Gadolinium in PDB 5klf: Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion

The structure of Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion, PDB code: 5klf was solved by M.V.Liberato, B.M.Campos, A.C.M.Zeri, F.M.Squina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.26 / 1.80
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	88.410, 88.410, 88.410, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Gadolinium atom in the Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion (pdb code 5klf). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 12 binding sites of Gadolinium where determined in the Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion, PDB code: 5klf:
Jump to Gadolinium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Gadolinium binding site 1 out of 12 in the Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd102 b:37.6 occ:0.37 O A:HOH255 2.7 27.2 1.0 OXT A:TRP97 4.4 26.9 1.0 OG1 A:THR39 4.5 19.0 1.0 O3E A:CE5101 4.6 74.9 0.7 O A:TRP97 4.6 26.8 1.0 O A:HOH293 4.9 27.9 1.0

Gadolinium binding site 2 out of 12 in the Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd103 b:21.1 occ:0.22 O A:SER87 2.6 13.8 1.0 O A:HOH225 2.8 38.4 1.0 C A:SER87 3.6 15.9 1.0 CA A:SER87 4.1 13.1 1.0 O A:HOH305 4.1 23.1 1.0 O A:HOH333 4.5 33.6 1.0 O A:ALA86 4.6 15.2 1.0 N A:ARG88 4.6 11.7 1.0 CB A:SER87 4.8 18.1 1.0

Gadolinium binding site 3 out of 12 in the Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd104 b:70.8 occ:0.44 O A:SER56 2.7 18.8 1.0 O A:HOH297 2.7 52.7 1.0 O A:HOH314 3.8 37.4 1.0 C A:SER56 3.8 19.2 1.0 CB A:SER56 3.9 23.1 1.0 CA A:SER56 4.4 17.1 1.0 O A:HOH317 4.5 33.7 1.0 O A:HOH300 4.7 24.5 1.0 O A:HOH312 4.8 42.1 1.0 N A:GLY57 4.9 15.7 1.0 OG A:SER56 5.0 22.7 1.0

Gadolinium binding site 4 out of 12 in the Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd105 b:53.4 occ:0.28 OD2 A:ASP78 2.7 27.4 1.0 O A:HOH206 2.9 56.2 1.0 GD A:GD106 3.1 73.0 0.4 CG A:ASP78 3.5 30.5 1.0 OD1 A:ASP78 3.8 29.1 1.0 O A:HOH228 4.1 32.3 1.0 O A:HOH202 4.4 31.7 1.0 O A:HOH260 4.4 27.1 1.0 CB A:ASP78 4.7 18.3 1.0 GD A:GD107 5.0 84.3 0.2

Gadolinium binding site 5 out of 12 in the Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 5 of Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd106 b:73.0 occ:0.37 O A:HOH228 3.0 32.3 1.0 O A:HOH206 3.0 56.2 1.0 GD A:GD105 3.1 53.4 0.3 OD2 A:ASP78 4.6 27.4 1.0 NZ A:LYS32 4.6 24.4 1.0 OD1 A:ASP78 4.7 29.1 1.0

Gadolinium binding site 6 out of 12 in the Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 6 of Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd107 b:84.3 occ:0.22 O A:HOH260 2.9 27.1 1.0 O A:HOH202 3.9 31.7 1.0 O A:HOH280 3.9 37.1 1.0 CB A:ASP78 4.4 18.3 1.0 OD2 A:ASP78 4.4 27.4 1.0 CG A:ASP78 4.8 30.5 1.0 N A:ASP78 4.8 18.9 1.0 O A:ASP78 4.9 21.5 1.0 O A:HOH256 4.9 33.7 1.0 GD A:GD105 5.0 53.4 0.3

Gadolinium binding site 7 out of 12 in the Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 7 of Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd108 b:80.5 occ:0.31 O A:HOH325 2.9 34.3 1.0 ND2 A:ASN91 4.1 30.1 1.0 OD1 A:ASN91 4.3 45.5 1.0 CG A:ASN91 4.7 28.6 1.0

Gadolinium binding site 8 out of 12 in the Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 8 of Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd109 b:46.6 occ:0.22 O A:HOH218 3.1 36.4 1.0 O A:HOH294 3.4 35.0 1.0 O A:HOH245 4.1 31.3 1.0 O6E A:CE5101 4.5 74.1 0.7 O A:ASN96 4.7 20.9 1.0 NZ A:LYS19 4.8 22.2 1.0 CE A:LYS19 4.9 23.2 1.0

Gadolinium binding site 9 out of 12 in the Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 9 of Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd110 b:72.9 occ:0.29 GD A:GD111 3.2 80.5 0.3 OE2 A:GLU22 4.0 61.7 1.0 O6A A:CE5101 4.6 74.1 0.7 O A:HOH313 4.6 26.8 1.0 OD1 A:ASN91 4.7 45.5 1.0 OE1 A:GLU22 4.8 52.0 1.0 CD A:GLU22 4.9 52.4 1.0

Gadolinium binding site 10 out of 12 in the Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 10 of Structure of CBM_E1, A Novel Carbohydrate-Binding Module Found By Sugar Cane Soil Metagenome, Complexed with Cellopentaose and Gadolinium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd111 b:80.5 occ:0.29 OE2 A:GLU22 2.9 61.7 1.0 GD A:GD110 3.2 72.9 0.3 CD A:GLU22 3.6 52.4 1.0 OE1 A:GLU22 3.8 52.0 1.0 O6A A:CE5101 4.1 74.1 0.7 CG A:GLU22 4.8 40.2 1.0

B.M.Campos, M.V.Liberato, T.M.Alvarez, L.M.Zanphorlin, G.C.Ematsu, H.Barud, I.Polikarpov, R.Ruller, H.J.Gilbert, A.C.Zeri, F.M.Squina. A Novel Carbohydrate-Binding Module From Sugar Cane Soil Metagenome Featuring Unique Structural and Carbohydrate Affinity Properties. J.Biol.Chem. V. 291 23734 2016.
ISSN: ESSN 1083-351X
PubMed: 27621314
DOI: 10.1074/JBC.M116.744383