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Gadolinium in PDB 3zty: The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27

Enzymatic activity of The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27

All present enzymatic activity of The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27:
3.1.3.70;

Protein crystallography data

The structure of The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27, PDB code: 3zty was solved by S.Goncalves, A.M.Esteves, H.Santos, N.Borges, P.M.Matias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.56 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.692, 70.835, 92.735, 90.00, 95.04, 90.00
R / Rfree (%) 19.5 / 25.3

Other elements in 3zty:

The structure of The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27 (pdb code 3zty). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 6 binding sites of Gadolinium where determined in the The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27, PDB code: 3zty:
Jump to Gadolinium binding site number: 1; 2; 3; 4; 5; 6;

Gadolinium binding site 1 out of 6 in 3zty

Go back to Gadolinium Binding Sites List in 3zty
Gadolinium binding site 1 out of 6 in the The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd261

b:42.6
occ:1.00
 O A:ASP8 2.4 35.3 1.0
OD2 A:ASP6 2.5 29.7 1.0
OD2 A:ASP202 2.6 38.3 1.0
OD1 A:ASP202 2.7 37.9 1.0
CG A:ASP202 3.0 38.7 1.0
O A:HOH2003 3.0 19.7 1.0
CG A:ASP6 3.4 28.4 1.0
C A:ASP8 3.5 37.7 1.0
OD1 A:ASP6 3.6 27.6 1.0
GD A:GD262 3.9 55.1 0.8
CB A:ASP8 4.1 37.4 1.0
GD A:GD263 4.1 53.6 0.8
CL A:CL264 4.3 42.6 1.0
CA A:ASP8 4.3 38.0 1.0
O A:HOH2085 4.3 28.1 1.0
O A:HOH2006 4.4 26.8 1.0
O A:HOH2004 4.5 23.6 1.0
N A:GLY9 4.5 40.0 1.0
N A:ASP8 4.5 36.2 1.0
CB A:SER203 4.6 39.3 1.0
CB A:ASP202 4.6 40.4 1.0
CA A:GLY9 4.6 39.9 1.0
OG1 A:THR10 4.7 32.6 1.0
OD2 A:ASP206 4.8 32.1 1.0
CB A:ASP6 4.8 27.8 1.0

Gadolinium binding site 2 out of 6 in 3zty

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Gadolinium binding site 2 out of 6 in the The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd262

b:55.1
occ:0.75
 OE2 A:GLU14 2.8 41.8 1.0
O A:HOH2089 3.2 31.1 1.0
CD A:GLU14 3.5 43.5 1.0
OE1 A:GLU14 3.6 42.5 1.0
GD A:GD263 3.6 53.6 0.8
GD A:GD261 3.9 42.6 1.0
OD2 A:ASP202 3.9 38.3 1.0
OD1 A:ASP202 4.1 37.9 1.0
CG A:ASP202 4.2 38.7 1.0
O A:ASP8 4.4 35.3 1.0
O A:HOH2007 4.5 23.6 1.0
CA A:GLY9 4.5 39.9 1.0
C A:ASP8 4.9 37.7 1.0
CG A:GLU14 4.9 46.9 1.0
N A:GLY9 4.9 40.0 1.0
O A:GLY165 5.0 33.8 1.0

Gadolinium binding site 3 out of 6 in 3zty

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Gadolinium binding site 3 out of 6 in the The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd263

b:53.6
occ:0.82
 O A:GLY165 2.6 33.8 1.0
O A:HOH2007 3.2 23.6 1.0
O A:HOH2089 3.4 31.1 1.0
O A:HOH2072 3.4 36.0 1.0
O A:HOH2006 3.5 26.8 1.0
O A:HOH2005 3.5 20.7 1.0
GD A:GD262 3.6 55.1 0.8
O A:HOH2085 3.6 28.1 1.0
C A:GLY165 3.7 33.8 1.0
O A:HOH2002 4.1 33.6 1.0
GD A:GD261 4.1 42.6 1.0
O A:HOH2071 4.3 27.9 1.0
OE1 A:GLU14 4.4 42.5 1.0
CA A:GLY165 4.5 31.8 1.0
N A:GLY166 4.7 35.7 1.0
CA A:GLY166 4.8 38.1 1.0
CB A:ASP8 4.9 37.4 1.0

Gadolinium binding site 4 out of 6 in 3zty

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Gadolinium binding site 4 out of 6 in the The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd261

b:35.7
occ:1.00
 OD1 B:ASP202 2.3 31.0 1.0
O B:HOH2002 2.4 14.1 1.0
OD2 B:ASP6 2.5 29.2 1.0
O B:ASP8 2.7 33.2 1.0
CG B:ASP202 3.0 31.8 1.0
OD2 B:ASP202 3.1 31.9 1.0
CG B:ASP6 3.3 28.3 1.0
O B:HOH2050 3.5 23.4 1.0
OD1 B:ASP6 3.5 28.1 1.0
CL B:CL264 3.6 52.0 1.0
C B:ASP8 3.8 35.3 1.0
O B:HOH2001 3.8 47.6 1.0
GD B:GD263 3.9 46.7 0.7
GD B:GD262 3.9 44.8 0.8
OG B:SER203 4.0 33.4 1.0
OD2 B:ASP206 4.3 30.7 1.0
CB B:ASP8 4.3 35.9 1.0
O B:HOH2003 4.3 25.9 1.0
CA B:ASP8 4.4 35.7 1.0
CB B:ASP202 4.5 33.1 1.0
N B:ASP8 4.6 34.2 1.0
CB B:ASP6 4.7 27.8 1.0
N B:SER203 4.7 32.7 1.0
O B:GLY165 4.7 29.9 1.0
N B:GLY9 4.8 37.2 1.0
CB B:SER203 4.9 33.9 1.0
OG1 B:THR10 4.9 31.6 1.0
OD1 B:ASN205 4.9 30.9 1.0

Gadolinium binding site 5 out of 6 in 3zty

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Gadolinium binding site 5 out of 6 in the The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 5 of The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd262

b:44.8
occ:0.81
 O B:GLY165 2.8 29.9 1.0
O B:HOH2050 3.1 23.4 1.0
O B:HOH2003 3.1 25.9 1.0
O B:HOH2057 3.4 26.3 1.0
C B:GLY165 3.5 28.2 1.0
GD B:GD263 3.6 46.7 0.7
O B:HOH2045 3.8 26.9 1.0
GD B:GD261 3.9 35.7 1.0
CA B:GLY165 3.9 26.1 1.0
O B:HOH2004 4.0 45.0 1.0
OE1 B:GLU14 4.2 38.9 1.0
O B:HOH2042 4.4 39.5 1.0
N B:GLY166 4.5 28.5 1.0
OG B:SER203 4.5 33.4 1.0
OE2 B:GLU14 4.7 38.4 1.0
CB B:ASP8 4.8 35.9 1.0
O B:HOH2043 4.9 44.9 1.0
CD B:GLU14 4.9 39.7 1.0
CA B:GLY166 4.9 31.0 1.0

Gadolinium binding site 6 out of 6 in 3zty

Go back to Gadolinium Binding Sites List in 3zty
Gadolinium binding site 6 out of 6 in the The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 6 of The 3-Dimensional Structure of the Gadolinium Derivative of Mpgp, the Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd263

b:46.7
occ:0.74
 OE2 B:GLU14 2.6 38.4 1.0
OD2 B:ASP202 2.8 31.9 1.0
O B:HOH2043 2.9 44.9 1.0
O B:HOH2057 3.4 26.3 1.0
CG B:ASP202 3.6 31.8 1.0
GD B:GD262 3.6 44.8 0.8
CD B:GLU14 3.6 39.7 1.0
OG B:SER203 3.6 33.4 1.0
O B:HOH2019 3.8 25.4 1.0
GD B:GD261 3.9 35.7 1.0
OD1 B:ASP202 3.9 31.0 1.0
OE1 B:GLU14 4.0 38.9 1.0
O B:GLY165 4.0 29.9 1.0
O B:ASP8 4.1 33.2 1.0
CA B:GLY9 4.3 37.1 1.0
C B:ASP8 4.6 35.3 1.0
CB B:ASP202 4.7 33.1 1.0
N B:GLY9 4.7 37.2 1.0
CG B:GLU14 4.9 42.6 1.0

Reference:

S.Goncalves, A.M.Esteves, H.Santos, N.Borges, P.M.Matias. The Three-Dimensional Structure of Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus HB27: A New Member of the Haloalkanoic Acid Dehalogenase Superfamily. Biochemistry V. 50 9551 2011.
ISSN: ISSN 0006-2960
PubMed: 21961705
DOI: 10.1021/BI201171H
Page generated: Sun Dec 13 18:59:32 2020

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