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Zinc in PDB 2wvl: Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II)

Enzymatic activity of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II)

All present enzymatic activity of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II):
2.4.1.217;

Protein crystallography data

The structure of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II), PDB code: 2wvl 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) 45.08 / 2.81
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 (%) 17.27 / 23.396

Other elements in 2wvl:

The structure of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II) (pdb code 2wvl). 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 in Complex with Gdp-Alpha-D-Mannose and Mg(II), PDB code: 2wvl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 2wvl

Go back to Zinc Binding Sites List in 2wvl
Zinc binding site 1 out of 5 in the Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II)


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 in Complex with Gdp-Alpha-D-Mannose and Mg(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1392

b:93.2
occ:1.00
 OE1 A:GLU19 2.0 79.8 1.0
ND1 A:HIS8 2.1 71.0 1.0
O A:HOH2016 2.1 30.7 1.0
OE2 A:GLU19 2.2 68.3 1.0
CD A:GLU19 2.3 71.0 1.0
CE1 A:HIS8 2.7 67.7 1.0
CG A:HIS8 3.2 65.7 1.0
CB A:HIS8 3.9 63.8 1.0
N A:HIS8 3.9 63.9 1.0
CG A:GLU19 3.9 62.2 1.0
NE2 A:HIS8 3.9 65.4 1.0
CB A:ASN7 4.0 66.1 1.0
ND2 A:ASN7 4.0 68.1 1.0
CD2 A:HIS8 4.2 66.5 1.0
CA A:HIS8 4.5 63.6 1.0
C A:ASN7 4.5 64.8 1.0
CG A:ASN7 4.6 67.5 1.0
CB A:GLU19 4.6 57.3 1.0
CA A:ASN7 4.8 65.6 1.0

Zinc binding site 2 out of 5 in 2wvl

Go back to Zinc Binding Sites List in 2wvl
Zinc binding site 2 out of 5 in the Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II)


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 in Complex with Gdp-Alpha-D-Mannose and Mg(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1393

b:0.9
occ:1.00
 OE1 A:GLU251 2.2 80.6 1.0
NE2 A:HIS311 2.2 85.5 1.0
ND1 A:HIS309 2.5 92.9 1.0
O A:HOH2017 2.7 65.2 1.0
CD A:GLU251 2.8 77.6 1.0
CE1 A:HIS309 2.9 56.5 1.0
CD2 A:HIS311 3.1 0.5 1.0
OE2 A:GLU251 3.1 79.9 1.0
CE1 A:HIS311 3.2 71.4 1.0
O A:HOH2015 3.4 56.2 1.0
CG A:HIS309 3.6 0.9 1.0
CG A:GLU251 4.0 70.8 1.0
NE2 A:HIS309 4.1 0.1 1.0
CG A:HIS311 4.2 0.1 1.0
ND1 A:HIS311 4.2 0.5 1.0
CB A:HIS309 4.2 0.8 1.0
O A:HOH2013 4.4 68.9 1.0
CD2 A:HIS309 4.4 80.8 1.0
CB A:GLU251 4.6 68.5 1.0
N A:GLU251 4.6 68.7 1.0
CE2 A:TYR179 4.9 65.5 1.0
OD1 A:ASP167 5.0 77.0 1.0

Zinc binding site 3 out of 5 in 2wvl

Go back to Zinc Binding Sites List in 2wvl
Zinc binding site 3 out of 5 in the Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II)


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 in Complex with Gdp-Alpha-D-Mannose and Mg(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1392

b:79.8
occ:1.00
 OE1 B:GLU19 2.0 70.9 1.0
NE2 B:HIS8 2.1 60.6 1.0
OD1 B:ASP242 2.1 37.7 1.0
OD2 B:ASP242 2.5 60.2 1.0
CG B:ASP242 2.6 93.9 1.0
O B:HOH2018 2.7 37.5 1.0
CD2 B:HIS8 2.8 38.7 1.0
CD B:GLU19 3.0 90.1 1.0
CE1 B:HIS8 3.3 53.3 1.0
CG B:GLU19 3.6 68.7 1.0
OE2 B:GLU19 4.0 61.5 1.0
CG B:HIS8 4.0 66.6 1.0
CB B:ASP242 4.2 37.5 1.0
ND1 B:HIS8 4.3 58.1 1.0
NZ B:LYS245 4.5 57.3 1.0
CB B:GLU19 4.5 42.1 1.0
C B:ASP242 4.7 57.9 1.0
OD1 B:ASN7 4.9 0.9 1.0
O B:ASP242 4.9 93.2 1.0
CA B:ASP242 4.9 36.4 1.0
N B:VAL243 5.0 42.6 1.0

Zinc binding site 4 out of 5 in 2wvl

Go back to Zinc Binding Sites List in 2wvl
Zinc binding site 4 out of 5 in the Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II)


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 in Complex with Gdp-Alpha-D-Mannose and Mg(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1393

b:0.7
occ:1.00
 NE2 B:HIS311 2.3 79.6 1.0
O B:HOH2019 2.4 61.8 1.0
OE1 B:GLU251 2.4 86.4 1.0
ND1 B:HIS309 2.8 0.1 1.0
CD B:GLU251 2.8 56.5 1.0
OE2 B:GLU251 3.0 0.5 1.0
CE1 B:HIS311 3.1 72.4 1.0
CE1 B:HIS309 3.3 59.9 1.0
CD2 B:HIS311 3.4 0.2 1.0
O B:HOH2015 3.5 80.9 1.0
CG B:HIS309 3.7 0.8 1.0
CG B:GLU251 4.0 58.7 1.0
CB B:HIS309 4.2 0.1 1.0
ND1 B:HIS311 4.3 0.7 1.0
NE2 B:HIS309 4.3 0.8 1.0
CG B:HIS311 4.4 0.4 1.0
O B:HOH2010 4.5 68.0 1.0
CD2 B:HIS309 4.5 70.8 1.0
C61 B:GDD400 4.6 84.6 1.0
CB B:GLU251 4.7 59.5 1.0
N B:GLU251 4.7 58.0 1.0
ND2 B:ASN170 4.8 63.5 1.0
CE2 B:TYR179 4.8 75.5 1.0
CA B:HIS309 4.9 68.3 1.0

Zinc binding site 5 out of 5 in 2wvl

Go back to Zinc Binding Sites List in 2wvl
Zinc binding site 5 out of 5 in the Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II)


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 in Complex with Gdp-Alpha-D-Mannose and Mg(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1394

b:86.5
occ:1.00
 OE2 B:GLU292 2.0 67.3 1.0
NE2 B:HIS296 2.1 60.6 1.0
OE1 B:GLU292 2.2 43.1 1.0
CD B:GLU292 2.4 58.3 1.0
CD2 B:HIS296 2.9 43.0 1.0
CE1 B:HIS296 3.2 67.8 1.0
CG B:GLU292 3.9 43.5 1.0
CG B:HIS296 4.1 54.6 1.0
ND1 B:HIS296 4.2 46.8 1.0
CB B:GLU292 4.6 58.0 1.0
CG B:GLN295 4.7 36.5 1.0
O B:HOH2013 4.7 81.0 1.0
CA B:GLU292 4.8 85.5 1.0

Reference:

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
Page generated: Thu Oct 17 05:01:36 2024

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