Gadolinium in PDB 6z1d: Crystal Structure of the Aaa Domain of Rubisco Activase From Nostoc Sp. (Strain Pcc 7120), Gadolinium Complex

The structure of Crystal Structure of the Aaa Domain of Rubisco Activase From Nostoc Sp. (Strain Pcc 7120), Gadolinium Complex, PDB code: 6z1d was solved by L.Popilka, A.Bracher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.63 / 2.71
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	111.990, 111.990, 283.818, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 25.9

The structure of Crystal Structure of the Aaa Domain of Rubisco Activase From Nostoc Sp. (Strain Pcc 7120), Gadolinium Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Gadolinium atom in the Crystal Structure of the Aaa Domain of Rubisco Activase From Nostoc Sp. (Strain Pcc 7120), Gadolinium Complex (pdb code 6z1d). 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 of the Aaa Domain of Rubisco Activase From Nostoc Sp. (Strain Pcc 7120), Gadolinium Complex, PDB code: 6z1d:
Jump to Gadolinium binding site number: 1; 2; 3; 4;

Gadolinium binding site 1 out of 4 in the Crystal Structure of the Aaa Domain of Rubisco Activase From Nostoc Sp. (Strain Pcc 7120), Gadolinium Complex


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 Aaa Domain of Rubisco Activase From Nostoc Sp. (Strain Pcc 7120), Gadolinium Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd401 b:85.4 occ:0.37 OE1 A:GLU204 2.9 75.9 1.0 OE2 A:GLU204 3.0 74.9 1.0 CD A:GLU204 3.3 73.8 1.0 HH22 A:ARG182 4.1 67.5 1.0 HH12 A:ARG182 4.1 67.9 1.0 CG A:GLU204 4.7 69.7 1.0 NH2 A:ARG182 4.9 56.3 1.0 NH1 A:ARG182 4.9 56.6 1.0 HG2 A:GLU204 5.0 83.7 1.0

Gadolinium binding site 2 out of 4 in the Crystal Structure of the Aaa Domain of Rubisco Activase From Nostoc Sp. (Strain Pcc 7120), Gadolinium Complex


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 Aaa Domain of Rubisco Activase From Nostoc Sp. (Strain Pcc 7120), Gadolinium Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd402 b:49.2 occ:0.13 HZ1 A:LYS185 2.9 59.8 1.0 HA A:LYS212 3.5 65.8 1.0 HZ3 A:LYS185 3.6 59.8 1.0 NZ A:LYS185 3.7 49.8 1.0 OE1 A:GLU179 3.7 73.6 1.0 HH12 A:ARG38 3.8 90.1 1.0 O A:PRO211 3.8 50.7 1.0 HH11 A:ARG38 3.9 90.1 1.0 NH1 A:ARG38 4.0 75.1 1.0 O A:LYS212 4.0 53.0 1.0 HE2 A:LYS185 4.1 58.9 1.0 HG3 A:GLU179 4.2 77.9 1.0 C A:LYS212 4.3 51.8 1.0 CA A:LYS212 4.3 54.9 1.0 HZ2 A:LYS185 4.3 59.8 1.0 HG2 A:GLU179 4.4 77.9 1.0 CE A:LYS185 4.4 49.1 1.0 CD A:GLU179 4.6 69.7 1.0 CG A:GLU179 4.6 64.9 1.0 O A:GLN213 4.6 46.1 1.0 HE3 A:LYS185 4.7 58.9 1.0 C A:PRO211 4.8 50.4 1.0 CZ A:ARG38 4.9 74.9 1.0 O A:PRO180 4.9 55.5 1.0 OE2 A:GLU41 4.9 54.1 1.0

Gadolinium binding site 3 out of 4 in the Crystal Structure of the Aaa Domain of Rubisco Activase From Nostoc Sp. (Strain Pcc 7120), Gadolinium Complex


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 Aaa Domain of Rubisco Activase From Nostoc Sp. (Strain Pcc 7120), Gadolinium Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd403 b:78.3 occ:0.14 HH21 A:ARG83 2.5 0.4 1.0 HH22 A:ARG83 2.9 0.4 1.0 NH2 A:ARG83 3.0 83.7 1.0 HD3 A:ARG83 3.7 89.4 1.0 CZ A:ARG83 4.2 81.9 1.0 HB3 A:ARG83 4.2 86.0 1.0 HB2 A:ARG83 4.3 86.0 1.0 HD23 A:LEU80 4.5 99.8 1.0 CD A:ARG83 4.6 74.5 1.0 HD12 A:LEU139 4.7 87.0 1.0 CB A:ARG83 4.7 71.7 1.0 HD13 A:LEU139 4.8 87.0 1.0 NE A:ARG83 4.8 77.8 1.0

Gadolinium binding site 4 out of 4 in the Crystal Structure of the Aaa Domain of Rubisco Activase From Nostoc Sp. (Strain Pcc 7120), Gadolinium Complex


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 Aaa Domain of Rubisco Activase From Nostoc Sp. (Strain Pcc 7120), Gadolinium Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Gd302 b:36.9 occ:0.10 HZ2 B:LYS39 2.7 82.8 1.0 O2B B:ADP301 2.9 47.7 1.0 HA2 B:GLY40 3.1 70.6 1.0 HG2 B:LYS39 3.1 74.0 1.0 O1A B:ADP301 3.2 54.8 1.0 H B:GLY40 3.3 69.0 1.0 HG3 B:LYS39 3.3 74.0 1.0 NZ B:LYS39 3.4 69.0 1.0 HH21 A:ARG169 3.5 98.2 1.0 H5'2 B:ADP301 3.5 70.5 1.0 HE3 B:LYS39 3.5 84.2 1.0 HZ1 B:LYS39 3.5 82.8 1.0 CG B:LYS39 3.7 61.7 1.0 N B:GLY40 3.7 57.5 1.0 CA B:GLY40 3.7 58.8 1.0 HA3 B:GLY40 3.8 70.6 1.0 NH2 A:ARG169 3.9 81.8 1.0 O3A B:ADP301 3.9 57.8 1.0 CE B:LYS39 3.9 70.2 1.0 HH22 A:ARG169 4.0 98.2 1.0 PB B:ADP301 4.1 48.0 1.0 HZ3 B:LYS39 4.1 82.8 1.0 PA B:ADP301 4.2 54.0 1.0 C5' B:ADP301 4.4 58.8 1.0 H5'1 B:ADP301 4.4 70.5 1.0 CD B:LYS39 4.4 66.8 1.0 C B:LYS39 4.6 57.9 1.0 O5' B:ADP301 4.8 58.2 1.0 CZ A:ARG169 4.8 81.0 1.0 HE A:ARG169 4.8 98.3 1.0 HE2 B:LYS39 4.8 84.2 1.0 O1B B:ADP301 4.9 48.1 1.0 HA B:LYS39 4.9 67.7 1.0 CB B:LYS39 4.9 59.5 1.0 HD2 B:LYS39 5.0 80.2 1.0

M.Flecken, H.Wang, L.Popilka, F.U.Hartl, A.Bracher, M.Hayer-Hartl. Dual Role of Rca-Like Protein in Rubisco Metabolic Repair and Carboxysome Organization To Be Published.