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Gadolinium in PDB 1v8m: Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd

Enzymatic activity of Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd

All present enzymatic activity of Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd:
3.6.1.13;

Protein crystallography data

The structure of Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd, PDB code: 1v8m was solved by S.Yoshiba, T.Ooga, N.Nakagawa, T.Shibata, Y.Inoue, S.Yokoyama, S.Kuramitsu, R.Masui, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.11 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 49.610, 49.610, 119.870, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 24.4

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd (pdb code 1v8m). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 4 binding sites of Gadolinium where determined in the Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd, PDB code: 1v8m:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in 1v8m

Go back to Gadolinium Binding Sites List in 1v8m
Gadolinium binding site 1 out of 4 in the Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd300

b:44.1
occ:0.25
 O A:HOH657 1.8 39.7 1.0
OE2 A:GLU86 2.2 21.7 1.0
O A:ALA66 2.3 13.9 1.0
O A:HOH632 2.4 21.4 1.0
O3A A:APR619 2.7 40.2 0.6
CD A:GLU86 3.1 20.8 1.0
O2B A:APR619 3.2 38.9 0.6
PB A:APR619 3.3 37.5 0.6
OE2 A:GLU82 3.4 19.4 1.0
C A:ALA66 3.5 14.1 1.0
O5D A:APR619 3.5 36.1 0.6
OE1 A:GLU86 3.7 21.6 1.0
GD A:GD301 3.7 55.5 0.4
CA A:GLY67 3.9 14.5 1.0
PA A:APR619 4.1 41.5 0.6
O1A A:APR619 4.1 41.6 0.6
CD A:GLU82 4.1 19.5 1.0
CG A:GLU86 4.1 19.3 1.0
N A:GLY67 4.2 13.2 1.0
NE2 A:GLN52 4.2 26.6 1.0
C5D A:APR619 4.3 34.1 0.6
OE1 A:GLU82 4.4 21.6 1.0
N A:ALA66 4.5 12.8 1.0
CA A:ALA66 4.6 13.3 1.0
O1B A:APR619 4.7 38.0 0.6
C5' A:APR619 4.7 45.3 0.6
O A:HOH656 4.8 35.9 1.0
O A:HOH622 4.8 15.7 1.0
O5' A:APR619 4.9 43.5 0.6

Gadolinium binding site 2 out of 4 in 1v8m

Go back to Gadolinium Binding Sites List in 1v8m
Gadolinium binding site 2 out of 4 in the Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd301

b:55.5
occ:0.37
 O A:HOH657 2.0 39.7 1.0
O A:HOH656 2.2 35.9 1.0
O1A A:APR619 2.7 41.6 0.6
OE1 A:GLU82 2.7 21.6 1.0
OE2 A:GLU82 2.8 19.4 1.0
CD A:GLU82 3.1 19.5 1.0
PA A:APR619 3.5 41.5 0.6
O A:HOH658 3.6 37.9 1.0
C5' A:APR619 3.7 45.3 0.6
O5' A:APR619 3.7 43.5 0.6
GD A:GD300 3.7 44.1 0.2
O3A A:APR619 3.9 40.2 0.6
OE1 A:GLU85 3.9 25.8 1.0
NH1 A:ARG81 3.9 19.4 1.0
C4' A:APR619 4.6 46.1 0.6
CG A:GLU82 4.6 17.9 1.0
OE2 A:GLU86 4.7 21.7 1.0
O2A A:APR619 4.8 42.7 0.6
O A:ALA66 4.9 13.9 1.0
CA A:GLY67 5.0 14.5 1.0

Gadolinium binding site 3 out of 4 in 1v8m

Go back to Gadolinium Binding Sites List in 1v8m
Gadolinium binding site 3 out of 4 in the Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd302

b:23.0
occ:0.50
 OE2 A:GLU140 2.1 21.8 1.0
OE2 A:GLU143 2.2 30.7 1.0
OE1 A:GLU143 2.5 31.3 1.0
OE1 A:GLU140 2.6 19.6 1.0
CD A:GLU140 2.7 19.6 1.0
CD A:GLU143 2.7 28.3 1.0
CG A:GLU140 4.2 20.1 1.0
CG A:GLU143 4.2 26.5 1.0
NH2 A:ARG147 4.5 39.0 1.0
CB A:GLU143 4.9 22.3 1.0

Gadolinium binding site 4 out of 4 in 1v8m

Go back to Gadolinium Binding Sites List in 1v8m
Gadolinium binding site 4 out of 4 in the Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Crystal Structure Analysis of Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Gd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd303

b:15.7
occ:0.59
 OE1 A:GLU122 2.1 44.1 1.0
OE2 A:GLU122 2.1 44.2 1.0
CD A:GLU122 2.4 45.3 1.0
O A:HOH647 3.0 27.5 1.0
CG A:GLU122 3.8 46.3 1.0
CB A:ASP126 4.1 58.6 1.0
O A:HIS124 4.1 62.0 1.0
OD2 A:ASP126 4.4 59.7 1.0
N A:ASP126 4.5 58.9 1.0
CB A:GLU122 4.8 47.2 1.0
CG A:ASP126 4.8 59.4 1.0
CA A:ASP126 4.8 57.8 1.0

Reference:

S.Yoshiba, T.Ooga, N.Nakagawa, T.Shibata, Y.Inoue, S.Yokoyama, S.Kuramitsu, R.Masui. Structural Insights Into the Thermus Thermophilus Adp-Ribose Pyrophosphatase Mechanism Via Crystal Structures with the Bound Substrate and Metal J.Biol.Chem. V. 279 37163 2004.
ISSN: ISSN 0021-9258
PubMed: 15210687
DOI: 10.1074/JBC.M403817200
Page generated: Sat Aug 10 21:19:14 2024

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