Sodium in PDB 6baq: Mus Musculus BPIFA1

The structure of Mus Musculus BPIFA1, PDB code: 6baq was solved by M.S.Little, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.79 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.200, 200.582, 89.499, 90.00, 126.15, 90.00
R / Rfree (%)	22.1 / 27.8

The structure of Mus Musculus BPIFA1 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 63;

Binding sites:

The binding sites of Sodium atom in the Mus Musculus BPIFA1 (pdb code 6baq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 63 binding sites of Sodium where determined in the Mus Musculus BPIFA1, PDB code: 6baq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 63 in the Mus Musculus BPIFA1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mus Musculus BPIFA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:49.5 occ:1.00 OG1 A:THR205 2.2 29.2 1.0 OG1 B:THR205 2.5 30.7 1.0 CG2 A:THR205 2.7 26.7 1.0 O B:HIS206 2.8 35.1 1.0 O A:HIS206 2.9 27.9 1.0 CB A:THR205 3.0 31.0 1.0 CG2 B:THR205 3.3 21.6 1.0 CB B:THR205 3.4 28.9 1.0 O A:HOH402 3.6 37.3 1.0 N A:HIS206 3.8 25.7 1.0 ND1 B:HIS206 3.8 30.7 1.0 CE1 B:HIS206 3.8 32.8 1.0 N B:HIS206 3.9 29.5 1.0 C B:HIS206 4.0 31.6 1.0 C A:HIS206 4.0 24.4 1.0 C A:THR205 4.0 27.2 1.0 CA A:THR205 4.1 29.4 1.0 ND1 A:HIS206 4.1 29.0 1.0 CG B:HIS206 4.3 33.2 1.0 CE1 A:HIS206 4.3 29.9 1.0 C B:THR205 4.3 27.9 1.0 NE2 B:HIS206 4.3 25.7 1.0 CA A:HIS206 4.4 25.0 1.0 CA B:THR205 4.4 26.8 1.0 CA B:HIS206 4.5 27.1 1.0 CG A:HIS206 4.5 32.6 1.0 O A:HOH428 4.6 33.5 0.9 CD2 B:HIS206 4.6 32.6 1.0 OE1 B:GLN242 4.6 34.3 1.0 O A:THR205 4.7 22.9 1.0 NE2 A:HIS206 4.8 29.8 1.0 CD B:PRO208 4.8 39.2 1.0 OE1 A:GLN242 4.8 36.3 1.0 CD2 A:HIS206 4.9 27.2 1.0 CD A:PRO208 5.0 34.2 1.0 CB B:HIS206 5.0 25.9 1.0 O B:THR205 5.0 23.9 1.0

Sodium binding site 2 out of 63 in the Mus Musculus BPIFA1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mus Musculus BPIFA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:52.0 occ:1.00 OD1 A:ASP70 2.3 45.1 1.0 OG1 A:THR69 3.0 40.8 1.0 O A:PHE274 3.0 36.1 1.0 N A:ASP70 3.2 43.4 1.0 CA A:ASP70 3.4 44.6 1.0 CG A:ASP70 3.4 45.5 1.0 C A:THR69 3.5 37.1 1.0 CA A:PHE274 3.8 31.4 1.0 O A:THR69 3.8 38.0 1.0 C A:PHE274 3.8 33.5 1.0 CB A:THR69 3.9 34.8 1.0 CB A:ASP70 4.0 41.6 1.0 CB A:PHE274 4.0 41.9 1.0 CD1 A:ILE276 4.1 53.1 1.0 ND2 A:ASN67 4.2 43.4 1.0 CA A:THR69 4.3 34.3 1.0 OD2 A:ASP70 4.4 55.8 1.0 NA A:NA310 4.5 44.5 1.0 CG1 A:ILE276 4.5 46.4 1.0 O A:ASN67 4.5 46.5 1.0 CG A:ASN67 4.6 48.1 1.0 C A:ASP70 4.7 40.9 1.0 CB A:ASN67 4.7 40.4 1.0 N A:THR69 4.9 33.4 1.0

Sodium binding site 3 out of 63 in the Mus Musculus BPIFA1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Mus Musculus BPIFA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:45.0 occ:1.00 OD1 A:ASP78 2.5 18.4 1.0 N E:GLY91 3.1 18.9 1.0 O A:HOH416 3.2 22.1 1.0 O E:HOH425 3.2 18.4 1.0 CG A:ASP78 3.5 24.1 1.0 OD2 A:ASP78 3.7 30.9 1.0 CB E:LEU90 3.7 18.5 1.0 CA E:GLY91 3.7 19.9 1.0 C E:LEU90 3.9 20.5 1.0 CA E:LEU90 4.1 21.4 1.0 N E:LEU90 4.1 17.7 1.0 O E:GLY88 4.3 26.0 1.0 CA E:GLY88 4.3 18.9 1.0 C E:GLY88 4.4 24.1 1.0 CG E:LEU90 4.7 19.0 1.0 O A:GLY74 4.9 23.8 1.0 CB A:ASP78 4.9 17.6 1.0 O E:LEU90 5.0 20.1 1.0

Sodium binding site 4 out of 63 in the Mus Musculus BPIFA1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Mus Musculus BPIFA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:45.7 occ:1.00 CG1 A:VAL170 2.6 53.9 1.0 N A:VAL170 2.6 43.0 1.0 CB A:VAL170 3.0 46.6 1.0 N A:PRO169 3.2 43.0 1.0 O A:ASN129 3.2 47.4 1.0 CB A:ASN129 3.3 51.8 1.0 CD A:PRO169 3.3 46.3 1.0 CA A:VAL170 3.4 46.5 1.0 C A:MET168 3.5 43.1 1.0 C A:PRO169 3.6 44.8 1.0 CG A:MET168 3.7 41.8 1.0 CA A:PRO169 3.8 45.7 1.0 ND2 A:ASN129 3.8 49.4 1.0 CG A:ASN129 3.9 53.3 1.0 O A:MET168 4.0 40.8 1.0 CA A:MET168 4.0 42.2 1.0 CA A:ASN129 4.0 44.8 1.0 C A:ASN129 4.1 47.2 1.0 CB A:PRO169 4.1 45.7 1.0 CG A:PRO169 4.2 49.1 1.0 CB A:MET168 4.4 40.5 1.0 C A:VAL170 4.4 50.0 1.0 CG2 A:VAL170 4.5 50.8 1.0 N A:VAL171 4.5 44.7 1.0 O A:PRO169 4.8 40.6 1.0 OD1 A:ASN129 4.8 54.7 1.0

Sodium binding site 5 out of 63 in the Mus Musculus BPIFA1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Mus Musculus BPIFA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:48.0 occ:1.00 O A:SER210 2.8 31.0 1.0 C A:SER210 3.7 30.9 1.0 CA A:SER210 3.9 32.6 1.0 CB A:SER210 3.9 25.4 1.0 CD A:LYS212 4.0 42.5 1.0 CB A:LYS180 4.1 26.1 1.0 O A:HOH437 4.1 32.5 1.0 OD1 A:ASN182 4.3 28.8 1.0 ND2 A:ASN182 4.3 21.0 1.0 CG A:ASN182 4.4 20.4 1.0 CE A:LYS212 4.6 38.5 1.0 N A:LEU181 4.6 25.8 1.0 C A:LYS180 4.6 24.9 1.0 NZ A:LYS212 4.6 61.6 1.0 OG A:SER210 4.8 23.7 1.0 O A:LYS180 4.8 28.2 1.0 CD A:LYS180 4.9 36.9 1.0 CG A:LYS212 4.9 35.4 1.0 CA A:LEU181 4.9 24.7 1.0 N A:LEU211 5.0 20.6 1.0 CA A:LYS180 5.0 27.8 1.0

Sodium binding site 6 out of 63 in the Mus Musculus BPIFA1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Mus Musculus BPIFA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:66.2 occ:1.00 CB A:PRO65 2.8 76.0 1.0 N A:SER66 3.2 68.0 1.0 CB A:PRO68 3.3 41.5 1.0 C A:PRO65 3.4 68.5 1.0 CG A:PRO65 3.4 79.3 1.0 CA A:PRO65 3.5 78.3 1.0 CD A:PRO65 3.6 77.4 1.0 CA A:PRO68 3.8 47.4 1.0 N A:PRO65 3.8 76.7 1.0 CD A:PRO68 3.8 42.9 1.0 CG A:PRO68 3.9 45.7 1.0 CA A:SER66 3.9 63.9 1.0 N A:PRO68 3.9 48.2 1.0 O A:PRO65 4.1 73.5 1.0 CB A:SER66 4.6 63.8 1.0 C A:ASN67 4.8 46.2 1.0

Sodium binding site 7 out of 63 in the Mus Musculus BPIFA1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Mus Musculus BPIFA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:42.3 occ:1.00 O A:LEU216 2.6 66.3 1.0 N A:GLN176 2.9 33.8 1.0 O A:LEU174 3.6 35.2 1.0 C A:LEU216 3.7 63.6 1.0 O A:GLN176 3.7 31.3 1.0 CB A:GLN176 3.7 35.9 1.0 CA A:GLN176 3.7 37.3 1.0 C A:LEU175 3.9 36.1 1.0 CA A:LEU175 3.9 37.7 1.0 C A:GLN176 4.2 34.0 1.0 CD1 A:LEU175 4.2 44.7 1.0 N A:LEU216 4.2 46.0 1.0 CB A:LEU216 4.3 38.4 1.0 CA A:LEU216 4.3 52.4 1.0 O A:HOH448 4.4 61.2 1.0 C A:LEU174 4.5 38.9 1.0 CG A:GLN176 4.6 42.1 1.0 N A:LEU175 4.7 40.0 1.0 N A:ASN217 4.8 62.2 1.0 CG1 C:VAL222 4.8 67.5 1.0 CB A:LEU175 4.9 33.7 1.0 OE1 A:GLN176 4.9 44.8 1.0 CG A:LEU175 4.9 32.9 1.0

Sodium binding site 8 out of 63 in the Mus Musculus BPIFA1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Mus Musculus BPIFA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:51.2 occ:1.00 O A:ILE135 2.4 25.6 1.0 C A:ILE135 3.5 29.1 1.0 CB A:GLU94 4.0 23.7 1.0 CG2 A:THR136 4.0 31.6 1.0 N A:ILE135 4.1 32.2 1.0 CG A:GLU94 4.1 28.3 1.0 O A:GLU94 4.3 33.1 1.0 N A:THR136 4.3 27.1 1.0 CA A:ILE135 4.4 29.6 1.0 CA A:THR136 4.4 28.0 1.0 CD A:GLU94 4.5 25.6 1.0 CA A:GLU94 4.6 25.2 1.0 OE1 A:GLU94 4.8 30.5 1.0 CB A:THR136 4.8 30.1 1.0 C A:GLU94 4.8 29.4 1.0 C A:LYS134 4.8 31.3 1.0 CB A:LYS134 4.9 30.3 1.0 CB A:ILE135 4.9 29.5 1.0 OE2 A:GLU94 5.0 26.4 1.0

Sodium binding site 9 out of 63 in the Mus Musculus BPIFA1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Mus Musculus BPIFA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:49.9 occ:1.00 NH2 A:ARG153 2.8 39.1 1.0 CG A:PRO149 3.3 42.4 1.0 CG A:ASP150 3.3 41.3 1.0 N A:ASP150 3.3 33.7 1.0 OD1 A:ASP150 3.5 45.4 1.0 CD A:PRO149 3.5 32.5 1.0 OD2 A:ASP150 3.6 44.0 1.0 CB A:ASP150 3.6 33.3 1.0 N A:PRO149 3.9 36.3 1.0 CZ A:ARG153 4.0 50.3 1.0 CA A:ASP150 4.1 28.7 1.0 CB A:SER148 4.1 34.5 1.0 O A:HOH434 4.1 40.4 1.0 CB A:PRO149 4.2 35.1 1.0 C A:PRO149 4.3 38.7 1.0 OG A:SER148 4.3 35.0 1.0 CA A:PRO149 4.4 37.7 1.0 NH1 A:ARG153 4.5 45.0 1.0 C A:SER148 4.6 30.1 1.0 CA A:SER148 4.9 30.0 1.0

Sodium binding site 10 out of 63 in the Mus Musculus BPIFA1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Mus Musculus BPIFA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:44.5 occ:1.00 O A:ASP70 2.3 39.5 1.0 O A:HOH424 2.7 30.7 1.0 C A:ASP70 2.8 40.9 1.0 O A:THR69 2.8 38.0 1.0 CA A:ASP70 3.2 44.6 1.0 O A:PHE274 3.2 36.1 1.0 N A:ALA73 3.2 25.6 1.0 CB A:ALA73 3.4 25.6 1.0 N A:LEU72 3.6 31.5 1.0 C A:THR69 3.8 37.1 1.0 N A:LEU71 3.8 33.9 1.0 O A:HOH404 3.8 26.5 1.0 CA A:ALA73 3.9 25.9 1.0 N A:ASP70 4.0 43.4 1.0 C A:LEU71 4.1 34.4 1.0 C A:PHE274 4.1 33.5 1.0 C A:LEU72 4.2 29.4 1.0 CA A:LEU72 4.3 33.3 1.0 CA A:LEU71 4.3 35.9 1.0 CA A:VAL275 4.4 35.2 1.0 NA A:NA302 4.5 52.0 1.0 CB A:ASP70 4.5 41.6 1.0 CB A:LEU72 4.5 30.0 1.0 CD1 A:PHE274 4.6 45.9 1.0 N A:VAL275 4.7 36.7 1.0 CB A:PHE274 4.7 41.9 1.0 O A:LEU71 4.7 30.2 1.0 CG A:PHE274 4.8 34.1 1.0 N A:ILE276 4.8 38.7 1.0 N A:GLY74 4.9 21.8 1.0

M.S.Little, M.R.Redinbo. Crystal Structure of the Mouse Innate Immunity Factor Bacterial Permeability-Increasing Family Member A1. Acta Crystallogr F Struct V. 74 268 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29717993
DOI: 10.1107/S2053230X18004600