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Chlorine in PDB 5y7c: Hapalindole A and Dmspp Bound AMBP3

Protein crystallography data

The structure of Hapalindole A and Dmspp Bound AMBP3, PDB code: 5y7c was solved by C.P.Wong, T.Awakawa, Y.Nakashima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.84 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.465, 54.724, 77.991, 105.23, 106.60, 98.51
R / Rfree (%) 19.5 / 24.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hapalindole A and Dmspp Bound AMBP3 (pdb code 5y7c). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Hapalindole A and Dmspp Bound AMBP3, PDB code: 5y7c:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5y7c

Go back to Chlorine Binding Sites List in 5y7c
Chlorine binding site 1 out of 2 in the Hapalindole A and Dmspp Bound AMBP3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hapalindole A and Dmspp Bound AMBP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:51.7
occ:1.00
CL01 A:8O0402 0.0 51.7 1.0
C14 A:8O0402 1.8 44.9 1.0
C15 A:8O0402 2.7 41.6 1.0
C13 A:8O0402 2.8 39.3 1.0
C19 A:8O0402 3.2 38.1 1.0
C20 A:8O0402 3.2 32.2 1.0
C16 A:8O0402 3.3 34.0 1.0
CB A:ALA44 3.7 18.0 1.0
C14 A:DST401 3.8 40.5 1.0
CG1 A:VAL284 3.8 40.0 1.0
C10 A:8O0402 4.2 44.7 1.0
C12 A:8O0402 4.2 43.2 1.0
OD2 A:ASP277 4.2 39.8 1.0
NH1 A:ARG60 4.3 27.9 1.0
CG A:ARG60 4.4 21.4 1.0
CG2 A:VAL284 4.4 31.6 1.0
CB A:ASP277 4.7 21.7 1.0
C09 A:8O0402 4.7 41.5 1.0
CB A:VAL284 4.7 35.3 1.0
CG A:ASP277 4.8 30.7 1.0
N02 A:8O0402 4.8 40.9 1.0
C12 A:DST401 4.8 47.8 1.0
C11 A:DST401 4.9 41.3 1.0
CD A:ARG60 4.9 24.2 1.0

Chlorine binding site 2 out of 2 in 5y7c

Go back to Chlorine Binding Sites List in 5y7c
Chlorine binding site 2 out of 2 in the Hapalindole A and Dmspp Bound AMBP3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hapalindole A and Dmspp Bound AMBP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:48.4
occ:1.00
CL01 B:8O0402 0.0 48.4 1.0
C14 B:8O0402 1.8 42.2 1.0
C15 B:8O0402 2.7 42.1 1.0
C13 B:8O0402 2.8 35.3 1.0
C19 B:8O0402 3.2 36.9 1.0
C16 B:8O0402 3.3 32.2 1.0
C20 B:8O0402 3.4 30.0 1.0
CB B:ALA44 3.6 18.9 1.0
CG1 B:VAL284 3.8 38.3 1.0
O B:HOH593 3.9 35.4 1.0
OD1 B:ASP277 3.9 40.6 1.0
C14 B:DST401 4.0 41.3 1.0
CD1 B:LEU259 4.1 35.0 1.0
C10 B:8O0402 4.2 41.6 1.0
C12 B:8O0402 4.2 40.6 1.0
NH1 B:ARG60 4.3 30.1 1.0
CG B:ARG60 4.3 23.3 1.0
CG2 B:VAL284 4.3 33.2 1.0
C12 B:DST401 4.4 47.5 1.0
CB B:ASP277 4.5 20.8 1.0
CG B:ASP277 4.6 34.0 1.0
CB B:VAL284 4.7 33.9 1.0
N02 B:8O0402 4.7 39.4 1.0
C09 B:8O0402 4.7 42.1 1.0
C13 B:DST401 4.8 42.2 1.0
CD B:ARG60 4.9 28.7 1.0
CA B:ALA44 5.0 22.1 1.0

Reference:

C.P.Wong, T.Awakawa, Y.Nakashima, T.Mori, Q.Zhu, X.Liu, I.Abe. Two Distinct Substrate Binding Modes For the Normal and Reverse Prenylation of Hapalindoles By the Prenyltransferase AMBP3 Angew. Chem. Int. Ed. Engl. V. 57 560 2018.
ISSN: ESSN 1521-3773
PubMed: 29178634
DOI: 10.1002/ANIE.201710682
Page generated: Sat Jul 12 10:52:22 2025

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