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Zinc in PDB 2wvm: H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II)

Enzymatic activity of H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II)

All present enzymatic activity of H309A Mutant 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 H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II), PDB code: 2wvm 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) 98.19 / 2.98
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 112.766, 112.766, 199.690, 90.00, 90.00, 90.00
R / Rfree (%) 17.355 / 23.163

Other elements in 2wvm:

The structure of H309A Mutant 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 H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II) (pdb code 2wvm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the H309A Mutant of Mannosyl-3-Phosphoglycerate Synthase From Thermus Thermophilus HB27 in Complex with Gdp-Alpha-D-Mannose and Mg(II), PDB code: 2wvm:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 2wvm

Go back to Zinc Binding Sites List in 2wvm
Zinc binding site 1 out of 3 in the H309A Mutant of 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 H309A Mutant 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:69.1
occ:1.00
 OE1 A:GLU19 2.1 63.3 1.0
ND1 A:HIS8 2.1 51.4 1.0
OE2 A:GLU19 2.4 56.2 1.0
CD A:GLU19 2.5 58.9 1.0
O A:HOH2007 2.5 12.3 1.0
CE1 A:HIS8 2.7 51.1 1.0
CG A:HIS8 3.2 50.3 1.0
ND2 A:ASN7 3.8 59.9 1.0
NE2 A:HIS8 3.8 51.2 1.0
CB A:HIS8 3.9 51.6 1.0
CG A:GLU19 4.0 53.9 1.0
CB A:ASN7 4.1 54.0 1.0
CD2 A:HIS8 4.1 51.7 1.0
N A:HIS8 4.3 52.6 1.0
CG A:ASN7 4.3 56.5 1.0
CA A:HIS8 4.8 52.2 1.0
CB A:GLU19 5.0 50.3 1.0

Zinc binding site 2 out of 3 in 2wvm

Go back to Zinc Binding Sites List in 2wvm
Zinc binding site 2 out of 3 in the H309A Mutant of 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 H309A Mutant 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:77.0
occ:1.00
 OE1 B:GLU19 2.0 61.2 1.0
OD1 B:ASP242 2.1 46.4 1.0
NE2 B:HIS8 2.1 53.7 1.0
OD2 B:ASP242 2.2 61.7 1.0
O B:HOH2008 2.3 40.9 1.0
CG B:ASP242 2.5 53.5 1.0
CD2 B:HIS8 2.9 58.5 1.0
CD B:GLU19 3.1 59.6 1.0
CE1 B:HIS8 3.2 45.0 1.0
CG B:GLU19 3.5 60.8 1.0
CB B:ASP242 4.1 49.5 1.0
CG B:HIS8 4.2 47.8 1.0
OE2 B:GLU19 4.2 48.8 1.0
NZ B:LYS245 4.2 61.2 1.0
ND1 B:HIS8 4.2 45.3 1.0
CB B:GLU19 4.6 41.1 1.0
C B:ASP242 4.8 49.7 1.0
CA B:ASP242 4.9 40.1 1.0
N B:VAL243 5.0 54.8 1.0
O B:ASP242 5.0 59.6 1.0

Zinc binding site 3 out of 3 in 2wvm

Go back to Zinc Binding Sites List in 2wvm
Zinc binding site 3 out of 3 in the H309A Mutant of 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 H309A Mutant 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:70.8
occ:1.00
 NE2 B:HIS296 2.1 42.3 1.0
OE2 B:GLU292 2.1 47.8 1.0
OE1 B:GLU292 2.2 41.8 1.0
CD B:GLU292 2.4 47.5 1.0
CD2 B:HIS296 2.8 48.5 1.0
CE1 B:HIS296 3.2 51.2 1.0
CG B:GLU292 3.9 51.1 1.0
CG B:HIS296 4.0 47.5 1.0
ND1 B:HIS296 4.2 54.4 1.0
CB B:GLU292 4.5 46.8 1.0
CA B:GLU292 4.7 47.8 1.0
CG B:GLN295 4.9 39.6 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 05:01:51 2024

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