Sodium in PDB 7zb1: S580A with 18MER

The structure of S580A with 18MER, PDB code: 7zb1 was solved by H.Song, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.84 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	70.01, 104.61, 110.65, 115.81, 98.87, 93.79
R / Rfree (%)	20.5 / 23.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the S580A with 18MER (pdb code 7zb1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the S580A with 18MER, PDB code: 7zb1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in the S580A with 18MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of S580A with 18MER within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:44.8 occ:1.00 O A:LEU504 2.5 34.0 1.0 O A:HOH967 2.5 32.6 1.0 N A:GLY500 3.0 25.8 1.0 CA A:GLY500 3.3 25.8 1.0 CA A:GLY533 3.4 28.9 1.0 N A:GLY501 3.5 23.9 1.0 N A:GLY533 3.6 29.7 1.0 CD2 A:TYR499 3.7 24.6 1.0 C A:LEU504 3.7 32.8 1.0 O A:HOH1069 3.7 31.2 1.0 C A:GLY500 3.9 25.5 1.0 CB A:TYR499 4.0 25.1 1.0 O A:GLY501 4.1 24.1 1.0 C A:TYR499 4.1 25.7 1.0 C A:GLY532 4.3 30.3 1.0 OE2 A:GLU535 4.4 26.2 1.0 CG A:TYR499 4.4 24.2 1.0 CG A:MET506 4.5 37.4 1.0 OE1 A:GLU535 4.5 30.1 1.0 O A:ILE530 4.5 26.0 1.0 CA A:TYR499 4.5 24.8 1.0 O A:GLY532 4.6 26.8 1.0 CA A:LEU504 4.6 33.0 1.0 N A:ALA505 4.6 28.9 1.0 N A:MET506 4.7 34.3 1.0 CA A:GLY501 4.7 24.3 1.0 N A:LEU504 4.7 30.4 1.0 CA A:ALA505 4.7 32.4 1.0 CE2 A:TYR499 4.8 25.2 1.0 CD A:GLU535 4.8 29.3 1.0 C A:GLY501 4.8 24.8 1.0 CB A:LEU504 4.8 33.3 1.0 CE A:MET506 4.9 45.5 1.0 C A:ALA505 4.9 33.0 1.0 C A:GLY533 4.9 28.9 1.0 N A:TYR499 4.9 25.6 1.0

Sodium binding site 2 out of 16 in the S580A with 18MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of S580A with 18MER within 5.0Å range: probe atom residue distance (Å) B Occ A:Na803 b:48.2 occ:1.00 OG1 A:THR602 2.8 28.4 1.0 O A:VAL600 2.8 33.8 1.0 O A:LEU658 3.2 34.1 1.0 N A:THR602 3.2 29.9 1.0 CB A:THR602 3.3 29.3 1.0 C A:VAL600 3.4 34.2 1.0 CE1 A:PHE659 3.5 32.3 1.0 CZ A:PHE659 3.5 31.7 1.0 CG1 A:VAL600 3.6 33.2 1.0 N A:LEU658 3.7 34.4 1.0 C A:LEU658 3.7 34.2 1.0 CE2 A:PHE659 3.7 32.1 1.0 CD1 A:PHE659 3.8 32.2 1.0 C A:ILE601 3.8 30.4 1.0 CA A:THR602 3.9 29.8 1.0 CB A:MET657 3.9 36.7 1.0 CD2 A:PHE659 4.0 31.6 1.0 N A:ILE601 4.0 33.2 1.0 CG A:PHE659 4.0 33.3 1.0 CB A:VAL600 4.0 33.1 1.0 CE A:MET657 4.0 37.1 1.0 CA A:ILE601 4.0 32.3 1.0 CA A:MET657 4.2 34.7 1.0 C A:MET657 4.2 34.7 1.0 N A:PHE659 4.3 33.6 1.0 CA A:VAL600 4.3 33.8 1.0 CA A:LEU658 4.4 34.8 1.0 CA A:PHE659 4.6 34.0 1.0 O A:ILE601 4.6 30.6 1.0 CG A:MET657 4.6 36.8 1.0 CG2 A:THR602 4.6 28.3 1.0 O A:THR602 4.9 29.1 1.0 CB A:PHE659 4.9 33.6 1.0 C A:THR602 4.9 29.7 1.0 SD A:MET657 5.0 37.4 1.0

Sodium binding site 3 out of 16 in the S580A with 18MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of S580A with 18MER within 5.0Å range: probe atom residue distance (Å) B Occ A:Na804 b:52.9 occ:1.00 O A:GLN56 2.5 48.3 1.0 OE1 A:GLN56 2.9 45.6 1.0 N A:MET693 3.0 41.8 1.0 C A:GLN56 3.4 50.0 1.0 O A:MET693 3.5 44.4 1.0 CB A:ALA60 3.6 46.7 1.0 CA A:GLN56 3.6 49.0 1.0 CB A:GLN56 3.7 47.0 1.0 N A:ALA60 3.7 49.2 1.0 CA A:LEU692 3.8 44.3 1.0 CD2 A:PHE59 3.8 50.3 1.0 C A:LEU692 3.8 42.2 1.0 CA A:MET693 3.9 45.0 1.0 CD A:GLN56 3.9 46.6 1.0 CB A:MET693 4.1 44.1 1.0 CA A:ALA60 4.1 47.2 1.0 C A:MET693 4.1 43.3 1.0 CD2 A:LEU692 4.1 53.5 1.0 CB A:PHE59 4.2 53.6 1.0 CB A:LEU692 4.3 48.9 1.0 NE2 A:GLN681 4.3 38.3 1.0 CG A:GLN56 4.4 47.2 1.0 CG A:PHE59 4.5 52.8 1.0 N A:ARG57 4.6 54.1 1.0 C A:PHE59 4.6 50.5 1.0 CE2 A:PHE59 4.8 50.1 1.0 O A:CYS691 4.8 41.5 1.0 CG A:LEU692 4.9 49.3 1.0 CA A:PHE59 4.9 54.3 1.0

Sodium binding site 4 out of 16 in the S580A with 18MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of S580A with 18MER within 5.0Å range: probe atom residue distance (Å) B Occ A:Na805 b:67.3 occ:1.00 OG A:SER219 2.9 37.0 1.0 O A:ILE206 3.2 46.9 1.0 N A:SER219 3.3 36.0 1.0 C A:TYR218 3.3 37.7 1.0 CA A:TYR218 3.5 36.9 1.0 N A:VAL267 3.6 36.6 1.0 CB A:SER266 3.7 35.5 1.0 CA A:SER266 3.8 35.2 1.0 CB A:SER219 3.9 38.3 1.0 O A:TYR218 3.9 36.7 1.0 N A:TYR218 3.9 39.4 1.0 O A:VAL267 3.9 36.5 1.0 CG2 A:VAL267 4.0 38.9 1.0 CG2 A:ILE206 4.0 45.0 1.0 CA A:SER219 4.1 36.0 1.0 CB A:ILE206 4.1 46.0 1.0 C A:SER266 4.2 37.3 1.0 C A:ILE206 4.2 46.3 1.0 C A:PHE217 4.4 39.4 1.0 O A:HOH1039 4.5 40.4 1.0 O A:PHE217 4.5 40.0 1.0 CG1 A:VAL239 4.6 33.4 1.0 CA A:VAL267 4.6 38.1 1.0 C A:VAL267 4.7 38.1 1.0 CA A:ILE206 4.8 40.2 1.0 CG2 A:VAL239 4.8 32.3 1.0 CB A:VAL267 4.9 37.8 1.0 OG A:SER266 4.9 34.9 1.0 CB A:TYR218 4.9 36.9 1.0 CB A:PHE217 4.9 35.2 1.0

Sodium binding site 5 out of 16 in the S580A with 18MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of S580A with 18MER within 5.0Å range: probe atom residue distance (Å) B Occ A:Na806 b:70.8 occ:1.00 O A:HOH926 2.3 35.7 1.0 OG A:SER470 3.1 32.9 1.0 NH1 A:ARG531 3.1 39.2 1.0 N A:ASP472 3.2 43.6 1.0 CG A:ASP472 3.4 38.5 1.0 N A:LYS471 3.4 43.9 1.0 CB A:LYS471 3.5 50.2 1.0 CB A:ASP554 3.6 30.8 1.0 OD2 A:ASP472 3.6 40.1 1.0 OD1 A:ASP472 3.6 37.6 1.0 CB A:SER470 3.7 35.7 1.0 CB A:ASP472 3.8 41.5 1.0 CA A:LYS471 3.8 46.3 1.0 OD2 A:ASP554 3.9 31.6 1.0 C A:LYS471 4.0 44.9 1.0 CA A:ASP472 4.1 41.5 1.0 OD1 A:ASN551 4.2 34.4 1.0 C A:SER470 4.2 40.9 1.0 OD1 A:ASP555 4.2 29.3 1.0 CG A:ASP554 4.2 32.6 1.0 CZ A:ARG531 4.4 33.9 1.0 CA A:SER470 4.6 37.7 1.0 O A:ASN551 4.6 32.0 1.0 CA A:ASN551 4.7 31.2 1.0 CA A:ASP554 4.8 30.1 1.0 CG A:ASN551 4.8 33.2 1.0 NH2 A:ARG531 4.8 34.5 1.0 C A:ASP554 4.9 29.6 1.0 CG A:LYS471 4.9 56.0 1.0 N A:ASP555 4.9 28.2 1.0 CB A:ASN551 5.0 32.4 1.0

Sodium binding site 6 out of 16 in the S580A with 18MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of S580A with 18MER within 5.0Å range: probe atom residue distance (Å) B Occ A:Na807 b:52.6 occ:1.00 O A:THR509 2.7 31.3 1.0 O A:HOH958 2.8 41.2 1.0 O A:HOH991 3.3 28.0 1.0 CB A:SER511 3.5 35.8 1.0 CE2 A:TYR525 3.5 36.0 1.0 N A:SER511 3.5 33.1 1.0 CD1 A:PHE427 3.7 34.3 1.0 OG1 A:THR514 3.7 28.0 0.5 C A:THR509 3.8 35.0 1.0 OH A:TYR525 4.0 35.9 1.0 CA A:SER511 4.1 34.2 1.0 C A:PHE510 4.1 34.4 1.0 CE1 A:PHE427 4.2 32.7 1.0 CG2 A:THR514 4.2 28.7 0.5 CZ A:TYR525 4.2 39.9 1.0 OG1 A:THR514 4.2 35.3 0.5 CD2 A:TYR525 4.4 36.2 1.0 CB A:THR514 4.4 29.3 0.5 CB A:THR514 4.5 34.0 0.5 CA A:PHE510 4.5 33.5 1.0 CB A:THR509 4.6 41.9 1.0 N A:PHE510 4.6 33.5 1.0 O A:SER511 4.6 36.2 1.0 OG A:SER511 4.6 35.8 1.0 CA A:THR509 4.7 36.2 1.0 O A:PHE510 4.8 32.1 1.0 CG A:PHE427 4.9 33.6 1.0 O A:HOH1068 4.9 42.9 1.0 C A:SER511 4.9 34.4 1.0 N A:THR509 4.9 32.5 1.0

Sodium binding site 7 out of 16 in the S580A with 18MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of S580A with 18MER within 5.0Å range: probe atom residue distance (Å) B Occ B:Na801 b:51.5 occ:1.00 O B:GLY544 2.4 33.2 1.0 OE1 B:GLU624 2.6 29.4 1.0 NZ B:LYS549 3.0 33.6 1.0 CD B:LYS549 3.4 34.5 1.0 CD B:GLU624 3.4 29.4 1.0 C B:GLY544 3.5 33.0 1.0 CG B:GLU624 3.6 29.7 1.0 CA B:MET545 3.6 34.2 1.0 CE B:LYS549 3.7 34.7 1.0 O B:GLY500 3.7 29.5 1.0 CA B:GLY501 3.7 30.2 1.0 CB B:MET545 3.8 33.8 1.0 N B:MET545 4.0 33.1 1.0 C B:GLY500 4.5 29.4 1.0 CA B:GLY532 4.5 31.5 1.0 OE2 B:GLU624 4.6 28.7 1.0 CG2 B:VAL552 4.6 28.8 1.0 N B:GLY501 4.6 29.9 1.0 O B:GLU624 4.7 34.0 1.0 N B:PHE502 4.7 31.4 1.0 CG B:LYS549 4.7 32.8 1.0 OD1 B:ASN581 4.8 36.7 1.0 CA B:GLY544 4.8 34.4 1.0 C B:GLY501 4.8 31.0 1.0 C B:MET545 4.9 33.9 1.0 CE1 B:TYR625 4.9 34.0 1.0 CD2 B:HIS541 4.9 31.1 1.0 CB B:GLU624 5.0 30.8 1.0

Sodium binding site 8 out of 16 in the S580A with 18MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of S580A with 18MER within 5.0Å range: probe atom residue distance (Å) B Occ B:Na802 b:45.1 occ:1.00 O B:TYR499 2.8 31.7 1.0 O B:ASN581 2.8 32.1 1.0 NZ B:LYS549 3.0 33.6 1.0 ND2 B:ASN581 3.2 31.9 1.0 O B:GLY500 3.3 29.5 1.0 OD1 B:ASN581 3.3 36.7 1.0 CG B:ASN581 3.5 32.8 1.0 CE B:LYS549 3.6 34.7 1.0 CB B:LEU585 3.6 32.1 1.0 C B:ASN581 3.7 31.8 1.0 N B:LEU585 3.7 31.9 1.0 C B:TYR499 4.0 30.2 1.0 CG1 B:VAL552 4.0 29.1 1.0 CA B:LEU585 4.0 32.3 1.0 CB B:VAL584 4.1 32.5 1.0 C B:GLY500 4.2 29.4 1.0 N B:GLY582 4.3 30.9 1.0 CA B:GLY582 4.4 30.6 1.0 CE1 B:PHE553 4.4 28.4 1.0 CA B:GLY500 4.5 29.4 1.0 C B:VAL584 4.6 32.1 1.0 CB B:ASN581 4.6 31.9 1.0 CA B:ASN581 4.6 32.2 1.0 N B:GLY500 4.7 29.3 1.0 CG B:LEU585 4.7 31.6 1.0 CD1 B:LEU585 4.8 32.1 1.0 CA B:VAL584 4.8 32.0 1.0 CG2 B:VAL584 4.8 34.8 1.0 CD B:LYS549 4.9 34.5 1.0 CG1 B:VAL584 4.9 32.8 1.0 C B:GLY582 4.9 31.0 1.0 CB B:VAL552 5.0 29.1 1.0 N B:VAL584 5.0 31.9 1.0

Sodium binding site 9 out of 16 in the S580A with 18MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of S580A with 18MER within 5.0Å range: probe atom residue distance (Å) B Occ B:Na803 b:50.4 occ:1.00 O B:HOH1005 2.8 37.2 1.0 O B:HOH931 2.8 43.2 1.0 O B:PHE262 2.9 36.0 1.0 C B:ARG282 3.3 33.7 1.0 O B:HOH940 3.5 50.8 1.0 O B:SER281 3.6 31.5 1.0 N B:ASP283 3.6 32.6 1.0 O B:ARG282 3.6 32.2 1.0 CA B:ARG282 3.7 34.0 1.0 C B:PHE262 3.8 36.7 1.0 CB B:SER620 3.9 33.2 1.0 C B:SER281 4.1 32.1 1.0 CA B:TRP263 4.1 36.5 1.0 CA B:ASP283 4.2 33.6 1.0 N B:ILE264 4.2 35.4 1.0 N B:ARG282 4.2 32.8 1.0 CD1 B:ILE264 4.2 40.2 1.0 CG1 B:ILE264 4.2 39.9 1.0 O B:HOH923 4.2 44.5 1.0 N B:TRP263 4.3 36.3 1.0 CA B:SER620 4.4 34.1 1.0 C B:TRP263 4.5 36.9 1.0 O B:ASP283 4.6 33.1 1.0 OG B:SER281 4.7 34.1 1.0 C B:ASP283 4.7 35.1 1.0 CB B:ILE264 4.8 37.6 1.0 CB B:PHE262 4.8 36.0 1.0 CA B:PHE262 4.9 36.3 1.0 N B:SER620 5.0 34.0 1.0

Sodium binding site 10 out of 16 in the S580A with 18MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of S580A with 18MER within 5.0Å range: probe atom residue distance (Å) B Occ B:Na804 b:61.9 occ:1.00 O B:ASN337 2.7 39.5 1.0 O B:TYR338 2.7 39.5 1.0 O B:ALA362 2.9 41.5 1.0 O B:HOH912 2.9 46.3 1.0 N B:ASP359 3.1 50.0 1.0 C B:ASN337 3.4 38.4 1.0 O B:ASP359 3.5 48.9 1.0 CB B:ASN337 3.6 38.7 1.0 CB B:ASP359 3.7 50.5 1.0 N B:LEU364 3.7 42.4 1.0 CA B:ASP359 3.7 49.9 1.0 CE1 B:TYR379 3.8 51.0 1.0 CB B:LEU364 3.8 42.4 1.0 C B:TYR338 3.9 39.5 1.0 C B:GLU358 4.0 47.3 1.0 C B:ASP359 4.0 49.3 1.0 CA B:GLU358 4.0 44.7 1.0 CG B:GLU358 4.1 42.3 1.0 C B:ALA362 4.1 41.8 1.0 CA B:ASN337 4.1 37.7 1.0 N B:TYR338 4.2 37.9 1.0 CA B:LEU364 4.3 42.1 1.0 C B:PHE363 4.4 42.2 1.0 CD1 B:TYR379 4.4 49.1 1.0 CA B:TYR338 4.5 37.8 1.0 CA B:PHE363 4.6 42.0 1.0 CB B:GLU358 4.7 44.3 1.0 N B:PHE363 4.8 42.1 1.0 OH B:TYR379 4.8 52.8 1.0 CZ B:TYR379 4.8 51.5 1.0 CG B:ASN337 4.8 38.6 1.0 O B:ALA357 4.9 45.7 1.0 N B:LYS339 5.0 40.1 1.0

H.Song, J.H.Naismith. S580A with 18MER To Be Published.