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Sodium in PDB 8pkx: Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec)

Protein crystallography data

The structure of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec), PDB code: 8pkx was solved by M.B.Braun, L.Bischof, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.24 / 1.79
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.43, 68.877, 78.252, 90, 117.68, 90
R / Rfree (%) 17.5 / 21

Other elements in 8pkx:

The structure of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec) (pdb code 8pkx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec), PDB code: 8pkx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8pkx

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Sodium binding site 1 out of 4 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na709

b:59.2
occ:1.00
OG A:SER508 2.8 36.5 0.7
OG A:SER555 3.0 46.7 1.0
O A:SER508 3.1 29.7 1.0
O A:HOH978 3.2 58.8 1.0
C A:SER508 3.4 27.8 1.0
CB A:TYR525 3.5 35.6 1.0
CB A:SER508 3.7 33.7 0.3
CB A:SER508 3.8 33.8 0.7
OG A:SER508 3.8 25.6 0.3
N A:GLY509 3.9 31.6 1.0
CA A:GLY509 4.0 37.8 1.0
CD2 A:TYR525 4.1 33.9 1.0
CA A:SER508 4.2 32.9 0.3
CA A:SER508 4.2 32.2 0.7
CG A:TYR525 4.3 34.1 1.0
CB A:SER555 4.3 33.3 1.0
N A:TYR525 4.5 34.0 1.0
CA A:TYR525 4.6 37.3 1.0
NH1 A:ARG415 4.7 31.9 1.0
O A:TYR525 4.8 33.6 1.0
NE A:ARG483 4.9 53.0 1.0
C A:GLY509 4.9 35.2 1.0
N A:SER508 5.0 32.5 1.0

Sodium binding site 2 out of 4 in 8pkx

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Sodium binding site 2 out of 4 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na710

b:47.8
occ:1.00
OG A:SER383 2.6 48.6 0.3
O A:HOH960 2.7 65.3 1.0
O A:ASN382 3.0 49.9 1.0
O A:SER338 3.0 30.8 1.0
OD1 A:ASN381 3.2 48.2 1.0
OE1 A:GLN337 3.5 46.3 0.5
CB A:PRO361 3.5 34.3 1.0
CB A:SER383 3.6 55.1 0.7
CB A:SER383 3.6 54.9 0.3
CG A:PRO361 3.7 41.2 1.0
CA A:SER383 3.8 56.8 0.7
CA A:SER383 3.8 56.1 0.3
N A:SER338 3.8 27.8 1.0
O A:HOH847 3.8 52.6 1.0
C A:ASN382 3.9 50.8 1.0
C A:SER338 3.9 30.3 1.0
CG A:GLN337 3.9 36.7 0.5
CB A:GLN337 3.9 35.2 0.5
CB A:GLN337 3.9 35.5 0.5
CD A:GLN337 4.0 40.3 0.5
O A:HOH950 4.1 56.4 1.0
CB A:SER338 4.1 28.6 1.0
CA A:SER338 4.1 28.1 1.0
N A:SER383 4.2 50.5 1.0
CG A:ASN381 4.3 45.4 1.0
C A:GLN337 4.5 30.6 0.5
C A:GLN337 4.6 30.9 0.5
ND2 A:ASN381 4.8 50.4 1.0
CA A:GLN337 4.8 35.5 0.5
CA A:GLN337 4.8 35.4 0.5
CD A:PRO384 4.8 67.2 1.0
CG A:GLN337 4.9 41.0 0.5
CD A:PRO361 4.9 32.0 1.0
CA A:PRO361 5.0 27.4 1.0
N A:ASN382 5.0 37.9 1.0
O A:HOH896 5.0 54.7 1.0

Sodium binding site 3 out of 4 in 8pkx

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Sodium binding site 3 out of 4 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na711

b:61.2
occ:1.00
O A:HOH956 2.7 30.2 1.0
O A:GLY367 2.8 31.0 1.0
O A:HOH897 2.8 50.2 1.0
CL A:CL702 3.0 64.2 1.0
O A:HOH835 3.0 45.5 1.0
O A:HOH945 3.1 56.1 1.0
CG2 A:VAL418 3.7 37.0 1.0
C A:GLY367 3.9 32.1 1.0
O A:VAL418 4.0 29.6 1.0
N A:GLY367 4.1 27.6 1.0
O A:HOH827 4.1 42.8 1.0
CB A:ALA366 4.1 28.7 1.0
O A:HOH870 4.3 41.8 1.0
O A:VAL606 4.4 31.7 0.7
O A:HOH881 4.4 42.1 1.0
O A:VAL606 4.5 25.1 0.3
O A:HOH930 4.6 44.2 1.0
CA A:GLY367 4.6 28.9 1.0
CA A:ALA366 4.8 27.8 1.0
C A:ALA366 4.8 28.1 1.0
N A:VAL418 4.8 28.5 1.0
C A:VAL418 4.8 31.6 1.0
O A:HOH958 4.8 32.9 1.0
O A:HOH974 4.9 54.2 1.0
CB A:VAL418 5.0 31.2 1.0
N A:CYS368 5.0 28.4 1.0

Sodium binding site 4 out of 4 in 8pkx

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Sodium binding site 4 out of 4 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:56.4
occ:1.00
O2 B:GOL703 2.8 48.2 1.0
O B:VAL604 2.9 48.1 1.0
C2 B:GOL703 3.0 61.2 1.0
O B:HOH849 3.1 49.8 1.0
O B:HOH804 3.1 50.9 1.0
O1 B:GOL703 3.1 63.9 1.0
O B:LEU365 3.2 48.6 1.0
O B:HOH816 3.3 42.9 1.0
O B:HOH831 3.6 46.6 1.0
C1 B:GOL703 3.6 63.3 1.0
CA B:ALA366 3.9 50.1 1.0
C B:VAL604 4.0 57.4 1.0
CA B:GLY605 4.0 47.4 1.0
CB B:ALA366 4.2 54.6 1.0
C B:LEU365 4.2 51.9 1.0
C3 B:GOL703 4.4 54.7 1.0
N B:GLY605 4.4 53.3 1.0
N B:ALA366 4.5 48.8 1.0
O B:HOH829 4.6 43.1 1.0
O3 B:GOL703 4.6 59.0 1.0
O B:LEU557 4.7 54.8 1.0
N B:VAL606 4.8 52.5 1.0
N B:GLY367 4.8 61.0 1.0
C B:ALA366 4.9 53.2 1.0
C B:GLY605 4.9 53.6 1.0
O B:HOH860 4.9 43.8 1.0

Reference:

F.Fonseca Lopez, J.Miao, J.Damjanovic, L.Bischof, M.B.Braun, Y.Ling, M.D.Hartmann, Y.S.Lin, J.A.Kritzer. Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of KEAP1 Binders. J.Chem.Inf.Model. 2023.
ISSN: ESSN 1549-960X
PubMed: 37917529
DOI: 10.1021/ACS.JCIM.3C01337
Page generated: Wed Oct 9 13:01:10 2024

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