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Sodium in PDB 6fmq: KEAP1 - Peptide Complex

Protein crystallography data

The structure of KEAP1 - Peptide Complex, PDB code: 6fmq was solved by S.K.Talapatra, F.Kozielski, G.Wells, N.D.Georgakopoulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.84 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.652, 76.129, 211.137, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20

Sodium Binding Sites:

The binding sites of Sodium atom in the KEAP1 - Peptide Complex (pdb code 6fmq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the KEAP1 - Peptide Complex, PDB code: 6fmq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 6fmq

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Sodium binding site 1 out of 7 in the KEAP1 - Peptide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of KEAP1 - Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na708

b:66.6
occ:1.00
 NH2 A:ARG415 3.0 74.7 1.0
O B:ASP385 3.1 55.2 0.6
OG A:SER508 3.2 52.7 1.0
O B:ASP385 3.5 55.4 0.4
O A:SER508 3.6 40.7 1.0
O A:HOH887 3.7 55.9 1.0
CA A:GLY509 3.8 41.5 1.0
OD1 B:ASP385 3.8 60.3 0.4
C A:SER508 3.9 36.7 1.0
CA B:ASP385 3.9 57.8 0.6
C B:ASP385 3.9 59.1 0.6
CZ A:ARG415 4.0 75.1 1.0
N A:GLY509 4.0 38.2 1.0
NH1 A:ARG415 4.0 68.6 1.0
C B:ASP385 4.0 58.4 0.4
CB A:TYR525 4.1 50.1 1.0
CA B:ASP385 4.1 57.5 0.4
OD1 B:ASP385 4.1 49.5 0.6
CB B:ASP385 4.2 56.6 0.6
CB A:SER555 4.2 43.6 1.0
CG B:ASP385 4.3 60.7 0.4
OG A:SER555 4.4 41.3 1.0
CH3 A:ACT706 4.4 37.8 0.9
CB A:SER508 4.5 40.3 1.0
O A:ACT706 4.6 60.1 0.9
CG B:ASP385 4.6 55.5 0.6
N A:ALA556 4.7 34.0 1.0
C A:GLY509 4.8 38.6 1.0
CB B:ASP385 4.8 54.0 0.4
CA A:SER508 4.8 39.0 1.0
C A:ACT706 4.8 47.7 0.9
N A:TYR525 4.9 44.8 1.0
OD2 B:ASP385 4.9 58.2 0.4
O A:GLY509 4.9 43.7 1.0

Sodium binding site 2 out of 7 in 6fmq

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Sodium binding site 2 out of 7 in the KEAP1 - Peptide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of KEAP1 - Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na709

b:65.0
occ:1.00
 O A:HOH958 2.1 58.6 1.0
O A:HOH919 3.0 57.8 1.0
N A:SER391 3.1 36.0 1.0
OG A:SER391 3.6 45.2 1.0
CA A:SER390 3.6 39.9 1.0
OG A:SER390 3.8 43.1 1.0
C A:SER390 3.9 39.2 1.0
N A:ALA392 4.1 37.2 1.0
O A:ASP389 4.1 39.8 1.0
CA A:SER391 4.1 40.4 1.0
CB A:SER390 4.2 37.5 1.0
CB A:SER391 4.3 37.2 1.0
C A:SER391 4.4 41.1 1.0
O A:HOH877 4.5 57.7 1.0
N A:SER390 4.7 38.9 1.0
CB A:ALA392 4.7 41.6 1.0
C A:ASP389 4.8 44.9 1.0
CA A:ALA392 4.8 41.1 1.0

Sodium binding site 3 out of 7 in 6fmq

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Sodium binding site 3 out of 7 in the KEAP1 - Peptide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of KEAP1 - Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na710

b:71.2
occ:1.00
 O A:HOH811 2.1 45.1 1.0
O A:HOH831 2.5 57.3 1.0
O A:HOH862 3.3 57.8 1.0
OH A:TYR491 3.6 44.7 1.0
CG2 A:ILE500 3.8 44.0 1.0
OH A:TYR473 4.4 42.8 1.0
SG A:CYS489 4.4 50.0 1.0
CB A:CYS489 4.5 43.3 1.0
CE2 A:TYR473 4.7 42.3 1.0
CZ A:TYR491 4.8 45.9 1.0
O A:HOH849 4.8 64.2 1.0
OE2 A:GLU542 4.9 98.4 1.0
CB A:ILE500 5.0 45.1 1.0
CZ A:TYR473 5.0 46.3 1.0

Sodium binding site 4 out of 7 in 6fmq

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Sodium binding site 4 out of 7 in the KEAP1 - Peptide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of KEAP1 - Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na705

b:67.4
occ:1.00
 O B:HOH889 2.3 61.7 1.0
O B:HOH957 2.6 60.8 1.0
OD1 B:ASN382 2.7 52.3 1.0
OH B:TYR334 2.8 47.0 1.0
CG B:ASN382 3.4 47.1 1.0
O B:ARG336 3.5 39.7 1.0
ND2 B:ASN382 3.6 41.6 1.0
CE2 B:TYR334 3.7 35.9 1.0
CZ B:TYR334 3.7 40.9 1.0
OXT D:LEU7 3.8 65.0 1.0
O B:HOH805 4.0 51.0 1.0
CB D:LEU7 4.3 56.0 1.0
N D:LEU7 4.3 48.9 1.0
C D:LEU7 4.3 63.3 1.0
C B:ARG336 4.4 44.7 1.0
O B:ASN382 4.4 36.5 1.0
O B:SER383 4.4 44.3 0.4
CA B:GLN337 4.5 32.6 1.0
CA D:LEU7 4.6 57.6 1.0
CB B:ASN382 4.6 37.6 1.0
OH A:TYR334 4.6 60.9 1.0
C B:ASN382 4.6 40.9 1.0
C B:SER383 4.7 47.8 0.4
O B:SER383 4.7 44.3 0.6
O D:HOH102 4.8 58.4 1.0
C B:SER383 4.8 47.7 0.6
N B:GLN337 4.9 33.3 1.0
CB B:GLN337 5.0 35.4 1.0
N B:SER383 5.0 39.8 0.4
N B:SER383 5.0 39.8 0.6

Sodium binding site 5 out of 7 in 6fmq

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Sodium binding site 5 out of 7 in the KEAP1 - Peptide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of KEAP1 - Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na706

b:77.0
occ:1.00
 O B:HOH943 2.1 54.6 1.0
ND1 B:HIS432 3.6 42.2 1.0
CE1 B:HIS432 4.0 49.8 1.0
CG1 B:VAL411 4.0 40.7 1.0
CD1 B:ILE435 4.4 49.3 1.0
CB B:VAL411 4.8 37.2 1.0
CG B:HIS432 4.8 46.6 1.0

Sodium binding site 6 out of 7 in 6fmq

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Sodium binding site 6 out of 7 in the KEAP1 - Peptide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of KEAP1 - Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na707

b:56.9
occ:1.00
 O B:HOH905 2.2 58.7 1.0
O B:HOH952 2.7 63.5 1.0
N B:HIS436 3.2 38.1 1.0
O B:HIS436 3.6 42.0 1.0
NH1 B:ARG459 3.7 53.9 1.0
CA B:ILE435 3.8 44.3 1.0
CD B:ARG459 3.9 44.4 1.0
C B:ILE435 4.0 45.4 1.0
CZ B:ARG459 4.0 53.8 1.0
O B:CYS434 4.0 43.8 1.0
CA B:HIS436 4.0 38.6 1.0
NE B:ARG459 4.1 51.6 1.0
CB B:HIS436 4.1 38.7 1.0
ND1 B:HIS436 4.2 54.5 1.0
C B:HIS436 4.2 44.1 1.0
CG2 B:ILE435 4.5 43.8 1.0
CB B:ILE435 4.6 42.4 1.0
CG B:HIS436 4.6 50.2 1.0
N B:ILE435 4.8 43.4 1.0
NH2 B:ARG459 4.8 53.7 1.0
C B:CYS434 4.8 43.2 1.0
CG1 B:ILE435 4.9 44.5 1.0

Sodium binding site 7 out of 7 in 6fmq

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Sodium binding site 7 out of 7 in the KEAP1 - Peptide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of KEAP1 - Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na708

b:61.0
occ:1.00
 NH2 B:ARG380 3.1 43.3 1.0
O B:HOH896 3.2 40.7 1.0
CZ B:ARG380 3.6 51.4 1.0
ND2 B:ASN414 3.7 38.1 1.0
CD B:ARG415 3.9 43.2 1.0
OG1 D:THR4 4.0 36.4 1.0
O B:HOH833 4.0 57.3 1.0
OE1 D:GLU6 4.1 42.2 1.0
NE B:ARG380 4.1 40.5 1.0
CD D:GLU6 4.1 42.8 1.0
CG2 D:THR4 4.3 36.5 1.0
NH1 B:ARG380 4.3 43.6 1.0
CG B:ARG415 4.5 39.7 1.0
O D:HOH101 4.5 41.1 1.0
OE2 D:GLU6 4.5 43.8 1.0
CB D:THR4 4.5 39.9 1.0
CG D:GLU6 4.6 39.8 1.0
O B:HOH903 4.6 36.8 1.0
CB D:GLU6 4.7 39.8 1.0
CG B:ASN414 4.7 34.0 1.0
CH3 D:ACE1 4.7 71.5 1.0
OD1 B:ASN414 4.8 35.9 1.0
NE B:ARG415 4.9 45.9 1.0

Reference:

N.D.Georgakopoulos, S.K.Talapatra, J.Gatliff, F.Kozielski, G.Wells. Modified Peptide Inhibitors of the KEAP1-NRF2 Protein-Protein Interaction Incorporating Unnatural Amino Acids. Chembiochem V. 19 1810 2018.
ISSN: ESSN 1439-7633
PubMed: 29927029
DOI: 10.1002/CBIC.201800170
Page generated: Tue Oct 8 08:49:11 2024

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