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Bromine in PDB 3v8n: Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with 8-Bromo-5'-Amino-5'-Deoxyadenosine, Reacted with A Citrate Molecule in N Site

Enzymatic activity of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with 8-Bromo-5'-Amino-5'-Deoxyadenosine, Reacted with A Citrate Molecule in N Site

All present enzymatic activity of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with 8-Bromo-5'-Amino-5'-Deoxyadenosine, Reacted with A Citrate Molecule in N Site:
2.7.1.23;

Protein crystallography data

The structure of Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with 8-Bromo-5'-Amino-5'-Deoxyadenosine, Reacted with A Citrate Molecule in N Site, PDB code: 3v8n was solved by M.Gelin, G.Poncet-Montange, L.Assairi, L.Morellato, V.Huteau, L.Dugu, O.Dussurget, S.Pochet, G.Labesse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.98 / 2.38
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 63.063, 75.966, 119.012, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.6

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with 8-Bromo-5'-Amino-5'-Deoxyadenosine, Reacted with A Citrate Molecule in N Site (pdb code 3v8n). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with 8-Bromo-5'-Amino-5'-Deoxyadenosine, Reacted with A Citrate Molecule in N Site, PDB code: 3v8n:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 3v8n

Go back to Bromine Binding Sites List in 3v8n
Bromine binding site 1 out of 2 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with 8-Bromo-5'-Amino-5'-Deoxyadenosine, Reacted with A Citrate Molecule in N Site


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 8-Bromo-5'-Amino-5'-Deoxyadenosine, Reacted with A Citrate Molecule in N Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br301

b:44.8
occ:0.60
BR8 A:5NB301 0.0 44.8 0.6
C8 A:5NB301 1.9 51.8 1.0
N9 A:5NB301 2.8 52.3 1.0
N7 A:5NB301 2.8 47.0 1.0
C1' A:5NB301 3.2 51.6 1.0
N A:GLY46 3.5 35.0 1.0
CD1 A:LEU49 3.6 38.4 1.0
O51 A:5CI302 3.6 58.9 0.9
C A:ASP45 3.7 37.7 1.0
CB A:ASP45 3.7 36.0 1.0
C21 A:5CI302 3.7 63.4 0.9
CA A:GLY46 3.8 30.3 1.0
C61 A:5CI302 3.9 56.0 0.9
O4' A:5NB301 3.9 53.2 1.0
C4 A:5NB301 3.9 46.5 1.0
C5 A:5NB301 3.9 42.9 1.0
O A:ASP45 3.9 37.3 1.0
N5' A:5CI302 4.2 56.6 0.9
ND2 A:ASN122 4.2 30.9 1.0
C4' A:5CI302 4.3 43.2 0.9
CA A:ASP45 4.3 38.6 1.0
C5' A:5CI302 4.3 40.1 0.9
CG A:LEU49 4.4 39.3 1.0
C2' A:5NB301 4.4 49.6 1.0
O2' A:5NB301 4.5 49.5 1.0
O21 A:5CI302 4.6 63.2 0.9
C31 A:5CI302 4.6 63.1 0.9
C11 A:5CI302 4.7 61.8 0.9
CG A:ASP45 5.0 38.0 1.0
CB A:LEU49 5.0 37.7 1.0

Bromine binding site 2 out of 2 in 3v8n

Go back to Bromine Binding Sites List in 3v8n
Bromine binding site 2 out of 2 in the Crystal Structure of Nad Kinase 1 From Listeria Monocytogenes in Complex with 8-Bromo-5'-Amino-5'-Deoxyadenosine, Reacted with A Citrate Molecule in N Site


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 8-Bromo-5'-Amino-5'-Deoxyadenosine, Reacted with A Citrate Molecule in N Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br302

b:52.8
occ:0.70
BR8 A:5CI302 0.0 52.8 0.7
C8 A:5CI302 1.9 43.0 0.9
N7 A:5CI302 2.8 43.0 0.9
N9 A:5CI302 2.9 41.1 0.9
O4' A:5CI302 3.3 42.4 0.9
O A:HOH429 3.4 48.1 1.0
C1' A:5CI302 3.4 40.5 0.9
C2' A:5CI302 3.4 42.4 0.9
C3' A:5CI302 3.5 43.5 0.9
C5 A:5CI302 3.9 42.6 0.9
C4 A:5CI302 4.0 42.2 0.9
CD2 A:TYR163 4.0 33.9 1.0
C4' A:5CI302 4.0 43.2 0.9
CE2 A:TYR163 4.2 35.6 1.0
O A:HOH411 4.3 28.9 1.0
C5' A:5CI302 4.5 40.1 0.9
CG A:TYR163 4.7 30.8 1.0
O3' A:5CI302 4.7 38.9 0.9
O A:ASP222 4.7 44.0 1.0
O2' A:5CI302 4.8 45.5 0.9

Reference:

M.Gelin, G.Poncet-Montange, L.Assairi, L.Morellato, V.Huteau, L.Dugue, O.Dussurget, S.Pochet, G.Labesse. Screening and in Situ Synthesis Using Crystals of A Nad Kinase Lead to A Potent Antistaphylococcal Compound. Structure V. 20 1107 2012.
ISSN: ISSN 0969-2126
PubMed: 22608967
DOI: 10.1016/J.STR.2012.03.024
Page generated: Sat Dec 12 02:16:28 2020

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