Magnesium in PDB 6s40: Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites

Protein crystallography data

The structure of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites, PDB code: 6s40 was solved by S.Leysen, X.Guillory, M.Wolter, S.Genet, B.Somsen, J.Patel, P.Castaldi, C.Ottmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.04 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.090, 112.115, 62.604, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19.7

Other elements in 6s40:

The structure of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites (pdb code 6s40). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites, PDB code: 6s40:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6s40

Go back to Magnesium Binding Sites List in 6s40
Magnesium binding site 1 out of 4 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:10.3
occ:1.00
OE2 A:GLU188 2.2 22.7 1.0
CD A:GLU188 3.3 23.6 1.0
CG A:GLU188 3.8 21.8 1.0
OE1 A:GLU188 4.4 22.8 1.0
O A:HOH594 4.5 31.1 1.0

Magnesium binding site 2 out of 4 in 6s40

Go back to Magnesium Binding Sites List in 6s40
Magnesium binding site 2 out of 4 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:26.4
occ:0.98
O A:HOH430 2.1 35.5 1.0
OE2 A:GLU89 2.3 16.5 1.0
O A:HOH479 2.4 36.4 1.0
CD A:GLU89 3.3 15.2 1.0
O A:HOH455 4.0 29.6 1.0
CG A:GLU89 4.1 14.6 1.0
O A:HOH552 4.1 38.3 1.0
OE1 A:GLU89 4.3 13.9 1.0
NH1 A:ARG85 4.3 17.8 1.0
OE1 A:GLN93 4.5 13.8 1.0
CG A:GLU86 4.6 20.4 1.0
CB A:GLU89 4.7 14.0 1.0
NE2 A:GLN93 4.8 14.0 1.0
O A:HOH570 4.9 32.5 1.0
OG1 A:THR90 4.9 13.2 0.7

Magnesium binding site 3 out of 4 in 6s40

Go back to Magnesium Binding Sites List in 6s40
Magnesium binding site 3 out of 4 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:7.8
occ:0.50
OE1 A:GLU2 2.4 13.2 1.0
O A:HOH429 2.5 13.3 1.0
CD A:GLU2 3.4 13.8 1.0
OE2 A:GLU2 3.7 14.2 1.0
O A:HOH530 4.3 10.2 1.0
O A:HOH606 4.5 16.3 1.0
CG A:GLU2 4.6 12.7 1.0
CA A:GLU2 4.8 11.2 1.0
N A:ARG3 4.9 10.5 1.0
CB A:GLU2 5.0 12.1 1.0

Magnesium binding site 4 out of 4 in 6s40

Go back to Magnesium Binding Sites List in 6s40
Magnesium binding site 4 out of 4 in the Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fragment Az-001 Binding at the P53PT387/14-3-3 Sigma Interface and Additional Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:44.2
occ:1.00
O A:HOH476 2.1 28.3 1.0
O A:HOH420 2.5 21.0 1.0
N A:MET-2 3.0 19.2 1.0
N A:ALA-3 3.3 26.2 1.0
OE1 A:GLU31 3.3 19.8 1.0
CB A:MET-2 3.4 16.0 1.0
CA A:GLY-4 3.4 31.8 1.0
O A:HOH473 3.4 11.8 1.0
C A:GLY-4 3.4 29.3 1.0
CG A:MET-2 3.6 16.9 1.0
CA A:MET-2 3.7 17.3 1.0
O A:HOH529 3.9 33.0 1.0
C A:ALA-3 4.0 21.6 1.0
O A:HOH604 4.0 36.0 1.0
O A:HOH544 4.1 29.6 1.0
CA A:ALA-3 4.1 27.4 1.0
O A:GLY-4 4.2 23.6 1.0
CA A:GLY28 4.2 10.2 1.0
C A:MET-2 4.3 15.1 1.0
N A:GLY-1 4.3 13.9 1.0
CD A:GLU31 4.5 15.5 1.0
CB A:ALA-3 4.6 28.6 1.0
N A:GLY28 4.7 10.1 1.0
NZ A:LYS27 4.7 14.8 1.0
O A:HOH470 4.7 13.4 1.0
N A:GLY-4 4.8 35.6 1.0

Reference:

X.Guillory, M.Wolter, S.Leysen, J.F.Neves, A.Kuusk, S.Genet, B.Somsen, J.Morrow, E.Rivers, L.Van Beek, J.Patel, R.Goodnow, H.Schoenherr, N.Fuller, Q.Cao, R.G.Doveston, L.Brunsveld, M.R.Arkin, M.P.Castaldi, H.Boyd, I.Landrieu, H.Chen, C.Ottmann. Fragment-Based Differential Targeting of Ppi Stabilizer Interfaces. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32501690
DOI: 10.1021/ACS.JMEDCHEM.9B01942
Page generated: Tue Dec 15 00:03:03 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy