Sodium in PDB 5dkp: Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.

All present enzymatic activity of Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.:
3.4.21.92;

The structure of Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556., PDB code: 5dkp was solved by J.D.Goodreid, J.Janetzko, J.P.Santa Maria Jr., K.Wong, E.Leung, B.T.Eger, S.Bryson, E.F.Pai, S.D.Gray-Owen, S.Walker, W.A.Houry, R.A.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.40 / 2.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	117.640, 198.850, 144.040, 90.00, 97.81, 90.00
R / Rfree (%)	19.6 / 23.9

The structure of Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556. also contains other interesting chemical elements:

Potassium

(K)

28 atoms

The binding sites of Sodium atom in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556. (pdb code 5dkp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556., PDB code: 5dkp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556. within 5.0Å range: probe atom residue distance (Å) B Occ c:Na302 b:25.1 occ:1.00 OE1 c:GLU56 2.3 28.7 1.0 O11 t:OTT1 2.7 25.5 1.0 CD c:GLU56 3.1 30.7 1.0 OE2 c:GLU56 3.2 28.4 1.0 CE1 c:PHE87 3.4 22.6 1.0 CD1 c:PHE87 3.6 16.1 1.0 C1 t:OTT1 3.6 22.0 1.0 CG2 c:ILE88 3.8 15.3 1.0 O c:HOH413 4.0 23.4 1.0 CD2 c:LEU53 4.1 14.9 1.0 CA t:PHE2 4.2 26.2 1.0 N t:SER3 4.3 27.4 1.0 N t:PHE2 4.3 15.8 1.0 CA c:ILE88 4.3 20.5 1.0 CB c:ILE88 4.4 22.3 1.0 O t:HOH101 4.4 44.0 1.0 CG c:GLU56 4.5 24.1 1.0 C2 t:OTT1 4.6 26.4 1.0 O t:SER3 4.6 16.1 1.0 C3 t:OTT1 4.6 31.9 1.0 CZ c:PHE87 4.7 19.1 1.0 C t:PHE2 4.8 22.2 1.0 CD1 t:PHE2 4.9 18.0 1.0 N c:ILE88 4.9 18.1 1.0 CG c:PHE87 5.0 23.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556. within 5.0Å range: probe atom residue distance (Å) B Occ h:Na302 b:37.1 occ:1.00 OE1 h:GLU56 2.7 31.4 1.0 CE2 h:PHE87 3.0 24.3 1.0 O11 y:OTT1 3.0 22.8 1.0 CD2 h:PHE87 3.3 24.6 1.0 OE2 h:GLU56 3.3 29.3 1.0 CD h:GLU56 3.3 32.7 1.0 O y:SER3 4.0 30.9 1.0 N y:SER3 4.1 26.1 1.0 CA h:ILE88 4.1 24.5 1.0 C1 y:OTT1 4.1 20.8 1.0 CG2 h:ILE88 4.1 16.3 1.0 CZ h:PHE87 4.3 23.3 1.0 O h:HOH409 4.3 17.2 1.0 CA y:PHE2 4.4 21.3 1.0 CB h:ILE88 4.5 25.2 1.0 CG h:PHE87 4.6 23.9 1.0 O h:PHE87 4.7 23.5 1.0 N h:ILE88 4.7 21.2 1.0 N y:PHE2 4.7 24.2 1.0 CD2 h:LEU53 4.7 15.3 1.0 CG h:GLU56 4.8 25.2 1.0 C y:PHE2 4.8 28.4 1.0 C y:SER3 4.9 32.0 1.0 C h:PHE87 4.9 20.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of N. Meningitidis Clpp in Complex with Agonist Adep A54556. within 5.0Å range: probe atom residue distance (Å) B Occ k:Na302 b:40.5 occ:1.00 OE1 k:GLU56 2.6 29.5 1.0 O11 1:OTT1 3.0 25.1 1.0 CE1 k:PHE87 3.4 20.1 1.0 CD k:GLU56 3.4 30.1 1.0 OE2 k:GLU56 3.4 28.0 1.0 CD1 k:PHE87 3.5 24.1 1.0 C1 1:OTT1 3.7 23.9 1.0 N 1:SER3 3.9 35.9 1.0 O 1:SER3 4.1 33.6 1.0 CA 1:PHE2 4.1 25.9 1.0 O k:HOH403 4.1 24.8 1.0 CG2 k:ILE88 4.1 16.3 1.0 N 1:PHE2 4.2 18.2 1.0 CD2 k:LEU53 4.3 15.8 1.0 CA k:ILE88 4.3 21.6 1.0 CZ k:PHE87 4.5 24.4 1.0 C 1:PHE2 4.6 28.5 1.0 CB k:ILE88 4.6 22.4 1.0 CG k:PHE87 4.7 27.1 1.0 C2 1:OTT1 4.8 24.1 1.0 CG k:GLU56 4.8 24.8 1.0 N k:ILE88 4.9 25.7 1.0 C3 1:OTT1 4.9 26.3 1.0 CD1 1:PHE2 4.9 15.4 1.0 C 1:SER3 4.9 28.6 1.0 CA 1:SER3 4.9 21.6 1.0

J.D.Goodreid, J.Janetzko, J.P.Santa Maria, K.S.Wong, E.Leung, B.T.Eger, S.Bryson, E.F.Pai, S.D.Gray-Owen, S.Walker, W.A.Houry, R.A.Batey. Development and Characterization of Potent Cyclic Acyldepsipeptide Analogues with Increased Antimicrobial Activity. J.Med.Chem. V. 59 624 2016.
ISSN: ISSN 0022-2623
PubMed: 26818454
DOI: 10.1021/ACS.JMEDCHEM.5B01451