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Iron in PDB 7vzz: The Structure of Gdmn in Complex with the Natural Tetrahedral Intermediate, Carbamoyl Adenylate, and 20-O-Methyl-19- Chloroproansamitocin

Protein crystallography data

The structure of The Structure of Gdmn in Complex with the Natural Tetrahedral Intermediate, Carbamoyl Adenylate, and 20-O-Methyl-19- Chloroproansamitocin, PDB code: 7vzz 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) 25.70 / 2.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.86, 111.86, 231.272, 90, 90, 120
R / Rfree (%) 17.5 / 22.5

Other elements in 7vzz:

The structure of The Structure of Gdmn in Complex with the Natural Tetrahedral Intermediate, Carbamoyl Adenylate, and 20-O-Methyl-19- Chloroproansamitocin also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the The Structure of Gdmn in Complex with the Natural Tetrahedral Intermediate, Carbamoyl Adenylate, and 20-O-Methyl-19- Chloroproansamitocin (pdb code 7vzz). 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 in Complex with the Natural Tetrahedral Intermediate, Carbamoyl Adenylate, and 20-O-Methyl-19- Chloroproansamitocin, PDB code: 7vzz:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 7vzz

Go back to Iron Binding Sites List in 7vzz
Iron binding site 1 out of 2 in the The Structure of Gdmn in Complex with the Natural Tetrahedral Intermediate, Carbamoyl Adenylate, and 20-O-Methyl-19- Chloroproansamitocin


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 in Complex with the Natural Tetrahedral Intermediate, Carbamoyl Adenylate, and 20-O-Methyl-19- Chloroproansamitocin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe712

b:33.2
occ:1.00
OD1 A:ASP333 2.3 30.1 1.0
NE2 A:HIS137 2.4 25.2 1.0
O51 A:8CW706 2.4 32.5 1.0
OD2 A:ASP156 2.6 31.8 1.0
NE2 A:HIS133 2.6 26.1 1.0
N50 A:8CW706 2.6 43.5 1.0
O13 A:8CW706 2.9 44.0 1.0
P12 A:8CW706 2.9 45.9 1.0
CE1 A:HIS137 3.3 27.0 1.0
CD2 A:HIS137 3.3 27.0 1.0
C14 A:8CW706 3.4 51.3 1.0
CG A:ASP156 3.4 39.1 1.0
CE1 A:HIS133 3.4 29.2 1.0
CG A:ASP333 3.5 31.1 1.0
CB A:ASP156 3.6 40.5 1.0
CD2 A:HIS133 3.6 28.1 1.0
O52 A:8CW706 3.9 35.2 1.0
O15 A:8CW706 4.0 40.4 1.0
OD2 A:ASP333 4.1 33.5 1.0
O11 A:8CW706 4.2 36.1 1.0
ND1 A:HIS137 4.4 29.5 1.0
CG A:HIS137 4.5 26.6 1.0
OD1 A:ASP156 4.5 38.2 1.0
CA A:ASP333 4.5 26.6 1.0
CB A:ASP333 4.6 29.8 1.0
N A:ASP333 4.6 26.1 1.0
ND1 A:HIS133 4.6 24.7 1.0
N A:GLY305 4.7 26.8 1.0
O16 A:8CW706 4.7 45.8 1.0
CG A:HIS133 4.7 29.8 1.0
O A:ARG158 4.9 33.3 1.0
C A:HIS332 4.9 26.3 1.0
CA A:GLY304 5.0 26.3 1.0

Iron binding site 2 out of 2 in 7vzz

Go back to Iron Binding Sites List in 7vzz
Iron binding site 2 out of 2 in the The Structure of Gdmn in Complex with the Natural Tetrahedral Intermediate, Carbamoyl Adenylate, and 20-O-Methyl-19- Chloroproansamitocin


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 in Complex with the Natural Tetrahedral Intermediate, Carbamoyl Adenylate, and 20-O-Methyl-19- Chloroproansamitocin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe707

b:43.5
occ:1.00
NE2 B:HIS133 2.4 26.3 1.0
OD1 B:ASP333 2.5 37.4 1.0
OD2 B:ASP156 2.5 28.4 1.0
NE2 B:HIS137 2.5 36.0 1.0
O1A B:CA0708 2.5 30.9 1.0
O3A B:CA0708 2.8 41.4 1.0
CB B:CA0708 3.0 40.7 0.0
PA B:CA0708 3.2 35.1 1.0
CE1 B:HIS133 3.2 32.0 1.0
N2B B:CA0708 3.2 37.6 1.0
CD2 B:HIS137 3.3 36.8 1.0
CG B:ASP156 3.4 43.5 1.0
CD2 B:HIS133 3.5 32.4 1.0
CB B:ASP156 3.5 37.3 1.0
CE1 B:HIS137 3.5 36.3 1.0
CG B:ASP333 3.6 38.7 1.0
O1B B:CA0708 3.9 37.4 1.0
OD2 B:ASP333 4.1 40.6 1.0
O5' B:CA0708 4.4 32.6 1.0
O B:ARG158 4.4 38.2 1.0
ND1 B:HIS133 4.4 29.3 1.0
O2A B:CA0708 4.4 39.0 1.0
CG B:HIS133 4.5 29.4 1.0
CG B:HIS137 4.5 31.3 1.0
OD1 B:ASP156 4.6 35.3 1.0
ND1 B:HIS137 4.6 34.5 1.0
CA B:ASP333 4.6 32.4 1.0
CB B:ASP333 4.6 34.9 1.0
N B:ASP333 4.7 32.9 1.0
N B:GLY305 4.9 31.7 1.0

Reference:

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
Page generated: Fri Aug 9 07:00:26 2024

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