Atomistry » Chlorine » PDB 6de4-6dov » 6dmg
Atomistry »
  Chlorine »
    PDB 6de4-6dov »
      6dmg »

Chlorine in PDB 6dmg: A Multiconformer Ligand Model of EK6 Bound to ERK2

Enzymatic activity of A Multiconformer Ligand Model of EK6 Bound to ERK2

All present enzymatic activity of A Multiconformer Ligand Model of EK6 Bound to ERK2:
2.7.11.24;

Protein crystallography data

The structure of A Multiconformer Ligand Model of EK6 Bound to ERK2, PDB code: 6dmg was solved by B.M.Hudson, G.C.P.Van Zundert, D.A.Keedy, R.Fonseca, A.Heliou, P.Suresh, K.Borrelli, T.Day, J.S.Fraser, H.Van Den Bedem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.93 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.780, 70.700, 60.860, 90.00, 110.11, 90.00
R / Rfree (%) 18.6 / 23.6

Other elements in 6dmg:

The structure of A Multiconformer Ligand Model of EK6 Bound to ERK2 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the A Multiconformer Ligand Model of EK6 Bound to ERK2 (pdb code 6dmg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the A Multiconformer Ligand Model of EK6 Bound to ERK2, PDB code: 6dmg:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6dmg

Go back to Chlorine Binding Sites List in 6dmg
Chlorine binding site 1 out of 4 in the A Multiconformer Ligand Model of EK6 Bound to ERK2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of A Multiconformer Ligand Model of EK6 Bound to ERK2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:37.5
occ:0.46
CL2 A:EK6407 0.0 37.5 0.5
CL2 A:EK6407 0.2 37.7 0.5
C27 A:EK6407 1.6 34.3 0.5
C27 A:EK6407 1.8 33.7 0.5
C26 A:EK6407 2.6 33.0 0.5
C6 A:EK6407 2.6 33.3 0.5
H1 A:EK6407 2.6 41.5 0.5
H12 A:EK6407 2.7 39.6 0.5
H3 A:EK6407 2.7 42.3 0.5
C6 A:EK6407 2.8 33.2 0.5
C26 A:EK6407 2.8 33.1 0.5
HA3 A:GLY30 2.8 57.3 1.0
H12 A:EK6407 2.8 39.7 0.5
H2 A:EK6407 2.9 41.3 0.5
C5 A:EK6407 2.9 34.6 0.5
HB A:VAL37 3.0 49.6 1.0
C5 A:EK6407 3.1 34.4 0.5
N1 A:EK6407 3.1 35.3 0.5
HG21 A:VAL37 3.2 44.1 1.0
N1 A:EK6407 3.3 35.4 0.5
HG23 A:VAL37 3.4 44.1 1.0
H25 A:EK6407 3.4 49.2 0.5
H25 A:EK6407 3.4 49.0 0.5
CA A:GLY30 3.5 47.8 1.0
CG2 A:VAL37 3.6 36.8 1.0
C A:GLY30 3.7 46.7 1.0
CB A:VAL37 3.7 41.3 1.0
H A:GLY30 3.8 52.9 1.0
C7 A:EK6407 3.8 32.0 0.5
C9 A:EK6407 3.8 32.3 0.5
O1 A:EK6407 3.9 38.8 0.5
H2 A:EK6407 3.9 41.5 0.5
H3 A:EK6407 3.9 42.5 0.5
N A:GLY30 3.9 44.0 1.0
HG22 A:ILE29 4.0 48.1 1.0
CL1 A:EK6407 4.0 50.6 0.5
O A:HOH546 4.0 32.4 1.0
H1 A:EK6407 4.0 41.3 0.5
C7 A:EK6407 4.0 32.0 0.5
C9 A:EK6407 4.0 32.1 0.5
O A:GLY30 4.1 50.0 1.0
CL1 A:EK6407 4.1 50.6 0.5
C3 A:EK6407 4.1 37.4 0.5
N A:GLU31 4.2 50.3 1.0
C4 A:EK6407 4.2 37.1 0.5
H20 A:EK6407 4.2 42.3 0.5
HG11 A:VAL37 4.2 47.0 1.0
H20 A:EK6407 4.3 41.9 0.5
C24 A:EK6407 4.3 40.9 0.5
H17 A:EK6407 4.3 38.5 0.5
C24 A:EK6407 4.3 41.0 0.5
H A:GLU31 4.3 60.4 1.0
C8 A:EK6407 4.3 31.9 0.5
HA2 A:GLY30 4.4 57.3 1.0
H A:VAL37 4.4 52.7 1.0
H17 A:EK6407 4.4 38.4 0.5
C4 A:EK6407 4.5 35.9 0.5
HG22 A:VAL37 4.5 44.1 1.0
H5 A:EK6407 4.5 44.5 0.5
C8 A:EK6407 4.6 31.7 0.5
H14 A:EK6407 4.6 38.4 0.5
CG1 A:VAL37 4.6 39.2 1.0
HB A:ILE29 4.6 56.1 1.0
HG21 A:ILE29 4.7 48.1 1.0
C23 A:EK6407 4.7 43.6 0.5
CG2 A:ILE29 4.7 40.1 1.0
O2 A:EK6407 4.7 40.2 0.5
O2 A:EK6407 4.7 36.1 0.5
C23 A:EK6407 4.7 43.6 0.5
C25 A:EK6407 4.8 32.1 0.5
H14 A:EK6407 4.8 38.4 0.5
N5 A:EK6407 4.8 35.3 0.5
C25 A:EK6407 4.8 32.0 0.5
H5 A:EK6407 4.8 43.1 0.5
N A:VAL37 4.8 43.9 1.0
N5 A:EK6407 4.9 34.9 0.5
CA A:VAL37 4.9 44.5 1.0
C A:ILE29 4.9 44.6 1.0
HA A:GLU31 4.9 64.5 1.0
H22 A:EK6407 5.0 43.2 0.5
HG12 A:VAL37 5.0 47.0 1.0
H23 A:EK6407 5.0 42.9 0.5

Chlorine binding site 2 out of 4 in 6dmg

Go back to Chlorine Binding Sites List in 6dmg
Chlorine binding site 2 out of 4 in the A Multiconformer Ligand Model of EK6 Bound to ERK2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of A Multiconformer Ligand Model of EK6 Bound to ERK2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:37.7
occ:0.54
CL2 A:EK6407 0.0 37.7 0.5
CL2 A:EK6407 0.2 37.5 0.5
C27 A:EK6407 1.8 34.3 0.5
C27 A:EK6407 2.0 33.7 0.5
H1 A:EK6407 2.7 41.5 0.5
H3 A:EK6407 2.7 42.3 0.5
C26 A:EK6407 2.8 33.0 0.5
C6 A:EK6407 2.8 33.3 0.5
HA3 A:GLY30 2.8 57.3 1.0
H12 A:EK6407 2.8 39.6 0.5
C26 A:EK6407 3.0 33.1 0.5
C6 A:EK6407 3.0 33.2 0.5
H12 A:EK6407 3.0 39.7 0.5
H2 A:EK6407 3.0 41.3 0.5
HB A:VAL37 3.0 49.6 1.0
C5 A:EK6407 3.1 34.6 0.5
HG21 A:VAL37 3.1 44.1 1.0
N1 A:EK6407 3.1 35.3 0.5
C5 A:EK6407 3.2 34.4 0.5
HG23 A:VAL37 3.3 44.1 1.0
H25 A:EK6407 3.3 49.2 0.5
H25 A:EK6407 3.3 49.0 0.5
N1 A:EK6407 3.4 35.4 0.5
CG2 A:VAL37 3.5 36.8 1.0
CA A:GLY30 3.5 47.8 1.0
C A:GLY30 3.6 46.7 1.0
O1 A:EK6407 3.7 38.8 0.5
CB A:VAL37 3.7 41.3 1.0
CL1 A:EK6407 3.7 50.6 0.5
CL1 A:EK6407 3.8 50.6 0.5
H A:GLY30 3.9 52.9 1.0
O A:GLY30 4.0 50.0 1.0
C3 A:EK6407 4.0 37.4 0.5
H2 A:EK6407 4.0 41.5 0.5
H3 A:EK6407 4.0 42.5 0.5
N A:GLY30 4.0 44.0 1.0
N A:GLU31 4.0 50.3 1.0
C7 A:EK6407 4.0 32.0 0.5
C9 A:EK6407 4.0 32.3 0.5
O A:HOH546 4.1 32.4 1.0
C24 A:EK6407 4.1 40.9 0.5
C24 A:EK6407 4.1 41.0 0.5
HG22 A:ILE29 4.2 48.1 1.0
H1 A:EK6407 4.2 41.3 0.5
H A:GLU31 4.2 60.4 1.0
H20 A:EK6407 4.2 42.3 0.5
C4 A:EK6407 4.2 37.1 0.5
C9 A:EK6407 4.3 32.1 0.5
H20 A:EK6407 4.3 41.9 0.5
C7 A:EK6407 4.3 32.0 0.5
H A:VAL37 4.3 52.7 1.0
HG11 A:VAL37 4.3 47.0 1.0
HA2 A:GLY30 4.4 57.3 1.0
H17 A:EK6407 4.4 38.5 0.5
HG22 A:VAL37 4.4 44.1 1.0
C23 A:EK6407 4.5 43.6 0.5
H17 A:EK6407 4.5 38.4 0.5
C23 A:EK6407 4.5 43.6 0.5
H5 A:EK6407 4.5 44.5 0.5
C4 A:EK6407 4.6 35.9 0.5
C8 A:EK6407 4.6 31.9 0.5
O2 A:EK6407 4.6 40.2 0.5
CG1 A:VAL37 4.6 39.2 1.0
O2 A:EK6407 4.7 36.1 0.5
N A:VAL37 4.7 43.9 1.0
HB A:ILE29 4.7 56.1 1.0
HA A:GLU31 4.8 64.5 1.0
H14 A:EK6407 4.8 38.4 0.5
C8 A:EK6407 4.8 31.7 0.5
N5 A:EK6407 4.8 35.3 0.5
CA A:VAL37 4.8 44.5 1.0
N5 A:EK6407 4.8 34.9 0.5
C25 A:EK6407 4.8 32.1 0.5
CA A:GLU31 4.9 53.8 1.0
HG21 A:ILE29 4.9 48.1 1.0
H5 A:EK6407 4.9 43.1 0.5
H23 A:EK6407 4.9 42.9 0.5
H22 A:EK6407 4.9 43.2 0.5
CG2 A:ILE29 4.9 40.1 1.0
C25 A:EK6407 4.9 32.0 0.5
C A:GLU31 5.0 55.2 1.0
C2 A:EK6407 5.0 38.6 0.5
H14 A:EK6407 5.0 38.4 0.5

Chlorine binding site 3 out of 4 in 6dmg

Go back to Chlorine Binding Sites List in 6dmg
Chlorine binding site 3 out of 4 in the A Multiconformer Ligand Model of EK6 Bound to ERK2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of A Multiconformer Ligand Model of EK6 Bound to ERK2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:50.6
occ:0.46
CL1 A:EK6407 0.0 50.6 0.5
CL1 A:EK6407 0.1 50.6 0.5
C23 A:EK6407 1.8 43.6 0.5
C23 A:EK6407 1.8 43.6 0.5
H A:GLY32 2.7 65.2 1.0
C22 A:EK6407 2.7 46.2 0.5
C24 A:EK6407 2.8 41.0 0.5
C22 A:EK6407 2.8 46.3 0.5
HA3 A:GLY32 2.8 65.6 1.0
C24 A:EK6407 2.8 40.9 0.5
HG23 A:VAL37 2.8 44.1 1.0
H25 A:EK6407 2.8 49.2 0.5
H25 A:EK6407 2.9 49.0 0.5
F A:EK6407 2.9 52.1 0.5
N A:GLY32 3.0 54.4 1.0
F A:EK6407 3.0 52.1 0.5
CA A:GLY32 3.3 54.7 1.0
O A:GLY35 3.4 49.9 1.0
HA A:MET36 3.5 62.3 1.0
HA A:GLU31 3.6 64.5 1.0
C A:GLY35 3.6 47.5 1.0
CG2 A:VAL37 3.7 36.8 1.0
C A:GLU31 3.7 55.2 1.0
HA2 A:GLY32 3.8 65.6 1.0
CL2 A:EK6407 3.8 37.7 0.5
HG21 A:VAL37 3.9 44.1 1.0
N A:MET36 3.9 49.6 1.0
HG3 A:LYS52 4.0 46.9 1.0
C21 A:EK6407 4.0 45.0 0.5
C19 A:EK6407 4.0 39.6 0.5
C21 A:EK6407 4.0 45.0 0.5
CA A:MET36 4.1 51.9 1.0
CL2 A:EK6407 4.1 37.5 0.5
HD2 A:LYS52 4.1 45.1 1.0
C19 A:EK6407 4.1 39.7 0.5
HG22 A:VAL37 4.1 44.1 1.0
CA A:GLU31 4.1 53.8 1.0
HA3 A:GLY35 4.1 59.5 1.0
O1 A:EK6407 4.2 38.8 0.5
H A:VAL37 4.2 52.7 1.0
C A:MET36 4.3 47.6 1.0
N A:VAL37 4.3 43.9 1.0
CA A:GLY35 4.4 49.6 1.0
H9 A:EK6407 4.4 48.3 0.5
HD3 A:LYS52 4.4 45.1 1.0
H A:GLY35 4.4 63.3 1.0
H A:MET36 4.5 59.5 1.0
N A:GLU31 4.5 50.3 1.0
C20 A:EK6407 4.6 41.0 0.5
O A:GLU31 4.6 57.9 1.0
CD A:LYS52 4.6 37.6 1.0
C20 A:EK6407 4.6 40.9 0.5
C A:GLY32 4.6 58.0 1.0
O A:GLY30 4.6 50.0 1.0
CG A:LYS52 4.7 39.1 1.0
HB A:VAL37 4.7 49.6 1.0
H26 A:EK6407 4.8 54.0 0.5
C A:GLY30 4.8 46.7 1.0
N A:GLY35 4.8 52.8 1.0
H7 A:EK6407 4.8 46.3 0.5
H26 A:EK6407 4.8 54.0 0.5
CB A:VAL37 4.8 41.3 1.0
C2 A:EK6407 4.9 38.6 0.5
O A:MET36 5.0 43.8 1.0
H A:GLU31 5.0 60.4 1.0

Chlorine binding site 4 out of 4 in 6dmg

Go back to Chlorine Binding Sites List in 6dmg
Chlorine binding site 4 out of 4 in the A Multiconformer Ligand Model of EK6 Bound to ERK2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of A Multiconformer Ligand Model of EK6 Bound to ERK2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:50.6
occ:0.54
CL1 A:EK6407 0.0 50.6 0.5
CL1 A:EK6407 0.1 50.6 0.5
C23 A:EK6407 1.8 43.6 0.5
C23 A:EK6407 1.8 43.6 0.5
H A:GLY32 2.7 65.2 1.0
C24 A:EK6407 2.7 41.0 0.5
C24 A:EK6407 2.8 40.9 0.5
H25 A:EK6407 2.8 49.2 0.5
C22 A:EK6407 2.8 46.2 0.5
C22 A:EK6407 2.8 46.3 0.5
HA3 A:GLY32 2.8 65.6 1.0
HG23 A:VAL37 2.8 44.1 1.0
H25 A:EK6407 2.8 49.0 0.5
N A:GLY32 3.0 54.4 1.0
F A:EK6407 3.0 52.1 0.5
F A:EK6407 3.1 52.1 0.5
CA A:GLY32 3.3 54.7 1.0
O A:GLY35 3.5 49.9 1.0
HA A:MET36 3.6 62.3 1.0
HA A:GLU31 3.6 64.5 1.0
C A:GLU31 3.7 55.2 1.0
CG2 A:VAL37 3.7 36.8 1.0
CL2 A:EK6407 3.7 37.7 0.5
C A:GLY35 3.7 47.5 1.0
HA2 A:GLY32 3.8 65.6 1.0
HG21 A:VAL37 3.8 44.1 1.0
CL2 A:EK6407 4.0 37.5 0.5
C19 A:EK6407 4.0 39.6 0.5
HG3 A:LYS52 4.0 46.9 1.0
C19 A:EK6407 4.0 39.7 0.5
C21 A:EK6407 4.0 45.0 0.5
C21 A:EK6407 4.1 45.0 0.5
N A:MET36 4.1 49.6 1.0
O1 A:EK6407 4.1 38.8 0.5
CA A:GLU31 4.1 53.8 1.0
HG22 A:VAL37 4.1 44.1 1.0
HD2 A:LYS52 4.1 45.1 1.0
CA A:MET36 4.1 51.9 1.0
H A:VAL37 4.2 52.7 1.0
HA3 A:GLY35 4.2 59.5 1.0
H9 A:EK6407 4.3 48.3 0.5
C A:MET36 4.4 47.6 1.0
N A:VAL37 4.4 43.9 1.0
HD3 A:LYS52 4.4 45.1 1.0
CA A:GLY35 4.5 49.6 1.0
N A:GLU31 4.5 50.3 1.0
O A:GLU31 4.5 57.9 1.0
H A:GLY35 4.5 63.3 1.0
C20 A:EK6407 4.5 41.0 0.5
C20 A:EK6407 4.6 40.9 0.5
O A:GLY30 4.6 50.0 1.0
H A:MET36 4.6 59.5 1.0
C A:GLY32 4.6 58.0 1.0
CD A:LYS52 4.6 37.6 1.0
H7 A:EK6407 4.7 46.3 0.5
HB A:VAL37 4.7 49.6 1.0
C A:GLY30 4.7 46.7 1.0
H26 A:EK6407 4.8 54.0 0.5
CB A:VAL37 4.8 41.3 1.0
H26 A:EK6407 4.8 54.0 0.5
CG A:LYS52 4.8 39.1 1.0
C2 A:EK6407 4.8 38.6 0.5
N A:GLY35 4.9 52.8 1.0
H A:GLU31 4.9 60.4 1.0
C1 A:EK6407 5.0 40.3 0.5

Reference:

G.C.P.Van Zundert, B.M.Hudson, S.H.P.De Oliveira, D.A.Keedy, R.Fonseca, A.Heliou, P.Suresh, K.Borrelli, T.Day, J.S.Fraser, H.Van Den Bedem. Qfit-Ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J. Med. Chem. V. 61 11183 2018.
ISSN: ISSN 1520-4804
PubMed: 30457858
DOI: 10.1021/ACS.JMEDCHEM.8B01292
Page generated: Sat Jul 12 12:52:59 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy