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Chlorine 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:

Iron (Fe) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7vzz

Go back to Chlorine Binding Sites List in 7vzz
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl706

b:46.2
occ:1.00
CL1 A:8CW706 0.0 46.2 1.0
C41 A:8CW706 1.8 47.5 1.0
C40 A:8CW706 2.7 48.8 1.0
C43 A:8CW706 2.8 46.8 1.0
N39 A:8CW706 2.9 44.8 1.0
O44 A:8CW706 3.0 46.8 1.0
CG1 B:VAL243 3.4 32.5 1.0
CD B:PRO244 3.6 33.5 1.0
O B:MET242 3.7 36.4 1.0
CA B:VAL243 3.8 31.0 1.0
CB B:VAL243 3.8 32.5 1.0
C38 A:8CW706 3.9 43.1 1.0
CG1 A:VAL91 4.0 19.3 1.0
C48 A:8CW706 4.0 50.0 1.0
ND1 A:HIS94 4.0 35.7 1.0
C46 A:8CW706 4.1 43.0 1.0
CE2 A:PHE25 4.1 41.2 1.0
CG2 A:VAL91 4.3 24.7 1.0
C45 A:8CW706 4.4 53.1 1.0
C47 A:8CW706 4.5 44.3 1.0
C37 A:8CW706 4.5 48.0 1.0
O49 A:8CW706 4.6 45.2 1.0
CB A:VAL91 4.6 22.6 1.0
N B:PRO244 4.6 37.2 1.0
CE1 A:HIS94 4.6 35.9 1.0
C B:MET242 4.6 33.5 1.0
CZ A:PHE25 4.7 37.2 1.0
CG A:HIS94 4.7 31.8 1.0
N B:VAL243 4.7 29.9 1.0
CG B:PRO244 4.7 30.0 1.0
C B:VAL243 4.8 33.1 1.0
CA A:VAL91 4.9 28.8 1.0
CB A:HIS94 4.9 28.9 1.0

Chlorine binding site 2 out of 2 in 7vzz

Go back to Chlorine Binding Sites List in 7vzz
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl709

b:47.4
occ:1.00
CL1 B:83Z709 0.0 47.4 1.0
C09 B:83Z709 1.8 48.4 1.0
C11 B:83Z709 2.7 45.3 1.0
C06 B:83Z709 2.8 42.4 1.0
N12 B:83Z709 2.9 48.8 1.0
O07 B:83Z709 3.1 42.8 1.0
CG1 A:VAL243 3.6 25.4 1.0
CD A:PRO244 3.6 33.6 1.0
O A:MET242 3.8 34.3 1.0
C13 B:83Z709 3.8 44.1 1.0
CA A:VAL243 3.8 34.8 1.0
CB A:VAL243 3.9 33.6 1.0
CG1 B:VAL91 3.9 30.4 1.0
C28 B:83Z709 4.0 42.0 1.0
C05 B:83Z709 4.1 46.5 1.0
ND1 B:HIS94 4.1 28.6 1.0
CE2 B:PHE25 4.2 42.7 1.0
C14 B:83Z709 4.4 44.5 1.0
C08 B:83Z709 4.5 45.8 1.0
CG2 B:VAL91 4.5 25.8 1.0
C04 B:83Z709 4.5 45.4 1.0
O27 B:83Z709 4.5 40.6 1.0
CG B:HIS94 4.6 29.8 1.0
CB B:VAL91 4.6 28.2 1.0
C A:MET242 4.6 31.5 1.0
N A:PRO244 4.7 35.2 1.0
CA B:VAL91 4.7 27.1 1.0
N A:VAL243 4.7 33.3 1.0
CB B:HIS94 4.7 25.7 1.0
CG A:PRO244 4.8 29.6 1.0
CE1 B:HIS94 4.8 30.7 1.0
C A:VAL243 4.8 34.5 1.0
CZ B:PHE25 4.9 41.3 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: Sun Jul 13 08:13:04 2025

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