5 69.6 1.0 CZ B:TYR179 4.7 73.9 1.0 CA B:HIS309 4.7 70.5 1.0 CD1 B:TYR179 5.0 72.9 1.0

Zinc binding site 5 out of 5 in the Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 Apoprotein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1394 b:91.8 occ:1.00 OE1 B:GLU292 2.0 67.4 1.0 NE2 B:HIS296 2.0 67.3 1.0 CE1 B:HIS296 2.7 69.0 1.0 CD B:GLU292 2.8 67.7 1.0 OE2 B:GLU292 3.0 67.3 1.0 CD2 B:HIS296 3.2 69.3 1.0 ND1 B:HIS296 3.9 70.6 1.0 CG B:GLU292 4.1 69.3 1.0 CG B:HIS296 4.2 70.3 1.0 CB B:GLU292 4.5 69.0 1.0 O B:HOH2023 4.6 89.4 1.0 CA B:GLU292 4.7 70.8 1.0 CG B:GLN295 4.9 70.1 1.0

S.Goncalves, N.Borges, A.M.Esteves, B.Victor, C.M.Soares, H.Santos, P.M.Matias. Structural Analysis of Thermus Thermophilus HB27 Mannosyl-3-Phosphoglycerate Synthase Provides Evidence For A Second Catalytic Metal Ion and New Insight Into the Retaining Mechanism of Glycosyltransferases. J.Biol.Chem. V. 285 17857 2010.
ISSN: ISSN 0021-9258
PubMed: 20356840
DOI: 10.1074/JBC.M109.095976