Gadolinium in PDB 7lji: Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Gd+3 Bound

The structure of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Gd+3 Bound, PDB code: 7lji was solved by C.A.Brambley, T.J.Yared, M.Gonzalez, A.L.Jansch, J.R.Wallen, M.H.Weiland, J.M.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	98.57 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.67, 147.87, 197.14, 90, 90, 90
R / Rfree (%)	14.5 / 16.2

The binding sites of Gadolinium atom in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Gd+3 Bound (pdb code 7lji). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 3 binding sites of Gadolinium where determined in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Gd+3 Bound, PDB code: 7lji:
Jump to Gadolinium binding site number: 1; 2; 3;

Gadolinium binding site 1 out of 3 in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Gd+3 Bound


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Gd+3 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd501 b:32.5 occ:1.00 OE2 A:GLU156 2.5 31.7 1.0 OE1 A:GLU155 2.5 33.8 1.0 OD1 A:ASP121 2.5 28.8 1.0 NE2 A:HIS94 2.6 23.9 1.0 OD2 A:ASP121 2.6 38.0 1.0 OD1 A:ASP184 2.6 32.4 1.0 O A:HOH624 2.6 30.8 1.0 OD2 A:ASP184 2.7 38.7 1.0 O A:HOH894 2.9 44.0 1.0 CG A:ASP121 2.9 44.4 1.0 CG A:ASP184 3.0 33.6 1.0 CD A:GLU156 3.3 44.7 1.0 CD A:GLU155 3.4 44.9 1.0 CE1 A:HIS94 3.4 29.2 1.0 CD2 A:HIS94 3.6 27.3 1.0 OE1 A:GLU156 3.8 38.3 1.0 OE2 A:GLU155 3.8 52.2 1.0 O A:HOH828 4.2 56.5 1.0 NE2 A:HIS374 4.4 57.5 1.0 CB A:ASP121 4.4 31.7 1.0 CG A:GLU156 4.4 31.2 1.0 CG A:GLU155 4.5 35.0 1.0 CB A:ASP184 4.5 31.7 1.0 ND1 A:HIS94 4.6 26.6 1.0 CG A:HIS94 4.7 27.5 1.0 O A:HOH654 4.7 37.2 1.0 CB A:ASP122 5.0 29.4 1.0 O A:HOH849 5.0 61.8 1.0

Gadolinium binding site 2 out of 3 in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Gd+3 Bound


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Gd+3 Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Gd501 b:29.4 occ:1.00 OD2 B:ASP184 2.4 42.9 1.0 OE1 B:GLU155 2.5 29.5 1.0 NE2 B:HIS94 2.5 24.6 1.0 OD2 B:ASP121 2.5 30.5 1.0 OD1 B:ASP121 2.5 30.0 1.0 O B:HOH601 2.6 33.9 1.0 OE2 B:GLU156 2.6 33.9 1.0 O B:HOH860 2.9 34.7 1.0 CG B:ASP121 2.9 31.4 1.0 OE2 B:GLU155 2.9 80.9 1.0 OD1 B:ASP184 3.0 77.4 1.0 CD B:GLU155 3.0 42.7 1.0 CG B:ASP184 3.0 33.1 1.0 CE1 B:HIS94 3.3 22.8 1.0 CD B:GLU156 3.4 32.4 1.0 CD2 B:HIS94 3.5 24.1 1.0 OE1 B:GLU156 3.8 31.4 1.0 CB B:ASP121 4.4 30.5 1.0 NE2 B:HIS374 4.4 44.5 1.0 ND1 B:HIS94 4.5 24.9 1.0 CG B:GLU155 4.5 34.8 1.0 CB B:ASP184 4.5 28.2 1.0 CG B:GLU156 4.5 27.7 1.0 CG B:HIS94 4.6 28.6 1.0 O B:HOH707 4.8 35.8 1.0 O B:HOH776 4.9 47.9 1.0 CB B:ASP122 5.0 26.2 1.0 O B:HOH880 5.0 45.9 1.0

Gadolinium binding site 3 out of 3 in the Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Gd+3 Bound


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Structure of Poly(Aspartic Acid) Hydrolase PAHZ2 with Gd+3 Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Gd502 b:40.1 occ:1.00 O B:HOH902 2.5 40.7 1.0 O B:ARG25 2.6 32.7 1.0 OD1 B:ASP28 2.6 33.1 1.0 OD2 B:ASP28 2.7 41.0 1.0 CG B:ASP28 3.0 45.4 1.0 C B:ARG25 3.8 40.1 1.0 CA B:ASP26 4.5 31.3 1.0 OD1 B:ASP26 4.5 38.4 1.0 CB B:ASP28 4.5 37.4 1.0 N B:ASP26 4.6 33.4 1.0 CG B:ARG25 4.7 32.4 1.0 CA B:ARG25 4.8 35.1 1.0 O B:HOH620 4.9 54.0 1.0

C.A.Brambley, T.J.Yared, M.Gonzalez, A.L.Jansch, J.R.Wallen, M.H.Weiland, J.M.Miller. Sphingomonas Sp. Kt-1 PAHZ2 Structure Reveals A Role For Conformational Dynamics in Peptide Bond Hydrolysis. J.Phys.Chem.B V. 125 5722 2021.
ISSN: ISSN 1089-5647
PubMed: 34060838
DOI: 10.1021/ACS.JPCB.1C01216