Gadolinium in PDB 1okj: Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma"

The structure of Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma", PDB code: 1okj was solved by C.Abergel, S.Jeudy, J.M.Claverie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20 / 2.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.340, 97.600, 141.940, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.7

The binding sites of Gadolinium atom in the Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma" (pdb code 1okj). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 8 binding sites of Gadolinium where determined in the Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma", PDB code: 1okj:
Jump to Gadolinium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Gadolinium binding site 1 out of 8 in the Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma"


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma" within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd1213 b:41.4 occ:0.26 O D:HOH2028 3.2 49.5 1.0

Gadolinium binding site 2 out of 8 in the Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma"


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma" within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd1214 b:16.2 occ:0.33 O B:HOH2029 3.0 48.7 1.0 O B:HOH2023 3.1 40.1 1.0 O B:HOH2068 3.3 54.7 1.0 O B:HOH2077 3.8 37.1 1.0 CB B:ASP182 4.2 41.2 1.0 CG B:ASP182 4.9 46.9 1.0 OG1 B:THR161 4.9 25.6 1.0 OD1 B:ASP182 5.0 50.0 1.0 CA B:ASP182 5.0 38.6 1.0

Gadolinium binding site 3 out of 8 in the Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma"


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma" within 5.0Å range:

Gadolinium binding site 4 out of 8 in the Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma"


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma" within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd1216 b:38.5 occ:0.21 NH2 B:ARG31 2.8 62.6 1.0 CZ B:ARG31 4.0 61.4 1.0 NE2 B:HIS33 4.3 34.0 1.0 O A:HOH2062 4.6 41.7 1.0 NH1 B:ARG31 4.7 63.9 1.0 CD2 B:HIS33 4.8 33.2 1.0 NE B:ARG31 4.9 57.8 1.0

Gadolinium binding site 5 out of 8 in the Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma"


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 5 of Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma" within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd1217 b:34.7 occ:0.12 O B:HOH2014 4.3 60.8 1.0

Gadolinium binding site 6 out of 8 in the Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma"


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 6 of Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma" within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd1218 b:57.8 occ:0.25 NH2 A:ARG31 2.8 72.0 1.0 NH1 A:ARG31 2.8 72.5 1.0 CZ A:ARG31 2.9 71.5 1.0 NE A:ARG31 3.7 69.4 1.0 CD A:ARG31 4.6 65.8 1.0

Gadolinium binding site 7 out of 8 in the Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma"


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 7 of Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma" within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd1219 b:35.5 occ:0.12 O B:HOH2041 3.5 39.9 1.0

Gadolinium binding site 8 out of 8 in the Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma"


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 8 of Crystal Structure of the Essential E. Coli Yeaz Protein By Mad Method Using the Gadolinium Complex "Dotma" within 5.0Å range:

M.Stelter, R.Molina, S.Jeudy, R.Kahn, C.Abergel, J.A.Hermoso. A Complement to the Modern Crystallographer'S Toolbox: Caged Gadolinium Complexes with Versatile Binding Modes. Acta Crystallogr.,Sect.D V. 70 1506 2014.
ISSN: ISSN 0907-4449
PubMed: 24914962
DOI: 10.1107/S1399004714005483