Cadmium in PDB 6r5w: Crystal Structure of the Receptor Binding Protein (GP15) of Listeria Phage Psa

The structure of Crystal Structure of the Receptor Binding Protein (GP15) of Listeria Phage Psa, PDB code: 6r5w was solved by M.Dunne, P.Ernst, A.Pluckthun, M.J.Loessner, S.Kilcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.09 / 1.70
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.700, 134.700, 79.360, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 21.1

The binding sites of Cadmium atom in the Crystal Structure of the Receptor Binding Protein (GP15) of Listeria Phage Psa (pdb code 6r5w). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of the Receptor Binding Protein (GP15) of Listeria Phage Psa, PDB code: 6r5w:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in the Crystal Structure of the Receptor Binding Protein (GP15) of Listeria Phage Psa


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 the Receptor Binding Protein (GP15) of Listeria Phage Psa within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:34.4 occ:1.00 OE1 A:GLN336 2.3 30.3 1.0 OE1 C:GLN336 2.3 33.0 1.0 O A:HOH561 2.3 36.2 1.0 OE1 B:GLN336 2.4 31.3 1.0 O B:HOH571 2.4 34.0 1.0 O C:HOH507 2.5 36.4 1.0 HB2 B:GLN336 3.2 33.5 1.0 HB2 A:GLN336 3.3 33.2 1.0 HB2 C:GLN336 3.3 29.6 1.0 CD B:GLN336 3.4 32.0 1.0 CD A:GLN336 3.4 33.3 1.0 CD C:GLN336 3.4 30.9 1.0 HG3 B:GLN336 3.8 38.4 1.0 CB B:GLN336 3.9 27.9 1.0 CG B:GLN336 3.9 31.9 1.0 CB A:GLN336 3.9 27.6 1.0 HG3 A:GLN336 4.0 36.2 1.0 HG3 C:GLN336 4.0 33.2 1.0 CB C:GLN336 4.0 24.7 1.0 CG A:GLN336 4.0 30.2 1.0 CG C:GLN336 4.0 27.6 1.0 HB3 B:GLN336 4.0 33.5 1.0 HB3 A:GLN336 4.1 33.2 1.0 O C:ALA333 4.2 33.8 1.0 HB3 C:GLN336 4.2 29.6 1.0 O A:ALA333 4.2 36.5 1.0 O B:ALA333 4.4 36.6 1.0 O C:HOH647 4.4 31.7 1.0 NE2 A:GLN336 4.4 31.4 1.0 NE2 B:GLN336 4.5 33.0 1.0 NE2 C:GLN336 4.5 30.6 1.0 HG C:SER325 4.5 35.0 0.5 HE22 A:GLN336 4.5 37.7 1.0 HE22 C:GLN336 4.6 36.8 1.0 HE22 B:GLN336 4.6 39.6 1.0 HA A:SER334 4.7 41.5 1.0 HG B:SER325 4.7 38.0 0.5 HA C:SER334 4.8 41.0 1.0 HG2 B:GLN336 4.8 38.4 1.0 HA B:SER334 4.8 40.2 1.0 HG2 A:GLN336 4.9 36.2 1.0 HG2 C:GLN336 4.9 33.2 1.0

Cadmium binding site 2 out of 9 in the Crystal Structure of the Receptor Binding Protein (GP15) of Listeria Phage Psa


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 the Receptor Binding Protein (GP15) of Listeria Phage Psa within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:38.6 occ:1.00 NE2 B:HIS221 2.4 40.4 1.0 NE2 A:HIS221 2.4 32.0 1.0 NE2 C:HIS214 2.5 36.5 1.0 NE2 B:HIS214 2.5 40.1 1.0 NE2 A:HIS214 2.5 50.0 1.0 NE2 C:HIS221 2.5 43.9 1.0 CD2 C:HIS214 3.2 44.0 1.0 HD2 C:HIS214 3.2 52.8 1.0 CD2 C:HIS221 3.3 41.4 1.0 CD2 B:HIS221 3.3 36.4 1.0 CD2 A:HIS221 3.4 39.0 1.0 HD2 C:HIS221 3.4 49.7 1.0 CE1 B:HIS221 3.4 37.2 1.0 CD2 B:HIS214 3.4 48.4 1.0 CE1 A:HIS221 3.4 43.6 1.0 CE1 B:HIS214 3.4 46.3 1.0 CD2 A:HIS214 3.5 47.5 1.0 CE1 A:HIS214 3.5 46.1 1.0 HD2 A:HIS221 3.5 46.8 1.0 HD2 B:HIS221 3.5 43.8 1.0 HD2 B:HIS214 3.5 58.1 1.0 HE1 B:HIS221 3.5 44.7 1.0 CE1 C:HIS214 3.5 43.7 1.0 HE1 A:HIS221 3.6 52.4 1.0 HD2 A:HIS214 3.6 57.0 1.0 CE1 C:HIS221 3.6 44.4 1.0 HE1 B:HIS214 3.6 55.6 1.0 HE1 A:HIS214 3.6 55.3 1.0 HE1 C:HIS221 3.8 53.3 1.0 HE1 C:HIS214 3.8 52.5 1.0 CG C:HIS214 4.4 42.4 1.0 ND1 B:HIS221 4.5 39.2 1.0 CG B:HIS221 4.5 42.0 1.0 ND1 A:HIS221 4.5 40.0 1.0 ND1 B:HIS214 4.5 49.0 1.0 CG A:HIS221 4.5 35.0 1.0 CG B:HIS214 4.5 50.3 1.0 ND1 C:HIS214 4.6 47.5 1.0 CG C:HIS221 4.6 45.8 1.0 ND1 A:HIS214 4.6 49.7 1.0 CG A:HIS214 4.6 50.0 1.0 ND1 C:HIS221 4.6 47.8 1.0

Cadmium binding site 3 out of 9 in the Crystal Structure of the Receptor Binding Protein (GP15) of Listeria Phage Psa


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 the Receptor Binding Protein (GP15) of Listeria Phage Psa within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:36.1 occ:1.00 OD2 A:ASP317 2.4 25.6 1.0 O A:HOH641 2.4 30.4 1.0 OD1 A:ASP317 2.5 31.3 1.0 O A:HOH632 2.5 33.1 1.0 O C:HOH608 2.6 30.5 1.0 O A:HOH629 2.7 26.4 1.0 CG A:ASP317 2.7 28.6 1.0 HH22 A:ARG287 3.6 39.3 1.0 HH21 C:ARG280 3.7 38.2 1.0 HH12 A:ARG287 3.8 38.4 1.0 HG2 A:LYS369 4.1 41.4 1.0 HE3 A:LYS369 4.2 57.8 1.0 O C:HOH503 4.2 40.5 1.0 CB A:ASP317 4.2 27.8 1.0 HZ2 A:LYS369 4.3 65.5 1.0 NH2 A:ARG287 4.4 32.7 1.0 NH2 C:ARG280 4.4 31.8 1.0 HE C:ARG280 4.5 34.9 1.0 HB2 A:ASP317 4.5 33.3 1.0 NH1 A:ARG287 4.6 32.0 1.0 HA A:LYS369 4.7 35.8 1.0 HB3 A:ASP317 4.7 33.3 1.0 HA A:ASP317 4.7 34.1 1.0 HZ1 A:LYS369 4.8 65.5 1.0 HH22 C:ARG280 4.9 38.2 1.0 NZ A:LYS369 4.9 54.5 1.0 H A:GLU370 4.9 36.4 1.0 CZ A:ARG287 5.0 34.9 1.0 HH21 A:ARG287 5.0 39.3 1.0 CE A:LYS369 5.0 48.2 1.0 CG A:LYS369 5.0 34.5 1.0

Cadmium binding site 4 out of 9 in the Crystal Structure of the Receptor Binding Protein (GP15) of Listeria Phage Psa


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 the Receptor Binding Protein (GP15) of Listeria Phage Psa within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd405 b:32.2 occ:1.00 OD2 A:ASP226 2.3 28.9 1.0 O A:HOH643 2.4 27.6 1.0 O C:HOH617 2.4 17.1 1.0 O C:HOH613 2.5 27.1 1.0 OD1 A:ASP226 2.6 33.2 1.0 CG A:ASP226 2.7 31.7 1.0 HG23 A:THR223 3.4 45.3 1.0 HD2 C:LYS227 3.7 51.2 1.0 H A:THR223 4.0 37.8 1.0 HZ2 C:LYS227 4.0 43.7 1.0 CB A:ASP226 4.2 28.8 1.0 HA A:VAL222 4.2 37.6 1.0 O A:HOH530 4.3 40.2 1.0 CG2 A:THR223 4.3 37.7 1.0 OG1 A:THR223 4.4 32.8 1.0 HB3 A:ASP226 4.5 34.6 1.0 HZ2 A:TRP230 4.5 35.4 1.0 HB2 A:ASP226 4.5 34.6 1.0 HG21 A:THR223 4.5 45.3 1.0 HD21 C:ASN231 4.6 36.9 1.0 CD C:LYS227 4.6 42.7 1.0 HH2 A:TRP230 4.6 38.9 1.0 N A:THR223 4.6 31.5 1.0 HD3 C:LYS227 4.7 51.2 1.0 O C:HOH549 4.8 30.2 1.0 NZ C:LYS227 4.9 36.4 1.0 HG1 A:THR223 4.9 39.3 1.0 CB A:THR223 4.9 34.3 1.0 HG22 A:THR223 5.0 45.3 1.0 CZ2 A:TRP230 5.0 29.4 1.0

Cadmium binding site 5 out of 9 in the Crystal Structure of the Receptor Binding Protein (GP15) of Listeria Phage Psa


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 the Receptor Binding Protein (GP15) of Listeria Phage Psa within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd406 b:82.4 occ:0.95 OE2 A:GLU370 2.5 67.6 1.0 CD A:GLU370 2.5 63.0 1.0 OE1 A:GLU370 2.6 65.5 1.0 O C:HOH602 2.8 29.9 1.0 HB2 C:SER259 3.3 39.0 0.4 HG2 A:GLU370 3.4 62.8 1.0 HB3 C:SER259 3.4 39.0 0.6 CG A:GLU370 3.5 52.3 1.0 HG3 A:GLU370 3.7 62.8 1.0 H A:ASN286 3.7 36.3 1.0 HE A:ARG287 3.9 36.1 1.0 HB2 A:ASN286 3.9 45.3 1.0 H C:VAL260 4.0 33.6 1.0 HG3 A:ARG287 4.2 33.5 1.0 CB C:SER259 4.2 32.5 0.4 CB C:SER259 4.3 32.5 0.6 O C:VAL260 4.3 32.0 1.0 OG C:SER259 4.3 31.2 0.6 HD22 A:ASN286 4.4 50.7 1.0 HB3 C:SER259 4.6 39.0 0.4 N C:VAL260 4.6 28.0 1.0 HA3 A:GLY285 4.6 46.0 1.0 N A:ASN286 4.6 30.2 1.0 NE A:ARG287 4.6 30.1 1.0 HB C:VAL260 4.7 35.2 1.0 CB A:GLU370 4.7 43.2 1.0 HA C:SER259 4.7 37.2 0.6 HA C:SER259 4.7 37.3 0.4 HB2 A:GLU370 4.8 51.9 1.0 CB A:ASN286 4.8 37.7 1.0 HA A:GLU370 4.9 37.6 1.0 OG C:SER259 4.9 33.2 0.4 HB2 C:SER259 5.0 39.0 0.6 HD2 A:ARG287 5.0 31.1 1.0 HH21 A:ARG287 5.0 39.3 1.0 CA C:SER259 5.0 31.0 0.4 CA C:SER259 5.0 31.0 0.6

Cadmium binding site 6 out of 9 in the Crystal Structure of the Receptor Binding Protein (GP15) of Listeria Phage Psa


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 the Receptor Binding Protein (GP15) of Listeria Phage Psa within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd403 b:50.3 occ:1.00 OD2 B:ASP317 2.5 36.4 1.0 O B:HOH507 2.5 49.3 1.0 OD1 B:ASP317 2.8 39.5 1.0 O B:HOH624 2.8 38.6 1.0 CG B:ASP317 2.9 33.3 1.0 O A:HOH619 3.3 45.5 1.0 HH22 B:ARG287 3.4 63.5 1.0 HH21 A:ARG280 3.6 43.0 1.0 HH12 B:ARG287 3.7 54.8 1.0 HE A:ARG280 4.2 36.8 1.0 NH2 B:ARG287 4.2 52.9 1.0 NH2 A:ARG280 4.4 35.8 1.0 CB B:ASP317 4.4 30.3 1.0 NH1 B:ARG287 4.5 45.6 1.0 HB2 B:ASP317 4.7 36.4 1.0 HH21 B:ARG287 4.8 63.5 1.0 HA B:LYS369 4.8 45.0 1.0 CZ B:ARG287 4.8 49.5 1.0 HH22 A:ARG280 4.9 43.0 1.0 HB3 B:ASP317 4.9 36.4 1.0 NE A:ARG280 4.9 30.6 1.0 H B:GLU370 5.0 60.9 1.0

Cadmium binding site 7 out of 9 in the Crystal Structure of the Receptor Binding Protein (GP15) of Listeria Phage Psa


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 the Receptor Binding Protein (GP15) of Listeria Phage Psa within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd402 b:39.3 occ:1.00 O C:HOH621 2.4 43.1 1.0 OD1 C:ASP317 2.5 32.0 1.0 O B:HOH629 2.5 35.9 1.0 O C:HOH626 2.5 37.1 1.0 OD2 C:ASP317 2.5 30.9 1.0 O C:HOH612 2.6 27.4 1.0 CG C:ASP317 2.8 31.7 1.0 HH22 C:ARG287 3.6 43.8 1.0 HH21 B:ARG280 3.7 41.0 1.0 HH12 C:ARG287 3.9 40.3 1.0 O B:HOH534 4.1 40.1 1.0 HZ2 C:LYS369 4.2 72.3 1.0 HG2 C:LYS369 4.2 50.1 1.0 HE3 C:LYS369 4.3 69.7 1.0 CB C:ASP317 4.3 28.8 1.0 O C:HOH624 4.3 54.7 1.0 O B:HOH671 4.4 55.2 1.0 NH2 C:ARG287 4.4 36.4 1.0 HA C:LYS369 4.5 37.8 1.0 NH2 B:ARG280 4.5 34.1 1.0 HZ1 C:LYS369 4.6 72.3 1.0 HB2 C:ASP317 4.6 34.6 1.0 NH1 C:ARG287 4.6 33.5 1.0 H C:GLU370 4.6 43.2 1.0 NZ C:LYS369 4.7 60.2 1.0 HE B:ARG280 4.7 35.4 1.0 HA C:ASP317 4.7 34.5 1.0 HB3 C:ASP317 4.8 34.6 1.0 HH22 B:ARG280 4.8 41.0 1.0 HG3 C:GLU370 5.0 70.7 1.0 HB3 C:LYS369 5.0 45.5 1.0 CE C:LYS369 5.0 58.1 1.0 HH21 C:ARG287 5.0 43.8 1.0 CZ C:ARG287 5.0 35.5 1.0

Cadmium binding site 8 out of 9 in the Crystal Structure of the Receptor Binding Protein (GP15) of Listeria Phage Psa


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 the Receptor Binding Protein (GP15) of Listeria Phage Psa within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd403 b:51.6 occ:0.33 OD1 C:ASP226 2.4 38.4 1.0 O B:HOH565 2.4 44.6 1.0 O B:HOH609 2.5 41.2 1.0 O C:HOH527 2.6 54.2 0.9 OD2 C:ASP226 2.7 40.3 1.0 CG C:ASP226 2.9 44.5 1.0 HZ2 B:LYS227 3.8 47.6 1.0 HG23 C:THR223 3.9 47.1 1.0 HD2 B:LYS227 3.9 53.1 1.0 CB C:ASP226 4.3 35.9 1.0 HD21 B:ASN231 4.5 49.0 1.0 OG1 C:THR223 4.5 37.4 1.0 O B:HOH531 4.6 41.1 1.0 HG1 C:THR223 4.6 44.9 1.0 HG21 C:THR223 4.6 47.1 1.0 H C:THR223 4.6 42.9 1.0 CG2 C:THR223 4.6 39.3 1.0 NZ B:LYS227 4.6 39.6 1.0 HB3 C:ASP226 4.7 43.1 1.0 O B:HOH658 4.7 61.6 1.0 HB2 C:ASP226 4.8 43.1 1.0 CD B:LYS227 4.8 44.2 1.0 HZ2 C:TRP230 4.8 45.3 1.0 HA C:VAL222 4.9 44.5 1.0 HA C:ASP226 4.9 41.7 1.0 HZ3 B:LYS227 5.0 47.6 1.0

Cadmium binding site 9 out of 9 in the Crystal Structure of the Receptor Binding Protein (GP15) of Listeria Phage Psa


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 the Receptor Binding Protein (GP15) of Listeria Phage Psa within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd404 b:56.5 occ:0.71 O A:HOH523 2.4 52.8 1.0 O C:HOH583 2.6 47.3 1.0 O A:HOH636 2.6 34.3 1.0 O C:HOH566 2.6 55.6 1.0 OE2 C:GLU255 2.7 65.5 1.0 OE1 C:GLU255 2.8 73.5 1.0 CD C:GLU255 2.9 64.6 1.0 O C:HOH531 3.0 52.3 1.0 HZ1 A:LYS283 4.0 70.2 1.0 HG2 C:GLU255 4.1 62.3 1.0 CG C:GLU255 4.2 51.9 1.0 HD21 A:ASN286 4.4 50.7 1.0 OD1 A:ASN286 4.7 39.3 1.0 HB3 C:GLU255 4.7 44.6 1.0 OXT A:THR373 4.7 59.4 1.0 HG3 C:GLU255 4.8 62.3 1.0 NZ A:LYS283 4.8 58.5 1.0 HZ2 A:LYS283 5.0 70.2 1.0

M.Dunne, B.Rupf, M.Tala, X.Qabrati, P.Ernst, Y.Shen, E.Sumrall, L.Heeb, A.Pluckthun, M.J.Loessner, S.Kilcher. Reprogramming Bacteriophage Host Range Through Structure-Guided Design of Chimeric Receptor Binding Proteins. Cell Rep V. 29 1336 2019.
ISSN: ESSN 2211-1247
PubMed: 31665644
DOI: 10.1016/J.CELREP.2019.09.062