Sodium in PDB 8vi8: Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound

The structure of Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound, PDB code: 8vi8 was solved by D.G.Boggs, S.Fatima, L.Olshansky, J.Bridwell-Rabb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.86 / 3.21
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.067, 145.797, 123.443, 90, 90.11, 90
R / Rfree (%)	28.4 / 29

The structure of Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound also contains other interesting chemical elements:

Cobalt

(Co)

6 atoms

Pages:

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

Binding sites:

The binding sites of Sodium atom in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound (pdb code 8vi8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound, PDB code: 8vi8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:85.7 occ:1.00 NZ A:LYS95 2.3 99.0 1.0 O A:HOH407 2.4 98.3 1.0 OD1 A:ASN149 2.5 104.0 1.0 CE A:LYS95 2.8 114.8 1.0 O A:HOH405 3.2 89.8 1.0 CG A:ASN149 3.5 104.9 1.0 ND2 A:ASN149 3.9 104.6 1.0 ND2 A:ASN97 4.0 105.4 1.0 OD1 A:ASN97 4.0 105.0 1.0 CD A:LYS95 4.2 95.3 1.0 CG A:ASN97 4.4 103.1 1.0 CB A:ASN149 4.8 91.6 1.0

Sodium binding site 2 out of 11 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:98.0 occ:1.00 NZ B:LYS95 2.3 102.1 1.0 O B:HOH405 2.5 101.9 1.0 OD1 B:ASN149 2.7 111.1 1.0 CE B:LYS95 2.9 112.7 1.0 CG B:ASN149 3.6 109.2 1.0 ND2 B:ASN149 3.9 112.2 1.0 ND2 B:ASN97 3.9 110.2 1.0 O B:HOH401 3.9 77.7 1.0 OD1 B:ASN97 4.3 120.8 1.0 CD B:LYS95 4.3 101.7 1.0 CG B:ASN97 4.4 115.1 1.0 O B:HOH406 4.7 94.1 1.0

Sodium binding site 3 out of 11 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:58.7 occ:1.00 O B:HOH403 2.4 89.8 1.0 OD1 B:ASN138 2.4 111.5 1.0 NZ B:LYS115 2.8 72.1 1.0 CG B:ASN138 3.3 111.5 1.0 CE B:LYS115 3.5 93.0 1.0 O B:HOH407 3.6 76.3 1.0 CD B:LYS115 4.0 89.0 1.0 ND2 B:ASN138 4.0 119.5 1.0 CA B:ASN138 4.1 88.4 1.0 CB B:ASN138 4.1 84.7 1.0 N B:ILE139 4.3 78.8 1.0 O B:PRO137 4.6 102.5 1.0 CG1 B:ILE139 4.7 86.8 1.0 C B:ASN138 4.7 86.0 1.0

Sodium binding site 4 out of 11 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Na305 b:87.7 occ:1.00 O C:HOH401 2.2 73.2 1.0 OH C:TYR43 2.5 100.8 1.0 CZ C:TYR43 3.1 102.8 1.0 CE1 C:TYR43 3.5 107.1 1.0 CE2 C:TYR43 3.9 109.4 1.0 O C:HOH408 4.5 84.4 1.0 CD1 C:TYR43 4.6 94.8 1.0 CD2 C:TYR43 4.9 109.3 1.0

Sodium binding site 5 out of 11 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Na306 b:91.0 occ:1.00 NZ C:LYS95 2.4 102.0 1.0 O B:HOH404 2.4 92.5 1.0 OH B:TYR43 2.5 100.8 1.0 OD1 C:ASN149 2.5 115.7 1.0 CZ B:TYR43 2.9 102.3 1.0 CE C:LYS95 2.9 111.0 1.0 CE1 B:TYR43 3.4 102.5 1.0 CG C:ASN149 3.4 109.5 1.0 ND2 C:ASN149 3.6 107.8 1.0 O C:HOH403 3.7 82.9 1.0 CE2 B:TYR43 3.7 108.4 1.0 ND2 C:ASN97 4.1 111.0 1.0 OD1 C:ASN97 4.3 115.6 1.0 CD C:LYS95 4.4 99.2 1.0 CD1 B:TYR43 4.4 85.3 1.0 CG C:ASN97 4.5 111.7 1.0 CD2 B:TYR43 4.7 102.9 1.0 CB C:ASN149 4.8 95.7 1.0

Sodium binding site 6 out of 11 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Na307 b:75.8 occ:1.00 O C:HOH405 2.1 109.4 1.0 OD1 C:ASN138 2.2 112.1 1.0 NZ C:LYS115 2.6 98.3 1.0 CG C:ASN138 3.1 115.9 1.0 CE C:LYS115 3.2 112.5 1.0 ND2 C:ASN138 3.9 130.6 1.0 CA C:ASN138 4.0 92.4 1.0 CD C:LYS115 4.0 102.8 1.0 CB C:ASN138 4.0 87.5 1.0 N C:ILE139 4.1 85.1 1.0 CG1 C:ILE139 4.5 96.0 1.0 O C:PRO137 4.5 107.2 1.0 C C:ASN138 4.6 90.3 1.0

Sodium binding site 7 out of 11 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Na304 b:76.5 occ:1.00 OD1 D:ASN138 2.3 114.1 1.0 O D:HOH402 2.3 92.3 1.0 NZ D:LYS115 2.7 99.6 1.0 CG D:ASN138 3.1 114.7 1.0 CE D:LYS115 3.4 107.0 1.0 ND2 D:ASN138 3.8 126.2 1.0 CB D:ASN138 4.1 84.5 1.0 CA D:ASN138 4.1 89.1 1.0 CD D:LYS115 4.2 92.8 1.0 N D:ILE139 4.3 87.5 1.0 CG1 D:ILE139 4.6 96.8 1.0 O D:PRO137 4.7 105.8 1.0 C D:ASN138 4.8 90.1 1.0

Sodium binding site 8 out of 11 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound within 5.0Å range: probe atom residue distance (Å) B Occ E:Na303 b:97.2 occ:1.00 NZ E:LYS95 2.3 98.0 1.0 OD1 E:ASN149 2.3 101.5 1.0 O E:HOH401 2.5 73.6 1.0 OH A:TYR43 2.6 86.9 1.0 O A:HOH409 2.7 104.8 1.0 CE E:LYS95 2.7 106.5 1.0 CZ A:TYR43 3.1 97.7 1.0 CG E:ASN149 3.2 95.5 1.0 ND2 E:ASN149 3.5 100.8 1.0 CE1 A:TYR43 3.5 95.0 1.0 CE2 A:TYR43 4.0 106.1 1.0 ND2 E:ASN97 4.0 109.4 1.0 O E:HOH403 4.1 82.1 1.0 OD1 E:ASN97 4.1 114.0 1.0 CD E:LYS95 4.1 92.2 1.0 O A:HOH410 4.3 89.8 1.0 CG E:ASN97 4.4 108.6 1.0 CD1 A:TYR43 4.6 77.7 1.0 CB E:ASN149 4.6 85.8 1.0 O A:HOH406 4.8 71.5 1.0 CD2 A:TYR43 4.9 96.9 1.0

Sodium binding site 9 out of 11 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound within 5.0Å range: probe atom residue distance (Å) B Occ E:Na304 b:78.6 occ:1.00 O E:HOH405 2.3 72.5 1.0 OH E:TYR43 2.4 94.5 1.0 CZ E:TYR43 3.1 102.7 1.0 CE1 E:TYR43 3.7 104.5 1.0 CE2 E:TYR43 3.8 102.1 1.0 O E:HOH408 4.3 88.0 1.0 CD1 E:TYR43 4.8 83.3 1.0 CD2 E:TYR43 4.9 94.7 1.0

Sodium binding site 10 out of 11 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound within 5.0Å range: probe atom residue distance (Å) B Occ E:Na305 b:73.8 occ:1.00 OD1 E:ASN138 2.3 113.9 1.0 O E:HOH402 2.3 77.9 1.0 O E:HOH407 2.4 100.2 1.0 CG E:ASN138 3.1 115.9 1.0 ND2 E:ASN138 3.5 128.1 1.0 NZ E:LYS115 4.1 82.6 1.0 CB E:ASN138 4.3 89.3 1.0 O E:HOH409 4.4 83.3 1.0 CA E:ASN138 4.6 84.5 1.0 CG1 E:ILE139 4.6 92.7 1.0 N E:ILE139 4.6 71.9 1.0 CE E:LYS115 4.7 101.9 1.0 OD2 E:ASP140 4.8 148.1 1.0

S.Fatima, B.Mehrafrooz, D.G.Boggs, N.Ali, S.Singh, M.C.Thielges, J.Bridwell-Rabb, A.Aksimentiev, L.Olshansky. Conformation-Dependent Hydrogen-Bonding Interactions in A Switchable Artificial Metalloprotein. Biochemistry V. 63 2040 2024.
ISSN: ISSN 0006-2960
PubMed: 39088332
DOI: 10.1021/ACS.BIOCHEM.4C00209