Cadmium in PDB 8b3k: Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State

The structure of Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State, PDB code: 8b3k was solved by R.Cowan, G.Hall, M.Carr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.67 / 2.69
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	266.692, 266.692, 108.728, 90, 90, 90
R / Rfree (%)	19.9 / 24.5

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>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State (pdb code 8b3k). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 14 binding sites of Cadmium where determined in the Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State, PDB code: 8b3k:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 14 in the Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd601 b:71.4 occ:1.00 OE2 B:GLU269 2.4 53.4 1.0 OE2 B:GLU399 2.5 51.7 1.0 O B:HOH704 2.5 29.9 1.0 NH1 B:ARG272 2.6 37.1 1.0 OE1 B:GLU269 2.8 44.8 1.0 CD B:GLU269 2.9 57.8 1.0 OE1 B:GLU399 2.9 49.0 1.0 CD B:GLU399 3.0 50.7 1.0 CZ B:ARG272 3.8 54.3 1.0 CG B:GLU399 4.4 37.7 1.0 CG B:GLU269 4.4 54.4 1.0 NH2 B:ARG272 4.4 39.6 1.0 NE B:ARG272 4.8 70.3 1.0 OH B:TYR273 5.0 34.3 1.0

Cadmium binding site 2 out of 14 in the Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd602 b:62.3 occ:1.00 NE2 B:HIS465 2.0 61.4 1.0 O B:HOH768 2.6 33.4 1.0 O B:HOH765 2.6 25.4 1.0 CE1 B:HIS465 2.7 47.5 1.0 CD2 B:HIS465 3.1 55.6 1.0 ND1 B:HIS465 3.9 42.4 1.0 CG B:HIS465 4.1 44.9 1.0 NZ B:LYS476 4.7 58.1 1.0 CB B:PRO478 4.8 39.3 1.0

Cadmium binding site 3 out of 14 in the Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd603 b:74.5 occ:1.00 NE2 B:HIS217 2.5 57.8 1.0 O B:HOH792 2.8 31.5 1.0 O B:HOH794 2.9 53.0 1.0 O B:HOH789 3.2 49.2 1.0 CD2 B:HIS217 3.3 49.8 1.0 CE1 B:HIS217 3.6 53.7 1.0 CG B:HIS217 4.5 47.7 1.0 ND1 B:HIS217 4.6 55.2 1.0

Cadmium binding site 4 out of 14 in the Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd604 b:74.9 occ:1.00 NE2 B:HIS416 2.6 54.3 1.0 CD2 B:HIS416 3.3 48.4 1.0 CE1 B:HIS416 3.7 61.4 1.0 CG B:HIS416 4.5 50.5 1.0 ND1 B:HIS416 4.7 60.8 1.0

Cadmium binding site 5 out of 14 in the Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd605 b:139.3 occ:1.00 ND1 B:HIS440 3.6 74.3 1.0 CE1 B:HIS440 4.1 66.8 1.0 CG B:HIS440 4.8 64.3 1.0 CG B:PRO441 4.9 37.8 1.0 CD B:PRO441 5.0 36.1 1.0

Cadmium binding site 6 out of 14 in the Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd606 b:72.0 occ:1.00 NE2 B:HIS485 2.2 69.7 1.0 O B:HOH800 2.7 35.0 1.0 CE1 B:HIS485 2.7 55.9 1.0 ND1 B:HIS494 2.8 73.2 1.0 CD2 B:HIS485 3.5 64.6 1.0 CE1 B:HIS494 3.5 66.0 1.0 CG B:HIS494 3.6 64.1 1.0 CB B:HIS494 3.8 54.5 1.0 CA B:HIS494 3.9 59.6 1.0 ND1 B:HIS485 4.0 58.4 1.0 O B:HOH784 4.1 49.9 1.0 NE2 B:GLN484 4.4 69.9 1.0 CG B:HIS485 4.4 61.0 1.0 N B:HIS494 4.4 64.5 1.0 NE2 B:HIS494 4.5 70.0 1.0 CD2 B:HIS494 4.6 59.1 1.0 O B:SER490 4.6 51.5 1.0 O B:HOH780 4.9 46.2 1.0 C B:ALA493 5.0 58.3 1.0

Cadmium binding site 7 out of 14 in the Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd607 b:54.8 occ:1.00 OD2 B:ASP456 2.5 51.5 1.0 OD1 B:ASP456 2.6 43.9 1.0 ND1 B:HIS37 2.7 37.7 1.0 CG B:ASP456 2.8 44.3 1.0 CG B:HIS37 3.4 36.6 1.0 CB B:HIS37 3.5 39.9 1.0 CE1 B:HIS37 3.7 37.1 1.0 CA B:HIS37 4.1 41.0 1.0 CB B:ASP456 4.3 41.3 1.0 CD2 B:HIS37 4.6 39.6 1.0 O B:GLN36 4.6 46.9 1.0 NE2 B:HIS37 4.7 46.4 1.0 OG B:SER454 4.8 32.4 1.0 N B:LEU38 4.8 31.4 1.0 N B:ASP456 5.0 36.4 1.0 C B:HIS37 5.0 40.0 1.0

Cadmium binding site 8 out of 14 in the Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd601 b:78.2 occ:1.00 NE2 A:HIS217 2.5 65.8 1.0 CE1 A:HIS217 3.2 61.8 1.0 CD2 A:HIS217 3.5 49.2 1.0 CG A:PRO309 3.7 90.9 1.0 CB A:PRO309 3.8 85.2 1.0 ND1 A:HIS217 4.3 54.4 1.0 CG A:HIS217 4.5 43.7 1.0

Cadmium binding site 9 out of 14 in the Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd602 b:53.7 occ:1.00 NE2 A:HIS465 2.4 46.0 1.0 O A:HOH775 2.6 30.1 1.0 O A:HOH782 2.6 27.7 1.0 CE1 A:HIS465 3.2 45.6 1.0 CD2 A:HIS465 3.5 42.5 1.0 ND1 A:HIS465 4.4 40.1 1.0 CG A:HIS465 4.5 38.6 1.0 CB A:PRO478 4.7 40.7 1.0 NZ A:LYS476 4.9 60.7 1.0

Cadmium binding site 10 out of 14 in the Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Human Plexin-B1 (20-535) in the Unbound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd603 b:71.0 occ:1.00 NE2 A:HIS416 2.6 45.1 1.0 O A:HOH792 2.9 50.2 1.0 CD2 A:HIS416 3.5 43.6 1.0 CE1 A:HIS416 3.6 50.1 1.0 CG A:HIS416 4.7 46.2 1.0 ND1 A:HIS416 4.7 49.0 1.0 O A:ASP414 5.0 46.4 1.0

R.Cowan, M.Trokter, A.Oleksy, M.Fedorova, K.Sawmynaden, T.Worzfeld, S.Offermanns, D.Matthews, M.D.Carr, G.Hall. Nanobody Inhibitors of Plexin-B1 Identify Allostery in Plexin-Semaphorin Interactions and Signalling. J.Biol.Chem. 04740 2023.
ISSN: ESSN 1083-351X
PubMed: 37088134
DOI: 10.1016/J.JBC.2023.104740