Iron in PDB 7vyp: The Structure of Gdmn Complex with the Natural Tetrahedral Intermediate, Carbamoylated Derivative, and Amp

The structure of The Structure of Gdmn Complex with the Natural Tetrahedral Intermediate, Carbamoylated Derivative, and Amp, PDB code: 7vyp was solved by J.Wei, J.Zheng, J.Zhou, Q.Kang, L.Bai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.76 / 2.88
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.029, 111.029, 231.276, 90, 90, 120
R / Rfree (%)	16.6 / 21.6

The structure of The Structure of Gdmn Complex with the Natural Tetrahedral Intermediate, Carbamoylated Derivative, and Amp also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the The Structure of Gdmn Complex with the Natural Tetrahedral Intermediate, Carbamoylated Derivative, and Amp (pdb code 7vyp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the The Structure of Gdmn Complex with the Natural Tetrahedral Intermediate, Carbamoylated Derivative, and Amp, PDB code: 7vyp:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the The Structure of Gdmn Complex with the Natural Tetrahedral Intermediate, Carbamoylated Derivative, and Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of Gdmn Complex with the Natural Tetrahedral Intermediate, Carbamoylated Derivative, and Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:32.6 occ:1.00 NE2 A:HIS133 2.3 30.9 1.0 OD2 A:ASP156 2.3 39.1 1.0 NE2 A:HIS137 2.4 29.9 1.0 OD1 A:ASP333 2.4 32.3 1.0 O3P A:AMP715 2.4 40.4 1.0 O2P A:AMP715 3.0 34.4 1.0 CD2 A:HIS137 3.0 29.1 1.0 N25 A:82Z714 3.1 40.1 0.8 CG A:ASP156 3.2 37.2 1.0 P A:AMP715 3.2 42.6 1.0 CE1 A:HIS133 3.2 29.3 1.0 CD2 A:HIS133 3.3 35.2 1.0 CG A:ASP333 3.4 35.9 1.0 CB A:ASP156 3.4 34.5 1.0 CE1 A:HIS137 3.5 28.5 1.0 OD2 A:ASP333 3.9 39.6 1.0 C24 A:82Z714 4.2 51.6 0.8 OD1 A:ASP156 4.2 40.6 1.0 O1P A:AMP715 4.3 46.0 1.0 CG A:HIS137 4.3 34.3 1.0 O5' A:AMP715 4.3 35.8 1.0 ND1 A:HIS133 4.3 32.2 1.0 CG A:HIS133 4.4 36.1 1.0 ND1 A:HIS137 4.5 36.2 1.0 O26 A:82Z714 4.5 41.6 0.8 CB A:ASP333 4.6 29.6 1.0 CA A:ASP333 4.7 29.7 1.0 N A:GLY305 4.9 31.3 1.0 N A:ASP333 4.9 33.2 1.0 CA A:ASP156 5.0 35.5 1.0 CB A:ALA336 5.0 27.4 1.0

Iron binding site 2 out of 2 in the The Structure of Gdmn Complex with the Natural Tetrahedral Intermediate, Carbamoylated Derivative, and Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of Gdmn Complex with the Natural Tetrahedral Intermediate, Carbamoylated Derivative, and Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe702 b:40.5 occ:1.00 OD1 B:ASP333 2.3 45.2 1.0 NE2 B:HIS133 2.3 29.0 1.0 OD2 B:ASP156 2.4 40.4 1.0 O52 B:8CW701 2.4 31.3 0.8 NE2 B:HIS137 2.4 44.4 1.0 N50 B:8CW701 2.7 46.0 0.8 CD2 B:HIS137 3.1 39.0 1.0 CE1 B:HIS133 3.3 34.3 1.0 CG B:ASP156 3.3 40.2 1.0 CD2 B:HIS133 3.3 36.9 1.0 P12 B:8CW701 3.4 36.3 0.8 CG B:ASP333 3.4 41.0 1.0 CE1 B:HIS137 3.5 42.4 1.0 O13 B:8CW701 3.5 48.6 0.8 CB B:ASP156 3.5 36.3 1.0 C14 B:8CW701 3.6 52.8 0.8 OD2 B:ASP333 4.0 42.4 1.0 O15 B:8CW701 4.0 40.8 0.8 O51 B:8CW701 4.3 41.7 0.8 CG B:HIS137 4.4 37.1 1.0 ND1 B:HIS133 4.4 28.3 1.0 OD1 B:ASP156 4.4 40.0 1.0 CG B:HIS133 4.4 32.4 1.0 ND1 B:HIS137 4.5 41.9 1.0 CA B:ASP333 4.6 36.2 1.0 CB B:ASP333 4.6 37.3 1.0 O11 B:8CW701 4.6 33.7 0.8 O B:ARG158 4.8 39.9 1.0 N B:ASP333 4.8 41.2 1.0 CA B:GLY304 4.9 40.4 1.0 N B:GLY305 4.9 32.8 1.0 O16 B:8CW701 5.0 50.5 0.8

J.Wei, X.Zhang, Y.Zhou, X.Cheng, Z.Lin, M.Tang, J.Zheng, B.Wang, Q.Kang, L.Bai. Endowing Homodimeric Carbamoyltransferase Gdmn with Iterative Functions Through Structural Characterization and Mechanistic Studies. Nat Commun V. 13 6617 2022.
ISSN: ESSN 2041-1723
PubMed: 36329057
DOI: 10.1038/S41467-022-34387-2