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Bromine in PDB 3v8r: Crystal Structure of Nad Kinase 1 H223E Mutant From Listeria Monocytogenes in Complex with 5'-Amino-8-Bromo-5'-Deoxyadenosine

Enzymatic activity of Crystal Structure of Nad Kinase 1 H223E Mutant From Listeria Monocytogenes in Complex with 5'-Amino-8-Bromo-5'-Deoxyadenosine

All present enzymatic activity of Crystal Structure of Nad Kinase 1 H223E Mutant From Listeria Monocytogenes in Complex with 5'-Amino-8-Bromo-5'-Deoxyadenosine:
2.7.1.23;

Protein crystallography data

The structure of Crystal Structure of Nad Kinase 1 H223E Mutant From Listeria Monocytogenes in Complex with 5'-Amino-8-Bromo-5'-Deoxyadenosine, PDB code: 3v8r 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) 55.42 / 2.39
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 62.718, 77.135, 118.358, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 26.4

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Nad Kinase 1 H223E Mutant From Listeria Monocytogenes in Complex with 5'-Amino-8-Bromo-5'-Deoxyadenosine (pdb code 3v8r). 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 H223E Mutant From Listeria Monocytogenes in Complex with 5'-Amino-8-Bromo-5'-Deoxyadenosine, PDB code: 3v8r:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 3v8r

Go back to Bromine Binding Sites List in 3v8r
Bromine binding site 1 out of 2 in the Crystal Structure of Nad Kinase 1 H223E Mutant From Listeria Monocytogenes in Complex with 5'-Amino-8-Bromo-5'-Deoxyadenosine


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 H223E Mutant From Listeria Monocytogenes in Complex with 5'-Amino-8-Bromo-5'-Deoxyadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br301

b:43.5
occ:0.75
BR8 A:5NB301 0.0 43.5 0.8
C8 A:5NB301 1.9 42.2 1.0
N9 A:5NB301 2.8 40.6 1.0
N7 A:5NB301 2.9 43.8 1.0
C1' A:5NB301 3.1 40.9 1.0
CD1 A:LEU49 3.5 28.3 1.0
N A:GLY46 3.7 32.2 1.0
CB A:ASP45 3.8 34.2 1.0
C A:ASP45 3.9 30.1 1.0
C4 A:5NB301 3.9 40.7 1.0
C5 A:5NB301 4.0 41.1 1.0
CA A:GLY46 4.0 28.9 1.0
ND2 A:ASN122 4.1 26.1 1.0
O4' A:5NB301 4.1 48.7 1.0
O A:ASP45 4.1 25.5 1.0
C4' A:5NB302 4.1 52.4 1.0
CG A:LEU49 4.2 32.8 1.0
C5' A:5NB302 4.3 48.1 1.0
O2' A:5NB301 4.3 44.9 1.0
C2' A:5NB301 4.3 42.0 1.0
CA A:ASP45 4.5 33.1 1.0
O3' A:5NB302 4.7 37.6 1.0
CB A:LEU49 5.0 31.9 1.0

Bromine binding site 2 out of 2 in 3v8r

Go back to Bromine Binding Sites List in 3v8r
Bromine binding site 2 out of 2 in the Crystal Structure of Nad Kinase 1 H223E Mutant From Listeria Monocytogenes in Complex with 5'-Amino-8-Bromo-5'-Deoxyadenosine


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 H223E Mutant From Listeria Monocytogenes in Complex with 5'-Amino-8-Bromo-5'-Deoxyadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br302

b:57.4
occ:0.60
BR8 A:5NB302 0.0 57.4 0.6
C8 A:5NB302 1.9 55.0 1.0
N7 A:5NB302 2.8 57.0 1.0
N9 A:5NB302 2.9 54.0 1.0
O4' A:5NB302 3.3 54.0 1.0
C1' A:5NB302 3.4 50.5 1.0
N5' A:5NB302 3.5 49.3 1.0
C2' A:5NB302 3.6 44.7 1.0
C3' A:5NB302 3.8 44.7 1.0
C5 A:5NB302 4.0 53.3 1.0
C4 A:5NB302 4.0 52.4 1.0
C4' A:5NB302 4.0 52.4 1.0
CD2 A:TYR163 4.2 24.6 0.8
CE2 A:TYR163 4.3 27.5 0.8
C5' A:5NB302 4.4 48.1 1.0
O A:HOH419 4.6 17.2 1.0
CG A:TYR163 5.0 21.0 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 02:16:31 2020

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