Cobalt in PDB 8okv: Lipoprotein BT2095 From Bacteroides Thetaiotamicron Bound to Cyanocobalamin Cncbl

The structure of Lipoprotein BT2095 From Bacteroides Thetaiotamicron Bound to Cyanocobalamin Cncbl, PDB code: 8okv was solved by J.Javier Abellon-Ruiz, B.Van Den Berg, K.Jana, U.Kleinekathofer, A.Silale, A.M.Frey, A.Basle, M.Trost, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.12 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.77, 131.04, 179.38, 90, 90, 90
R / Rfree (%)	21.8 / 27.6

The binding sites of Cobalt atom in the Lipoprotein BT2095 From Bacteroides Thetaiotamicron Bound to Cyanocobalamin Cncbl (pdb code 8okv). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Lipoprotein BT2095 From Bacteroides Thetaiotamicron Bound to Cyanocobalamin Cncbl, PDB code: 8okv:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Lipoprotein BT2095 From Bacteroides Thetaiotamicron Bound to Cyanocobalamin Cncbl


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Lipoprotein BT2095 From Bacteroides Thetaiotamicron Bound to Cyanocobalamin Cncbl within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:81.8 occ:1.00 CO B:CNC401 0.0 81.8 1.0 C1A B:CNC401 1.8 73.9 1.0 N21 B:CNC401 1.8 80.6 1.0 N23 B:CNC401 1.9 103.5 1.0 N24 B:CNC401 1.9 85.1 1.0 N22 B:CNC401 1.9 84.1 1.0 N3B B:CNC401 2.2 71.0 1.0 C19 B:CNC401 2.7 78.1 1.0 C1 B:CNC401 2.8 69.4 1.0 C9 B:CNC401 2.8 97.2 1.0 C4 B:CNC401 2.8 82.0 1.0 C14 B:CNC401 2.9 102.3 1.0 C11 B:CNC401 2.9 123.9 1.0 C6 B:CNC401 2.9 76.7 1.0 N1A B:CNC401 2.9 79.6 1.0 C16 B:CNC401 3.0 72.6 1.0 H201 B:CNC401 3.1 63.2 1.0 C9B B:CNC401 3.2 77.9 1.0 C2B B:CNC401 3.2 94.5 1.0 C10 B:CNC401 3.2 120.1 1.0 C5 B:CNC401 3.3 86.9 1.0 H4B B:CNC401 3.3 73.1 1.0 C15 B:CNC401 3.3 87.1 1.0 C20 B:CNC401 3.4 60.4 1.0 H2B B:CNC401 3.4 85.4 1.0 H203 B:CNC401 3.7 63.1 1.0 C4B B:CNC401 3.7 72.8 1.0 C2 B:CNC401 4.0 58.8 1.0 H261 B:CNC401 4.0 61.2 1.0 C18 B:CNC401 4.1 74.5 1.0 C3 B:CNC401 4.1 62.6 1.0 C8 B:CNC401 4.2 82.9 1.0 C13 B:CNC401 4.2 107.7 1.0 C7 B:CNC401 4.2 71.0 1.0 C12 B:CNC401 4.2 124.5 1.0 H10 B:CNC401 4.2 114.1 1.0 H371 B:CNC401 4.2 56.1 1.0 C17 B:CNC401 4.2 74.7 1.0 H471 B:CNC401 4.3 123.3 1.0 H202 B:CNC401 4.3 63.1 1.0 H18 B:CNC401 4.3 73.0 1.0 N1B B:CNC401 4.4 85.8 1.0 H412 B:CNC401 4.4 78.1 1.0 C8B B:CNC401 4.4 82.1 1.0 C26 B:CNC401 4.5 63.1 1.0 H542 B:CNC401 4.6 75.6 1.0 H262 B:CNC401 4.6 61.2 1.0 C47 B:CNC401 4.7 123.0 1.0 C37 B:CNC401 4.7 49.5 1.0 H561 B:CNC401 4.7 78.5 1.0 H3 B:CNC401 4.8 66.4 1.0 C35 B:CNC401 4.8 92.1 1.0 H473 B:CNC401 4.8 123.4 1.0 H13 B:CNC401 4.8 109.6 1.0 H301 B:CNC401 4.8 67.3 1.0 H8 B:CNC401 4.8 82.0 1.0 C53 B:CNC401 4.8 97.5 1.0 H302 B:CNC401 4.8 67.4 1.0 C41 B:CNC401 4.9 77.7 1.0 HH2 B:TRP183 4.9 59.2 1.0 H481 B:CNC401 4.9 108.8 1.0 C30 B:CNC401 4.9 68.7 1.0 H482 B:CNC401 4.9 108.7 1.0 C54 B:CNC401 4.9 76.0 1.0 C48 B:CNC401 5.0 107.8 1.0

Cobalt binding site 2 out of 4 in the Lipoprotein BT2095 From Bacteroides Thetaiotamicron Bound to Cyanocobalamin Cncbl


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Lipoprotein BT2095 From Bacteroides Thetaiotamicron Bound to Cyanocobalamin Cncbl within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:62.8 occ:1.00 CO A:CNC401 0.0 62.8 1.0 N24 A:CNC401 1.8 49.4 1.0 C1A A:CNC401 1.8 77.3 1.0 N23 A:CNC401 1.8 64.8 1.0 N21 A:CNC401 1.9 54.5 1.0 N22 A:CNC401 1.9 49.9 1.0 N3B A:CNC401 2.5 37.9 1.0 C19 A:CNC401 2.7 50.2 1.0 C9 A:CNC401 2.8 57.1 1.0 C14 A:CNC401 2.8 61.1 1.0 C4 A:CNC401 2.8 48.7 1.0 C16 A:CNC401 2.8 51.8 1.0 C11 A:CNC401 2.9 66.6 1.0 C1 A:CNC401 2.9 43.8 1.0 C6 A:CNC401 2.9 46.4 1.0 N1A A:CNC401 3.0 50.2 1.0 H201 A:CNC401 3.1 41.2 1.0 C10 A:CNC401 3.2 56.3 1.0 C15 A:CNC401 3.2 47.8 1.0 H2B A:CNC401 3.3 41.3 1.0 C5 A:CNC401 3.3 40.7 1.0 C2B A:CNC401 3.3 39.1 1.0 C20 A:CNC401 3.5 40.0 1.0 C9B A:CNC401 3.6 38.8 1.0 H4B A:CNC401 3.6 44.5 1.0 H203 A:CNC401 4.0 41.2 1.0 H261 A:CNC401 4.0 56.6 1.0 C4B A:CNC401 4.1 45.5 1.0 C18 A:CNC401 4.1 56.3 1.0 C2 A:CNC401 4.1 57.1 1.0 C8 A:CNC401 4.1 53.8 1.0 C3 A:CNC401 4.1 53.9 1.0 C17 A:CNC401 4.2 58.9 1.0 H10 A:CNC401 4.2 58.9 1.0 C12 A:CNC401 4.2 71.3 1.0 C13 A:CNC401 4.2 64.6 1.0 C7 A:CNC401 4.2 50.6 1.0 H371 A:CNC401 4.3 62.2 1.0 H202 A:CNC401 4.3 41.3 1.0 H18 A:CNC401 4.3 56.7 1.0 H471 A:CNC401 4.5 73.9 1.0 C26 A:CNC401 4.5 61.0 1.0 H542 A:CNC401 4.6 59.2 1.0 H412 A:CNC401 4.6 60.2 1.0 N1B A:CNC401 4.6 46.1 1.0 H3 A:CNC401 4.7 53.6 1.0 H262 A:CNC401 4.7 56.6 1.0 C53 A:CNC401 4.8 57.2 1.0 H13 A:CNC401 4.8 66.6 1.0 H8 A:CNC401 4.8 54.8 1.0 C8B A:CNC401 4.8 45.7 1.0 C54 A:CNC401 4.8 59.4 1.0 C37 A:CNC401 4.8 69.4 1.0 C47 A:CNC401 4.9 75.1 1.0 C41 A:CNC401 4.9 59.0 1.0 C35 A:CNC401 4.9 34.4 1.0 HH2 A:TRP183 4.9 62.4 1.0 H543 A:CNC401 4.9 59.3 1.0 H302 A:CNC401 5.0 57.0 1.0 H561 A:CNC401 5.0 66.1 1.0

Cobalt binding site 3 out of 4 in the Lipoprotein BT2095 From Bacteroides Thetaiotamicron Bound to Cyanocobalamin Cncbl


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Lipoprotein BT2095 From Bacteroides Thetaiotamicron Bound to Cyanocobalamin Cncbl within 5.0Å range: probe atom residue distance (Å) B Occ C:Co401 b:97.0 occ:1.00 CO C:CNC401 0.0 97.0 1.0 C1A C:CNC401 1.8 77.9 1.0 N21 C:CNC401 1.9 104.5 1.0 N24 C:CNC401 1.9 116.6 1.0 N23 C:CNC401 1.9 126.0 1.0 N22 C:CNC401 1.9 118.0 1.0 N3B C:CNC401 2.1 70.2 1.0 C19 C:CNC401 2.7 92.8 1.0 C14 C:CNC401 2.8 138.6 1.0 C4 C:CNC401 2.8 101.6 1.0 C9 C:CNC401 2.8 109.0 1.0 C1 C:CNC401 2.9 84.8 1.0 C16 C:CNC401 2.9 115.5 1.0 N1A C:CNC401 2.9 86.4 1.0 C6 C:CNC401 2.9 99.6 1.0 C11 C:CNC401 2.9 120.9 1.0 C9B C:CNC401 3.1 86.2 1.0 C2B C:CNC401 3.2 89.9 1.0 C15 C:CNC401 3.2 130.3 1.0 C5 C:CNC401 3.3 101.0 1.0 C10 C:CNC401 3.3 119.0 1.0 H2B C:CNC401 3.3 87.6 1.0 H4B C:CNC401 3.4 85.2 1.0 H201 C:CNC401 3.4 81.3 1.0 C20 C:CNC401 3.7 79.9 1.0 C4B C:CNC401 3.7 83.9 1.0 H261 C:CNC401 3.9 76.7 1.0 C13 C:CNC401 4.1 133.2 1.0 H203 C:CNC401 4.1 81.3 1.0 C2 C:CNC401 4.1 82.0 1.0 C18 C:CNC401 4.1 83.9 1.0 C3 C:CNC401 4.1 77.9 1.0 C8 C:CNC401 4.2 92.1 1.0 H482 C:CNC401 4.2 140.2 1.0 C17 C:CNC401 4.2 89.4 1.0 C7 C:CNC401 4.2 75.7 1.0 H371 C:CNC401 4.2 73.3 1.0 H10 C:CNC401 4.2 116.7 1.0 H462 C:CNC401 4.3 101.4 1.0 C12 C:CNC401 4.3 110.8 1.0 N1B C:CNC401 4.3 101.0 1.0 H18 C:CNC401 4.4 83.2 1.0 H412 C:CNC401 4.4 82.8 1.0 C8B C:CNC401 4.4 92.1 1.0 H202 C:CNC401 4.5 81.3 1.0 C26 C:CNC401 4.5 76.6 1.0 C53 C:CNC401 4.6 118.4 1.0 C37 C:CNC401 4.6 69.2 1.0 H372 C:CNC401 4.6 73.2 1.0 C48 C:CNC401 4.7 138.4 1.0 H262 C:CNC401 4.7 76.7 1.0 H533 C:CNC401 4.7 121.8 1.0 H3 C:CNC401 4.7 80.1 1.0 H562 C:CNC401 4.8 89.5 1.0 C35 C:CNC401 4.8 92.2 1.0 H13 C:CNC401 4.8 130.3 1.0 C46 C:CNC401 4.8 97.4 1.0 H542 C:CNC401 4.8 81.6 1.0 H8 C:CNC401 4.9 89.2 1.0 C41 C:CNC401 4.9 80.2 1.0 H532 C:CNC401 4.9 121.9 1.0

Cobalt binding site 4 out of 4 in the Lipoprotein BT2095 From Bacteroides Thetaiotamicron Bound to Cyanocobalamin Cncbl


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Lipoprotein BT2095 From Bacteroides Thetaiotamicron Bound to Cyanocobalamin Cncbl within 5.0Å range: probe atom residue distance (Å) B Occ D:Co401 b:66.1 occ:1.00 CO D:CNC401 0.0 66.1 1.0 N22 D:CNC401 1.8 48.3 1.0 N23 D:CNC401 1.8 54.5 1.0 C1A D:CNC401 1.8 93.1 1.0 N24 D:CNC401 1.9 64.1 1.0 N21 D:CNC401 1.9 57.0 1.0 N3B D:CNC401 2.7 47.9 1.0 C9 D:CNC401 2.7 49.6 1.0 C19 D:CNC401 2.7 60.1 1.0 C14 D:CNC401 2.8 53.1 1.0 C11 D:CNC401 2.8 58.3 1.0 C4 D:CNC401 2.8 46.2 1.0 C1 D:CNC401 2.9 54.6 1.0 C6 D:CNC401 2.9 50.7 1.0 C16 D:CNC401 2.9 54.2 1.0 N1A D:CNC401 3.0 76.7 1.0 H201 D:CNC401 3.1 62.7 1.0 C10 D:CNC401 3.2 46.5 1.0 C5 D:CNC401 3.3 40.3 1.0 C15 D:CNC401 3.3 51.0 1.0 C20 D:CNC401 3.5 66.9 1.0 C9B D:CNC401 3.6 43.5 1.0 C2B D:CNC401 3.6 44.4 1.0 H4B D:CNC401 3.6 43.4 1.0 H2B D:CNC401 3.7 47.2 1.0 H421 D:CNC401 3.9 73.8 1.0 H261 D:CNC401 4.0 55.2 1.0 H471 D:CNC401 4.0 67.9 1.0 C8 D:CNC401 4.0 60.3 1.0 C4B D:CNC401 4.0 39.1 1.0 C18 D:CNC401 4.0 63.1 1.0 H203 D:CNC401 4.0 62.7 1.0 C13 D:CNC401 4.1 67.9 1.0 C2 D:CNC401 4.1 54.6 1.0 C12 D:CNC401 4.1 69.6 1.0 C3 D:CNC401 4.2 47.5 1.0 H10 D:CNC401 4.2 50.2 1.0 C17 D:CNC401 4.2 61.7 1.0 C7 D:CNC401 4.2 54.7 1.0 H202 D:CNC401 4.3 62.6 1.0 H18 D:CNC401 4.3 63.8 1.0 H412 D:CNC401 4.4 67.5 1.0 C26 D:CNC401 4.5 58.4 1.0 C41 D:CNC401 4.5 68.1 1.0 H371 D:CNC401 4.5 65.1 1.0 C47 D:CNC401 4.5 67.3 1.0 H542 D:CNC401 4.6 65.1 1.0 C42 D:CNC401 4.6 75.4 1.0 H262 D:CNC401 4.7 55.3 1.0 N1B D:CNC401 4.7 51.6 1.0 H3 D:CNC401 4.7 49.5 1.0 H8 D:CNC401 4.7 58.4 1.0 HH2 D:TRP183 4.8 60.4 1.0 C8B D:CNC401 4.8 54.3 1.0 H13 D:CNC401 4.8 67.5 1.0 C53 D:CNC401 4.8 53.4 1.0 H473 D:CNC401 4.8 68.0 1.0 C54 D:CNC401 4.9 66.6 1.0 C35 D:CNC401 4.9 37.3 1.0 H481 D:CNC401 4.9 81.0 1.0 H482 D:CNC401 5.0 81.1 1.0 H302 D:CNC401 5.0 53.6 1.0 C48 D:CNC401 5.0 82.1 1.0 C37 D:CNC401 5.0 67.5 1.0 H541 D:CNC401 5.0 65.0 1.0

J.Abellon-Ruiz, K.Jana, A.Silale, A.M.Frey, A.Basle, M.Trost, U.Kleinekathofer, B.Van Den Berg. Btub Tonb-Dependent Transporters and Btug Surface Lipoproteins Form Stable Complexes For Vitamin B 12 Uptake in Gut Bacteroides. Nat Commun V. 14 4714 2023.
ISSN: ESSN 2041-1723
PubMed: 37543597
DOI: 10.1038/S41467-023-40427-2