Cadmium in PDB 7daa: Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment

The structure of Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment, PDB code: 7daa was solved by T.Sakuragi, R.Kanai, H.Narita, E.Onishi, T.Miyazaki, T.Baba, A.Nakagawa, C.Toyoshima, S.Nagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	123.68 / 2.51
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	117.345, 247.352, 52.251, 90, 90, 90
R / Rfree (%)	22.8 / 28.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment (pdb code 7daa). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 16 binding sites of Cadmium where determined in the Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment, PDB code: 7daa:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 16 in the Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment


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 Basigin Complexed with Anti-Basigin Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:72.5 occ:1.00 OD2 A:ASP194 2.7 56.1 1.0 OD1 A:ASP194 2.7 50.3 1.0 CG A:ASP194 3.1 58.8 1.0 O A:GLN195 4.1 50.1 1.0 O A:VAL107 4.4 65.0 1.0 CB A:ASP194 4.6 54.2 1.0 N A:VAL107 4.9 49.8 1.0 CG A:ARG106 4.9 86.6 1.0 N A:GLN195 5.0 39.6 1.0

Cadmium binding site 2 out of 16 in the Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment


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 Basigin Complexed with Anti-Basigin Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:170.7 occ:1.00 OE2 A:GLU129 3.8 103.9 1.0 OH L:TYR50 4.4 42.5 1.0 NZ A:LYS127 4.5 59.3 1.0 CD A:GLU129 4.9 104.5 1.0 CG L:ASP54 4.9 61.1 1.0 OD2 L:ASP54 5.0 79.0 1.0 CE A:LYS127 5.0 55.7 1.0

Cadmium binding site 3 out of 16 in the Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment


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 Basigin Complexed with Anti-Basigin Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd301 b:139.4 occ:1.00 OD1 L:ASP54 2.8 62.2 1.0 OD2 L:ASP54 2.9 79.0 1.0 CG L:ASP54 3.2 61.1 1.0 NZ A:LYS127 3.7 59.3 1.0 OG L:SER53 4.6 47.5 1.0 CB L:ASP54 4.7 36.0 1.0 CE A:LYS127 4.8 55.7 1.0

Cadmium binding site 4 out of 16 in the Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment


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 Basigin Complexed with Anti-Basigin Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd302 b:41.6 occ:1.00 OD2 L:ASP78 2.7 29.7 1.0 OD1 L:ASP78 2.7 64.1 1.0 CG L:ASP78 3.1 41.8 1.0 CB L:ASP78 4.6 31.5 1.0 CA L:GLY17 4.8 26.6 1.0

Cadmium binding site 5 out of 16 in the Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment


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 Basigin Complexed with Anti-Basigin Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd303 b:98.2 occ:1.00 OE2 L:GLU80 2.8 63.5 1.0 OE1 L:GLU80 3.0 52.2 1.0 CD L:GLU80 3.3 52.9 1.0 CG L:GLU80 4.8 51.7 1.0 NE L:ARG62 4.8 30.1 1.0 NH2 L:ARG62 4.9 23.5 1.0

Cadmium binding site 6 out of 16 in the Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment


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 Basigin Complexed with Anti-Basigin Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd304 b:62.4 occ:1.00 OE2 L:GLU107 2.6 41.0 1.0 OE1 L:GLU169 2.9 44.3 1.0 OE2 L:GLU169 2.9 41.2 1.0 OE1 L:GLU107 2.9 36.0 1.0 CD L:GLU107 3.0 43.9 1.0 CD L:GLU169 3.2 32.2 1.0 CG L:GLU107 4.5 48.8 1.0 CG L:GLU169 4.8 19.2 1.0

Cadmium binding site 7 out of 16 in the Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment


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 Basigin Complexed with Anti-Basigin Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd305 b:148.5 occ:1.00 OD2 L:ASP171 2.8 66.5 1.0 CE L:LYS173 3.2 78.2 1.0 CG L:ASP171 3.7 54.7 1.0 OD1 L:ASP171 3.7 72.1 1.0 CD L:LYS173 3.9 89.9 1.0 CD L:CD306 4.0 81.2 1.0 CG L:LYS173 4.0 71.8 1.0 NZ L:LYS173 4.3 64.5 1.0 N H:GLY161 4.7 35.1 1.0 NE2 H:HIS163 4.8 45.1 1.0

Cadmium binding site 8 out of 16 in the Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment


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 Basigin Complexed with Anti-Basigin Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd306 b:81.2 occ:1.00 OD1 L:ASN142 2.9 47.6 1.0 CE1 H:HIS163 2.9 34.9 1.0 NE2 H:HIS163 3.0 45.1 1.0 ND2 L:ASN142 3.2 39.4 1.0 CG L:ASN142 3.3 36.8 1.0 OD2 L:ASP171 3.7 66.5 1.0 OD2 L:ASP174 3.9 32.3 1.0 CD L:CD305 4.0 148.5 1.0 ND1 H:HIS163 4.2 37.9 1.0 CD2 H:HIS163 4.4 32.6 1.0 NZ L:LYS173 4.5 64.5 1.0 CA H:GLY161 4.7 29.1 1.0 CE L:LYS173 4.7 78.2 1.0 CB L:ASN142 4.8 21.4 1.0 OD1 L:ASN141 4.8 36.4 1.0 CG L:ASP174 4.9 34.4 1.0 CG L:ASP171 4.9 54.7 1.0 CG H:HIS163 4.9 35.8 1.0 OG1 L:THR176 5.0 33.8 1.0

Cadmium binding site 9 out of 16 in the Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment


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 Basigin Complexed with Anti-Basigin Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd307 b:152.8 occ:1.00 OE2 L:GLU165 3.1 49.7 1.0 OE1 L:GLU165 3.3 54.2 1.0 O L:ALA148 3.4 47.8 1.0 CD L:GLU165 3.5 48.9 1.0 N L:VAL150 4.0 34.2 1.0 CA L:LYS149 4.0 31.5 1.0 C L:ALA148 4.4 29.2 1.0 C L:LYS149 4.6 35.1 1.0 N L:LYS149 4.7 29.9 1.0 CB L:LYS149 4.8 31.5 1.0 CG L:LYS149 4.9 51.7 1.0 O L:VAL150 4.9 39.5 1.0 CG L:GLU165 5.0 32.4 1.0

Cadmium binding site 10 out of 16 in the Crystal Structure of Basigin Complexed with Anti-Basigin Fab Fragment


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 Basigin Complexed with Anti-Basigin Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd308 b:73.2 occ:1.00 OE1 L:GLU199 2.7 56.9 1.0 OE2 L:GLU199 2.8 52.9 1.0 CD L:GLU199 3.1 52.3 1.0 NZ L:LYS153 4.3 46.8 1.0 CE L:LYS153 4.3 50.5 1.0 CG L:GLU199 4.6 42.3 1.0

T.Sakuragi, R.Kanai, A.Tsutsumi, H.Narita, E.Onishi, K.Nishino, T.Miyazaki, T.Baba, H.Kosako, A.Nakagawa, M.Kikkawa, C.Toyoshima, S.Nagata. The Tertiary Structure of the Human XKR8-Basigin Complex That Scrambles Phospholipids at Plasma Membranes. Nat.Struct.Mol.Biol. V. 28 825 2021.
ISSN: ESSN 1545-9985
PubMed: 34625749
DOI: 10.1038/S41594-021-00665-8