Cobalt 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:

Sodium

(Na)

11 atoms

The binding sites of Cobalt 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 Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound, PDB code: 8vi8:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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:Co301 b:131.1 occ:1.00 CO01 A:X5Z301 0.0 131.1 1.0 N10 A:X5Z301 1.9 101.2 1.0 N12 A:X5Z301 1.9 123.9 1.0 N09 A:X5Z301 1.9 111.9 1.0 N11 A:X5Z301 1.9 126.5 1.0 N13 A:X5Z301 2.0 126.8 1.0 SG A:CYS72 2.4 100.7 1.0 N14 A:X5Z301 2.7 128.7 1.0 C20 A:X5Z301 2.7 103.2 1.0 C21 A:X5Z301 2.7 92.3 1.0 C22 A:X5Z301 2.7 121.3 1.0 C23 A:X5Z301 2.7 126.6 1.0 O04 A:X5Z301 2.8 108.4 1.0 O03 A:X5Z301 2.8 102.7 1.0 O06 A:X5Z301 2.9 125.2 1.0 O05 A:X5Z301 2.9 123.2 1.0 N15 A:X5Z301 3.7 134.6 1.0 CB A:CYS72 4.1 99.5 1.0 C25 A:X5Z301 4.2 85.3 1.0 C24 A:X5Z301 4.2 94.3 1.0 C27 A:X5Z301 4.2 130.5 1.0 C26 A:X5Z301 4.2 107.2 1.0 CA A:CYS72 4.4 99.6 1.0 N A:ASP73 4.5 97.8 1.0 C A:CYS72 4.8 100.0 1.0 N A:GLU74 4.9 100.6 1.0

Cobalt binding site 2 out of 6 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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:Co301 b:129.5 occ:1.00 CO01 B:X5Z301 0.0 129.5 1.0 N10 B:X5Z301 1.9 103.7 1.0 N12 B:X5Z301 1.9 124.6 1.0 N09 B:X5Z301 1.9 122.4 1.0 N11 B:X5Z301 1.9 128.4 1.0 N13 B:X5Z301 2.0 129.0 1.0 SG B:CYS72 2.4 109.4 1.0 N14 B:X5Z301 2.7 129.5 1.0 C20 B:X5Z301 2.7 113.7 1.0 C21 B:X5Z301 2.7 97.5 1.0 C22 B:X5Z301 2.7 122.3 1.0 C23 B:X5Z301 2.7 124.5 1.0 O04 B:X5Z301 2.8 113.2 1.0 O03 B:X5Z301 2.8 117.7 1.0 O06 B:X5Z301 2.9 125.7 1.0 O05 B:X5Z301 2.9 123.9 1.0 N15 B:X5Z301 3.7 128.4 1.0 CB B:CYS72 4.0 106.9 1.0 C25 B:X5Z301 4.2 85.5 1.0 C24 B:X5Z301 4.2 103.2 1.0 C27 B:X5Z301 4.2 124.3 1.0 C26 B:X5Z301 4.2 113.4 1.0 CA B:CYS72 4.3 100.3 1.0 N B:ASP73 4.5 104.6 1.0 C B:CYS72 4.8 103.8 1.0 N B:GLU74 4.9 115.4 1.0

Cobalt binding site 3 out of 6 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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 C:Co301 b:136.0 occ:1.00 CO01 C:X5Z301 0.0 136.0 1.0 N10 C:X5Z301 1.9 97.7 1.0 N12 C:X5Z301 1.9 123.0 1.0 N09 C:X5Z301 1.9 108.6 1.0 N11 C:X5Z301 1.9 121.8 1.0 N13 C:X5Z301 2.0 119.2 1.0 SG C:CYS72 2.3 102.0 1.0 N14 C:X5Z301 2.7 116.9 1.0 C20 C:X5Z301 2.7 102.3 1.0 C21 C:X5Z301 2.7 89.5 1.0 C22 C:X5Z301 2.7 118.2 1.0 C23 C:X5Z301 2.7 120.8 1.0 O04 C:X5Z301 2.8 102.9 1.0 O03 C:X5Z301 2.8 98.1 1.0 O06 C:X5Z301 2.9 120.2 1.0 O05 C:X5Z301 2.9 121.4 1.0 N15 C:X5Z301 3.7 124.0 1.0 CB C:CYS72 4.0 98.7 1.0 C25 C:X5Z301 4.2 78.2 1.0 C24 C:X5Z301 4.2 106.7 1.0 C27 C:X5Z301 4.2 126.1 1.0 C26 C:X5Z301 4.2 116.2 1.0 CA C:CYS72 4.3 94.4 1.0 N C:ASP73 4.5 102.0 1.0 C C:CYS72 4.8 102.1 1.0 N C:GLU74 4.9 109.0 1.0

Cobalt binding site 4 out of 6 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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 D:Co301 b:141.7 occ:1.00 CO01 D:X5Z301 0.0 141.7 1.0 N10 D:X5Z301 1.9 105.4 1.0 N12 D:X5Z301 1.9 122.1 1.0 N09 D:X5Z301 1.9 105.9 1.0 N11 D:X5Z301 1.9 128.8 1.0 N13 D:X5Z301 2.0 128.3 1.0 SG D:CYS72 2.3 111.7 1.0 N14 D:X5Z301 2.7 127.0 1.0 C20 D:X5Z301 2.7 102.4 1.0 C21 D:X5Z301 2.7 95.9 1.0 C22 D:X5Z301 2.7 124.8 1.0 C23 D:X5Z301 2.7 124.7 1.0 O04 D:X5Z301 2.8 109.4 1.0 O03 D:X5Z301 2.8 95.6 1.0 O06 D:X5Z301 2.9 123.0 1.0 O05 D:X5Z301 2.9 124.8 1.0 N15 D:X5Z301 3.7 132.4 1.0 CB D:CYS72 4.0 103.9 1.0 C25 D:X5Z301 4.2 85.3 1.0 C24 D:X5Z301 4.2 91.0 1.0 C27 D:X5Z301 4.2 127.0 1.0 C26 D:X5Z301 4.2 122.2 1.0 CA D:CYS72 4.5 99.6 1.0 N D:ASP73 4.6 109.2 1.0 N D:GLU74 4.9 112.3 1.0 C D:CYS72 4.9 106.7 1.0

Cobalt binding site 5 out of 6 in the Engineered Glutamine Binding Protein and A Cobaloxime Ligand - No Gln Bound


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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 E:Co301 b:135.0 occ:1.00 CO01 E:X5Z301 0.0 135.0 1.0 N10 E:X5Z301 1.9 105.4 1.0 N12 E:X5Z301 1.9 120.3 1.0 N09 E:X5Z301 1.9 113.9 1.0 N11 E:X5Z301 1.9 123.9 1.0 N13 E:X5Z301 2.0 128.8 1.0 SG E:CYS72 2.3 104.8 1.0 N14 E:X5Z301 2.7 130.6 1.0 C20 E:X5Z301 2.7 108.6 1.0 C21 E:X5Z301 2.7 97.3 1.0 C22 E:X5Z301 2.7 116.3 1.0 C23 E:X5Z301 2.7 119.1 1.0 O04 E:X5Z301 2.8 113.8 1.0 O03 E:X5Z301 2.8 103.6 1.0 O06 E:X5Z301 2.9 122.8 1.0 O05 E:X5Z301 2.9 121.5 1.0 N15 E:X5Z301 3.7 132.9 1.0 CB E:CYS72 4.0 102.2 1.0 C25 E:X5Z301 4.2 83.8 1.0 C24 E:X5Z301 4.2 102.3 1.0 C27 E:X5Z301 4.2 124.9 1.0 C26 E:X5Z301 4.2 108.5 1.0 CA E:CYS72 4.4 103.2 1.0 N E:ASP73 4.6 104.2 1.0 C E:CYS72 4.9 106.6 1.0 N E:GLU74 4.9 112.8 1.0

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co 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 F:Co301 b:137.2 occ:1.00 CO01 F:X5Z301 0.0 137.2 1.0 N10 F:X5Z301 1.9 107.2 1.0 N12 F:X5Z301 1.9 119.2 1.0 N09 F:X5Z301 1.9 119.6 1.0 N11 F:X5Z301 1.9 129.1 1.0 N13 F:X5Z301 2.0 133.1 1.0 SG F:CYS72 2.3 105.2 1.0 N14 F:X5Z301 2.7 134.9 1.0 C20 F:X5Z301 2.7 111.0 1.0 C21 F:X5Z301 2.7 103.2 1.0 C22 F:X5Z301 2.7 123.4 1.0 C23 F:X5Z301 2.7 123.0 1.0 O04 F:X5Z301 2.8 120.5 1.0 O03 F:X5Z301 2.8 108.1 1.0 O06 F:X5Z301 2.9 120.8 1.0 O05 F:X5Z301 2.9 128.7 1.0 N15 F:X5Z301 3.7 137.4 1.0 CB F:CYS72 4.0 105.2 1.0 C25 F:X5Z301 4.2 96.8 1.0 C24 F:X5Z301 4.2 92.3 1.0 C27 F:X5Z301 4.2 124.3 1.0 C26 F:X5Z301 4.2 110.8 1.0 CA F:CYS72 4.4 98.2 1.0 N F:ASP73 4.5 105.7 1.0 N F:GLU74 4.8 111.4 1.0 C F:CYS72 4.8 103.3 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