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Sodium in PDB 8pkw: Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 5 (Ortho-Wrcdeetgec)

Protein crystallography data

The structure of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 5 (Ortho-Wrcdeetgec), PDB code: 8pkw 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) 42.13 / 1.54
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.684, 68.97, 77.965, 90, 117.86, 90
R / Rfree (%) 15.8 / 19.9

Other elements in 8pkw:

The structure of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 5 (Ortho-Wrcdeetgec) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 5 (Ortho-Wrcdeetgec) (pdb code 8pkw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 5 (Ortho-Wrcdeetgec), PDB code: 8pkw:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8pkw

Go back to Sodium Binding Sites List in 8pkw
Sodium binding site 1 out of 3 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 5 (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 5 (Ortho-Wrcdeetgec) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na707

b:63.9
occ:1.00
OG A:SER508 2.9 32.4 0.7
O A:HOH839 3.0 54.5 1.0
OG A:SER555 3.1 42.4 1.0
O A:SER508 3.2 29.4 1.0
C A:SER508 3.4 29.8 1.0
CB A:TYR525 3.6 30.8 1.0
N A:GLY509 3.8 27.2 1.0
CB A:SER508 3.8 30.6 0.3
OG A:SER508 3.8 31.2 0.3
CB A:SER508 3.9 29.8 0.7
O A:HOH824 3.9 46.2 1.0
CA A:GLY509 3.9 28.1 1.0
CD2 A:TYR525 4.2 31.6 1.0
CA A:SER508 4.2 29.9 0.3
CA A:SER508 4.3 29.8 0.7
CG A:TYR525 4.3 32.3 1.0
CB A:SER555 4.4 33.5 1.0
N A:TYR525 4.5 31.4 1.0
NH1 A:ARG415 4.6 32.0 1.0
CA A:TYR525 4.6 31.4 1.0
NE A:ARG483 4.8 41.4 1.0
O A:TYR525 4.9 33.3 1.0
C A:GLY509 4.9 30.4 1.0

Sodium binding site 2 out of 3 in 8pkw

Go back to Sodium Binding Sites List in 8pkw
Sodium binding site 2 out of 3 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 5 (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 5 (Ortho-Wrcdeetgec) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na708

b:67.7
occ:1.00
OG1 A:THR545 2.7 44.2 1.0
O A:HOH951 2.7 52.1 1.0
O A:THR543 2.9 42.5 0.8
O A:HOH867 3.0 61.1 1.0
O A:THR543 3.0 36.7 0.2
O A:ARG536 3.2 36.5 1.0
CB A:THR545 3.3 37.1 1.0
N A:THR545 3.5 34.1 1.0
C A:THR543 3.7 41.2 0.8
OG1 A:THR543 3.7 41.2 0.2
C A:THR543 3.7 38.1 0.2
CB A:ASP538 3.8 57.8 1.0
N A:ASP538 3.9 42.8 1.0
C A:TRP544 3.9 35.2 1.0
CA A:THR545 4.0 35.2 1.0
CA A:TRP544 4.1 34.7 1.0
C A:ARG536 4.2 34.3 1.0
N A:TRP544 4.3 37.5 1.0
CB A:THR543 4.3 47.5 0.8
CB A:THR543 4.4 40.9 0.2
CA A:ASP538 4.5 51.2 1.0
CG2 A:THR543 4.5 50.4 0.8
C A:TYR537 4.5 39.0 1.0
CG2 A:THR545 4.6 42.5 1.0
CA A:THR543 4.6 44.9 0.8
CA A:TYR537 4.6 33.5 1.0
CA A:THR543 4.6 40.9 0.2
O A:TRP544 4.6 41.1 1.0
OG1 A:THR541 4.7 52.5 1.0
O A:HOH1023 4.7 73.1 1.0
CG A:ARG536 4.8 44.8 1.0
N A:TYR537 4.8 32.4 1.0

Sodium binding site 3 out of 3 in 8pkw

Go back to Sodium Binding Sites List in 8pkw
Sodium binding site 3 out of 3 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 5 (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 5 (Ortho-Wrcdeetgec) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:46.9
occ:1.00
O B:SER383 2.7 33.6 1.0
OD1 B:ASN382 2.8 38.0 1.0
O B:GLY386 3.0 31.2 1.0
N B:SER383 3.8 34.6 1.0
C B:SER383 3.8 36.8 1.0
C B:GLY386 3.9 30.6 1.0
CG B:ASN382 4.0 36.2 1.0
CB B:ASN387 4.1 31.5 1.0
O B:HOH825 4.2 46.5 1.0
CG B:ASN387 4.2 35.4 1.0
C B:ASN382 4.4 33.6 1.0
CA B:SER383 4.5 33.9 1.0
ND2 B:ASN387 4.5 39.4 1.0
CA B:ASN382 4.6 31.2 1.0
N B:GLY386 4.6 29.9 1.0
CA B:ASN387 4.7 29.4 1.0
N B:ASN387 4.7 28.6 1.0
OD1 B:ASN387 4.7 36.4 1.0
O B:HOH860 4.7 46.3 1.0
O B:HOH897 4.8 59.8 1.0
ND2 B:ASN382 4.8 34.2 1.0
CA B:GLY386 4.8 29.2 1.0
N B:PRO384 4.8 35.7 1.0
CB B:ASN382 4.9 34.0 1.0
CA B:PRO384 5.0 34.0 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 13:01:09 2024

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