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Bromine in PDB 5dht: Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor

Enzymatic activity of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor

All present enzymatic activity of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor:
2.7.1.23;

Protein crystallography data

The structure of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor, PDB code: 5dht was solved by M.Gelin, J.Paoletti, L.Assairi, V.Huteau, S.Pochet, G.Labesse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.32 / 2.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.781, 119.072, 67.347, 90.00, 100.03, 90.00
R / Rfree (%) 22.9 / 27.1

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor (pdb code 5dht). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor, PDB code: 5dht:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 5dht

Go back to Bromine Binding Sites List in 5dht
Bromine binding site 1 out of 4 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br303

b:38.9
occ:0.50
BR A:5A9303 0.0 38.9 0.5
CBD A:5A9303 1.9 41.5 1.0
CBE A:5A9303 2.8 41.5 1.0
CBC A:5A9303 2.8 42.4 1.0
C6 A:5A9303 3.7 39.8 1.0
NH1 C:ARG148 3.8 69.2 1.0
C5 A:5A9303 3.8 44.3 1.0
CD1 C:ILE187 3.9 44.0 0.5
N1 A:5A9303 3.9 39.7 1.0
C4 A:5A9303 4.0 46.6 1.0
C2 A:5A9303 4.1 42.0 1.0
N3 A:5A9303 4.1 45.0 1.0
CAV A:5A9303 4.1 44.0 1.0
CAX A:5A9303 4.1 43.0 1.0
N6 A:5A9303 4.2 37.6 1.0
N7 A:5A9303 4.4 46.8 1.0
CG C:ARG148 4.4 60.0 1.0
CD C:ARG148 4.5 62.8 1.0
CB C:PRO132 4.5 72.5 1.0
CB C:ILE187 4.6 39.3 0.9
N9 A:5A9303 4.6 52.2 1.0
CAW A:5A9303 4.7 43.9 1.0
CG1 C:ILE187 4.7 41.9 0.8
C8 A:5A9303 4.8 49.6 1.0
CA C:GLY149 4.9 50.9 1.0
CZ C:ARG148 4.9 69.1 1.0
CG2 C:ILE187 4.9 39.7 0.8

Bromine binding site 2 out of 4 in 5dht

Go back to Bromine Binding Sites List in 5dht
Bromine binding site 2 out of 4 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br302

b:69.8
occ:0.80
BR B:5A9302 0.0 69.8 0.8
CBD B:5A9302 1.8 62.4 1.0
CBC B:5A9302 2.7 61.5 1.0
CBE B:5A9302 2.7 61.6 1.0
N1 B:5A9302 3.5 44.8 1.0
NE D:ARG148 3.5 52.4 1.0
C6 B:5A9302 3.5 46.4 1.0
C2 B:5A9302 3.7 44.5 1.0
C5 B:5A9302 3.7 47.1 1.0
N3 B:5A9302 3.9 45.8 1.0
C4 B:5A9302 3.9 46.8 1.0
CAV B:5A9302 4.0 61.3 1.0
CG D:ARG148 4.0 53.2 1.0
CAX B:5A9302 4.0 61.6 1.0
N6 B:5A9302 4.0 47.7 1.0
NH2 D:ARG148 4.1 55.5 1.0
CZ D:ARG148 4.2 54.6 1.0
CD D:ARG148 4.2 52.2 1.0
N7 B:5A9302 4.4 49.1 1.0
CA D:GLY149 4.4 63.3 1.0
CB D:PRO132 4.5 63.8 1.0
CAW B:5A9302 4.5 61.5 1.0
N D:GLY149 4.6 63.3 1.0
N9 B:5A9302 4.6 50.7 1.0
O D:GLY149 4.7 69.3 1.0
CD1 D:ILE187 4.8 51.4 1.0
C D:GLY149 4.9 65.8 1.0
C8 B:5A9302 4.9 50.7 1.0
C D:ARG148 5.0 57.1 1.0
CB D:ILE187 5.0 46.1 1.0
CG D:PRO132 5.0 66.6 1.0

Bromine binding site 3 out of 4 in 5dht

Go back to Bromine Binding Sites List in 5dht
Bromine binding site 3 out of 4 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br301

b:47.0
occ:0.50
BR C:5A9301 0.0 47.0 0.5
CBD C:5A9301 1.8 40.2 1.0
CBC C:5A9301 2.7 41.4 1.0
CBE C:5A9301 2.8 40.8 1.0
NE A:ARG148 3.6 58.5 1.0
C5 C:5A9301 3.7 39.5 1.0
C6 C:5A9301 3.7 38.8 1.0
C4 C:5A9301 3.8 41.3 1.0
N1 C:5A9301 3.9 39.0 1.0
N3 C:5A9301 4.0 39.7 1.0
C2 C:5A9301 4.0 39.7 1.0
CAV C:5A9301 4.0 44.9 1.0
CAX C:5A9301 4.1 41.3 1.0
CG A:ARG148 4.1 51.4 1.0
N7 C:5A9301 4.2 40.8 1.0
CD A:ARG148 4.3 55.2 1.0
N6 C:5A9301 4.3 41.4 1.0
NH2 A:ARG148 4.3 65.5 1.0
CZ A:ARG148 4.3 65.0 1.0
CB A:PRO132 4.3 57.5 1.0
N9 C:5A9301 4.3 44.7 1.0
CA A:GLY149 4.5 43.8 1.0
C8 C:5A9301 4.5 43.1 1.0
CAW C:5A9301 4.6 42.7 1.0
CD1 A:ILE187 4.7 46.0 0.5
N A:GLY149 4.7 43.0 1.0
O A:GLY149 4.8 49.8 1.0
C A:GLY149 5.0 46.9 1.0

Bromine binding site 4 out of 4 in 5dht

Go back to Bromine Binding Sites List in 5dht
Bromine binding site 4 out of 4 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with A Novel Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br302

b:95.0
occ:0.60
BR D:5A9302 0.0 95.0 0.6
CBD D:5A9302 1.7 0.4 1.0
CBC D:5A9302 2.6 1.0 1.0
CBE D:5A9302 2.8 0.2 1.0
N7 D:5A9302 3.5 65.4 1.0
C5 D:5A9302 3.6 65.0 1.0
C8 D:5A9302 3.7 66.9 1.0
C4 D:5A9302 3.9 65.0 1.0
CAV D:5A9302 3.9 0.7 1.0
N9 D:5A9302 4.0 66.3 1.0
CB B:PRO132 4.0 75.8 1.0
CAX D:5A9302 4.0 0.1 1.0
C6 D:5A9302 4.1 65.7 1.0
NH2 B:ARG148 4.2 93.9 1.0
CG B:PRO132 4.3 80.2 1.0
CA B:PRO132 4.3 74.4 1.0
SAH D:5A9302 4.3 67.8 1.0
N6 D:5A9302 4.3 65.2 1.0
CZ B:ARG148 4.4 91.3 1.0
CAW D:5A9302 4.5 0.9 1.0
NAK D:5A9302 4.5 98.8 1.0
NH1 B:ARG148 4.5 91.0 1.0
OAS D:5A9302 4.6 68.9 1.0
N3 D:5A9302 4.6 64.0 1.0
N1 D:5A9302 4.8 65.3 1.0
O B:GLY149 4.8 67.2 1.0
CAR D:5A9302 4.8 68.2 1.0
CAM D:5A9302 5.0 0.1 1.0
C2 D:5A9302 5.0 64.3 1.0

Reference:

J.Paoletti, L.Assairi, M.Gelin, V.Huteau, M.A.Nahori, O.Dussurget, G.Labesse, S.Pochet. 8-Thioalkyl-Adenosine Derivatives Inhibit Listeria Monocytogenes Nad Kinase Through A Novel Binding Mode. Eur.J.Med.Chem. V. 124 1041 2016.
ISSN: ISSN 0223-5234
PubMed: 27783975
DOI: 10.1016/J.EJMECH.2016.10.033
Page generated: Wed Jul 10 23:25:26 2024

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