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Gadolinium in PDB 2yeu: Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd

Enzymatic activity of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd

All present enzymatic activity of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd:
3.6.1.19;

Protein crystallography data

The structure of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd, PDB code: 2yeu was solved by A.M.D.Goncalves, D.De Sanctis, S.M.Mcsweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.06 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.820, 110.750, 165.980, 90.00, 90.00, 90.00
R / Rfree (%) 18.787 / 23.15

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd (pdb code 2yeu). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 6 binding sites of Gadolinium where determined in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd, PDB code: 2yeu:
Jump to Gadolinium binding site number: 1; 2; 3; 4; 5; 6;

Gadolinium binding site 1 out of 6 in 2yeu

Go back to Gadolinium Binding Sites List in 2yeu
Gadolinium binding site 1 out of 6 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1151

b:23.1
occ:1.00
O A:HOH2079 2.3 27.1 1.0
OE1 A:GLU50 2.3 25.2 1.0
OD2 A:ASP82 2.3 16.4 1.0
OE1 A:GLU79 2.5 14.3 1.0
O A:HOH2080 2.6 18.8 1.0
O A:HOH2054 2.6 27.2 1.0
OE1 A:GLU47 2.6 19.4 1.0
OE2 A:GLU47 2.6 22.6 1.0
CD A:GLU47 3.0 19.4 1.0
CD A:GLU79 3.4 19.9 1.0
CG A:ASP82 3.4 15.7 1.0
CD A:GLU50 3.4 25.1 1.0
H32 A:GOL1148 3.5 30.7 1.0
OE2 A:GLU79 3.6 21.3 1.0
HB3 A:ASP82 3.6 14.7 1.0
HB2 A:ASP82 3.7 14.7 1.0
CB A:ASP82 3.8 14.7 1.0
OE2 A:GLU50 3.9 29.7 1.0
HA A:GLU79 4.0 14.1 1.0
HB2 A:GLU50 4.3 19.3 1.0
H12 A:GOL1148 4.3 31.1 1.0
HA A:GLU47 4.4 15.2 1.0
HO3 A:GOL1148 4.4 38.7 1.0
HB3 A:GLU50 4.5 19.3 1.0
OD1 A:ASP82 4.5 17.0 1.0
C3 A:GOL1148 4.5 30.7 1.0
CG A:GLU47 4.5 17.1 1.0
CG A:GLU50 4.6 21.1 1.0
CB A:GLU50 4.7 19.3 1.0
CG A:GLU79 4.8 14.4 1.0
HB3 A:GLU79 4.8 13.4 1.0
H31 A:GOL1148 4.9 30.7 1.0
HG2 A:GLU47 5.0 17.1 1.0

Gadolinium binding site 2 out of 6 in 2yeu

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Gadolinium binding site 2 out of 6 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd1152

b:23.2
occ:1.00
O B:HOH2074 2.1 19.1 1.0
OE1 B:GLU79 2.4 16.7 1.0
OE1 B:GLU50 2.4 24.0 1.0
OD2 B:ASP82 2.5 15.4 1.0
O B:HOH2052 2.5 22.2 1.0
OE1 B:GLU47 2.5 21.1 1.0
O B:HOH2075 2.6 20.8 1.0
OE2 B:GLU47 2.7 24.4 1.0
CD B:GLU47 3.0 20.8 1.0
CD B:GLU50 3.4 24.2 1.0
CD B:GLU79 3.4 15.8 1.0
CG B:ASP82 3.5 15.8 1.0
HB3 B:ASP82 3.6 13.2 1.0
OE2 B:GLU79 3.7 21.5 1.0
OE2 B:GLU50 3.8 28.6 1.0
HB2 B:ASP82 3.8 13.2 1.0
CB B:ASP82 3.9 13.2 1.0
HA B:GLU79 4.0 11.7 1.0
HB2 B:GLU50 4.3 16.1 1.0
HB3 B:GLU50 4.4 16.1 1.0
HA B:GLU47 4.5 15.0 1.0
CG B:GLU47 4.6 18.1 1.0
OD1 B:ASP82 4.6 14.0 1.0
CG B:GLU50 4.6 20.2 1.0
CB B:GLU50 4.7 16.1 1.0
CG B:GLU79 4.8 10.4 1.0
HB3 B:GLU79 4.8 11.4 1.0
O B:HOH2049 4.8 25.7 1.0
CA B:GLU79 5.0 11.7 1.0

Gadolinium binding site 3 out of 6 in 2yeu

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Gadolinium binding site 3 out of 6 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd1149

b:20.1
occ:1.00
OD2 C:ASP82 2.3 15.6 1.0
O C:HOH2099 2.4 17.5 1.0
OE1 C:GLU79 2.5 13.4 1.0
OE1 C:GLU50 2.5 23.3 1.0
O C:HOH2097 2.5 15.8 1.0
O C:HOH2062 2.5 20.4 1.0
OE1 C:GLU47 2.6 18.2 1.0
OE2 C:GLU47 2.7 17.4 1.0
CD C:GLU47 3.0 16.2 1.0
CG C:ASP82 3.4 14.8 1.0
CD C:GLU79 3.4 17.8 1.0
CD C:GLU50 3.4 23.9 1.0
H32 C:GOL1148 3.6 32.7 1.0
OE2 C:GLU79 3.6 21.4 1.0
HB3 C:ASP82 3.6 12.1 1.0
OE2 C:GLU50 3.8 27.5 1.0
HB2 C:ASP82 3.8 12.1 1.0
CB C:ASP82 3.8 12.1 1.0
HA C:GLU79 4.0 12.9 1.0
HO3 C:GOL1148 4.1 28.7 1.0
H11 C:GOL1148 4.2 25.8 1.0
HB2 C:GLU50 4.3 16.3 1.0
HA C:GLU47 4.4 14.0 1.0
OD1 C:ASP82 4.5 16.8 1.0
CG C:GLU47 4.5 15.4 1.0
C3 C:GOL1148 4.6 32.7 1.0
HB3 C:GLU50 4.6 16.3 1.0
CG C:GLU50 4.7 20.7 1.0
H12 C:GOL1148 4.7 25.8 1.0
CB C:GLU50 4.8 16.3 1.0
CG C:GLU79 4.8 11.8 1.0
O3 C:GOL1148 4.8 28.7 1.0
O C:HOH2063 4.8 32.7 1.0
O C:HOH2098 4.9 15.3 1.0
HB3 C:GLU79 4.9 12.3 1.0
C1 C:GOL1148 5.0 25.8 1.0
HG2 C:GLU47 5.0 15.4 1.0

Gadolinium binding site 4 out of 6 in 2yeu

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Gadolinium binding site 4 out of 6 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Gd1153

b:19.9
occ:1.00
OE1 D:GLU50 2.4 23.8 1.0
O D:HOH2077 2.4 23.4 1.0
O D:HOH2051 2.4 20.3 1.0
OE1 D:GLU79 2.4 13.3 1.0
OD2 D:ASP82 2.5 16.3 1.0
O D:HOH2054 2.5 21.0 1.0
OE1 D:GLU47 2.6 22.6 1.0
OE2 D:GLU47 2.7 20.6 1.0
CD D:GLU47 3.0 17.6 1.0
CD D:GLU50 3.3 21.2 1.0
CD D:GLU79 3.3 14.8 1.0
CG D:ASP82 3.5 13.8 1.0
OE2 D:GLU79 3.5 20.5 1.0
HB3 D:ASP82 3.6 13.2 1.0
H32 D:GOL1148 3.6 32.6 1.0
OE2 D:GLU50 3.7 26.1 1.0
HB2 D:ASP82 3.8 13.2 1.0
CB D:ASP82 3.9 13.2 1.0
HA D:GLU79 4.0 13.6 1.0
HO3 D:GOL1148 4.2 30.3 1.0
HB2 D:GLU50 4.2 13.4 1.0
H11 D:GOL1148 4.4 27.0 1.0
HB3 D:GLU50 4.4 13.4 1.0
HA D:GLU47 4.5 15.4 1.0
OD1 D:ASP82 4.5 17.3 1.0
CG D:GLU50 4.5 18.3 1.0
CG D:GLU47 4.5 16.2 1.0
C3 D:GOL1148 4.6 32.6 1.0
CB D:GLU50 4.7 13.4 1.0
CG D:GLU79 4.8 12.6 1.0
HB3 D:GLU79 4.8 13.0 1.0
HE2 D:HIS78 4.8 21.5 1.0
O D:HOH2055 4.8 28.4 1.0
O D:HOH2076 4.8 20.9 1.0
O3 D:GOL1148 4.9 30.3 1.0
HG2 D:GLU47 5.0 16.2 1.0

Gadolinium binding site 5 out of 6 in 2yeu

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Gadolinium binding site 5 out of 6 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 5 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Gd1150

b:26.4
occ:1.00
OD2 E:ASP82 2.2 16.2 1.0
O E:HOH2039 2.2 31.8 1.0
O E:HOH2052 2.2 18.4 1.0
OE1 E:GLU79 2.4 25.5 1.0
OE1 E:GLU50 2.4 33.4 1.0
OE1 E:GLU47 2.5 25.7 1.0
O E:HOH2056 2.6 24.7 1.0
OE2 E:GLU47 2.8 25.1 1.0
CD E:GLU47 3.0 24.0 1.0
CG E:ASP82 3.3 19.0 1.0
CD E:GLU79 3.3 22.1 1.0
CD E:GLU50 3.5 32.3 1.0
HB3 E:ASP82 3.5 15.8 1.0
OE2 E:GLU79 3.5 27.0 1.0
HB2 E:ASP82 3.7 15.8 1.0
CB E:ASP82 3.7 15.8 1.0
OE2 E:GLU50 3.9 34.3 1.0
HA E:GLU79 4.1 19.5 1.0
HB2 E:GLU50 4.3 24.4 1.0
OD1 E:ASP82 4.4 18.2 1.0
HA E:GLU47 4.4 19.9 1.0
HB3 E:GLU50 4.4 24.4 1.0
CG E:GLU47 4.5 22.1 1.0
CG E:GLU50 4.7 27.4 1.0
CG E:GLU79 4.7 21.3 1.0
CB E:GLU50 4.7 24.4 1.0
O E:HOH2036 4.8 24.6 1.0
HB3 E:GLU79 4.9 19.5 1.0
O E:HOH2055 5.0 24.4 1.0
HG3 E:GLU47 5.0 22.1 1.0

Gadolinium binding site 6 out of 6 in 2yeu

Go back to Gadolinium Binding Sites List in 2yeu
Gadolinium binding site 6 out of 6 in the Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 6 of Structural and Functional Insights of DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans, Complex with Gd within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Gd1150

b:27.4
occ:1.00
OE1 F:GLU50 1.8 19.9 1.0
OD2 F:ASP82 2.0 24.1 1.0
O F:HOH2045 2.2 26.6 1.0
OE1 F:GLU79 2.5 21.0 1.0
O F:HOH2046 2.5 36.5 1.0
OE1 F:GLU47 2.6 29.0 1.0
O F:HOH2022 2.7 26.1 1.0
OE2 F:GLU47 2.7 30.0 1.0
CD F:GLU47 3.0 28.4 1.0
CD F:GLU50 3.0 28.3 1.0
CG F:ASP82 3.2 23.3 1.0
CD F:GLU79 3.4 25.1 1.0
HB3 F:ASP82 3.5 21.6 1.0
OE2 F:GLU79 3.7 26.7 1.0
HO2 F:GOL1148 3.7 41.1 1.0
HB2 F:ASP82 3.7 21.6 1.0
OE2 F:GLU50 3.7 31.6 1.0
CB F:ASP82 3.7 21.6 1.0
HA F:GLU79 4.0 20.1 1.0
OD1 F:ASP82 4.2 24.1 1.0
HB3 F:GLU50 4.2 22.9 1.0
CG F:GLU50 4.3 23.4 1.0
HB2 F:GLU50 4.3 22.9 1.0
H12 F:GOL1148 4.4 41.9 1.0
HA F:GLU47 4.4 24.7 1.0
H31 F:GOL1148 4.4 40.5 1.0
CB F:GLU50 4.5 22.9 1.0
O F:HOH2047 4.5 25.8 1.0
CG F:GLU47 4.6 26.8 1.0
O2 F:GOL1148 4.7 41.1 1.0
HG2 F:GLU50 4.7 23.4 1.0
CG F:GLU79 4.8 20.6 1.0
HB3 F:GLU79 4.9 19.1 1.0

Reference:

A.M.D.Goncalves, D.Desanctis, S.M.Mcsweeney. Structural and Functional Insights Into DR2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans. J.Biol.Chem. V. 286 30691 2011.
ISSN: ISSN 0021-9258
PubMed: 21733847
DOI: 10.1074/JBC.M111.247999
Page generated: Sun Dec 13 18:59:22 2020

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