Magnesium in PDB 7qlr: Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1

The structure of Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1, PDB code: 7qlr was solved by R.Wallis, A.Dowah, M.R.J.Clokie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	102.64 / 2.46
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	114.99, 178.206, 227.621, 90, 90, 90
R / Rfree (%)	19.5 / 21.9

The binding sites of Magnesium atom in the Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1 (pdb code 7qlr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1, PDB code: 7qlr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg700 b:64.8 occ:1.00 O A:ASP540 2.4 63.4 1.0 OD1 A:ASP540 2.4 64.4 1.0 O A:GLY606 2.5 67.8 1.0 OE1 A:GLN602 2.7 70.5 1.0 OD1 A:ASP605 2.7 77.7 1.0 NE2 A:GLN602 3.1 53.8 1.0 CD A:GLN602 3.3 60.6 1.0 C A:ASP540 3.3 61.0 1.0 CG A:ASP605 3.4 66.5 1.0 N A:GLY606 3.4 66.7 1.0 C A:GLY606 3.5 60.2 1.0 CG A:ASP540 3.5 75.2 1.0 C A:ASP605 3.7 72.0 1.0 O A:HOH817 3.8 68.6 1.0 CA A:ASP605 3.8 62.5 1.0 OD2 A:ASP605 3.9 70.8 1.0 CA A:ASP540 4.0 58.6 1.0 MG A:MG701 4.0 63.7 1.0 CA A:GLY606 4.0 62.0 1.0 O A:HOH827 4.1 61.6 1.0 CB A:ASP605 4.2 65.3 1.0 OD1 A:ASP541 4.3 69.7 1.0 N A:ASP541 4.3 59.9 1.0 CB A:ASP540 4.3 58.2 1.0 OD2 A:ASP540 4.4 84.4 1.0 O A:ASP605 4.4 71.0 1.0 N A:TYR607 4.6 58.2 1.0 CA A:ASP541 4.6 52.8 1.0 CG A:GLN602 4.7 57.9 1.0 O A:GLY604 5.0 64.7 1.0 CA A:TYR607 5.0 50.5 1.0

Magnesium binding site 2 out of 8 in the Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:63.7 occ:1.00 OD1 A:ASP605 2.1 77.7 1.0 O A:HOH817 2.4 68.6 1.0 O A:HOH827 2.4 61.6 1.0 CG A:ASP605 3.1 66.5 1.0 OD2 A:ASP605 3.7 70.8 1.0 OD1 A:ASP540 3.8 64.4 1.0 MG A:MG700 4.0 64.8 1.0 CB A:ASP605 4.1 65.3 1.0 OD1 A:ASP541 4.3 69.7 1.0 CG A:ASP540 4.7 75.2 1.0 CA A:ASP605 4.7 62.5 1.0 OD2 A:ASP540 5.0 84.4 1.0

Magnesium binding site 3 out of 8 in the Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg700 b:76.0 occ:1.00 O B:HOH818 2.0 71.8 1.0 OD1 B:ASP605 2.5 77.0 1.0 OD1 B:ASP540 2.8 101.0 1.0 O B:HOH806 3.3 63.7 1.0 OD1 B:ASP541 3.5 85.1 1.0 CG B:ASP605 3.5 66.9 1.0 CG B:ASP540 3.6 89.3 1.0 OD2 B:ASP605 3.9 58.1 1.0 OD2 B:ASP540 3.9 88.5 1.0 MG B:MG701 3.9 68.4 1.0 CG B:ASP541 4.5 86.0 1.0 CB B:ASP540 4.7 68.2 1.0 CB B:ASP605 4.9 65.4 1.0 O B:ASP540 4.9 59.6 1.0 OD2 B:ASP541 4.9 75.8 1.0

Magnesium binding site 4 out of 8 in the Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:68.4 occ:1.00 OE1 B:GLN602 3.0 71.8 1.0 OD1 B:ASP605 3.1 77.0 1.0 O B:HOH806 3.2 63.7 1.0 CA B:ASP605 3.7 72.7 1.0 O B:GLY604 3.8 68.2 1.0 MG B:MG700 3.9 76.0 1.0 CD B:GLN602 4.0 70.0 1.0 CG B:ASP605 4.1 66.9 1.0 CB B:ASP605 4.2 65.4 1.0 N B:ASP605 4.2 75.8 1.0 C B:GLY604 4.2 64.1 1.0 OD1 B:ASP541 4.4 85.1 1.0 NE2 B:GLN602 4.7 65.2 1.0 N B:GLY606 4.8 59.7 1.0 C B:ASP605 4.8 74.5 1.0

Magnesium binding site 5 out of 8 in the Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg700 b:54.2 occ:1.00 OD1 C:ASP540 2.3 75.5 1.0 OD1 C:ASP605 2.6 73.5 1.0 CG C:ASP540 3.0 73.3 1.0 OD2 C:ASP540 3.3 72.7 1.0 CG C:ASP605 3.5 75.3 1.0 MG C:MG701 3.5 62.5 1.0 OD1 C:ASP541 3.6 78.0 1.0 OD2 C:ASP605 3.7 73.8 1.0 CB C:ASP540 4.2 64.3 1.0 CG C:ASP541 4.6 81.4 1.0 O C:ASP540 4.7 71.8 1.0 C C:ASP540 4.8 67.3 1.0 CB C:ASP605 4.9 64.2 1.0

Magnesium binding site 6 out of 8 in the Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:62.5 occ:1.00 OD1 C:ASP540 2.4 75.5 1.0 O C:GLY606 2.5 66.5 1.0 OD1 C:ASP605 2.6 73.5 1.0 O C:ASP540 2.6 71.8 1.0 OE1 C:GLN602 2.8 65.0 1.0 CG C:ASP605 3.1 75.3 1.0 N C:GLY606 3.3 68.9 1.0 NE2 C:GLN602 3.4 65.0 1.0 CD C:GLN602 3.4 59.9 1.0 C C:ASP605 3.4 74.1 1.0 C C:GLY606 3.4 62.9 1.0 MG C:MG700 3.5 54.2 1.0 CG C:ASP540 3.5 73.3 1.0 CA C:ASP605 3.5 65.8 1.0 C C:ASP540 3.5 67.3 1.0 OD2 C:ASP605 3.6 73.8 1.0 CB C:ASP605 3.9 64.2 1.0 CA C:GLY606 3.9 62.5 1.0 CA C:ASP540 4.1 69.4 1.0 O C:ASP605 4.2 73.8 1.0 OD2 C:ASP540 4.3 72.7 1.0 CB C:ASP540 4.4 64.3 1.0 OD1 C:ASP541 4.4 78.0 1.0 N C:ASP541 4.5 62.7 1.0 N C:TYR607 4.6 56.8 1.0 O C:GLY604 4.8 72.8 1.0 CG C:GLN602 4.8 63.6 1.0 N C:ASP605 4.9 66.2 1.0 CA C:ASP541 4.9 58.6 1.0 CB C:TYR560 5.0 67.2 1.0

Magnesium binding site 7 out of 8 in the Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg700 b:56.9 occ:1.00 OD1 D:ASP605 2.4 77.4 1.0 OD1 D:ASP540 2.6 73.6 1.0 CG D:ASP605 3.4 67.9 1.0 MG D:MG701 3.5 63.1 1.0 OD1 D:ASP541 3.5 76.5 1.0 CG D:ASP540 3.5 73.5 1.0 OD2 D:ASP605 3.8 75.7 1.0 OD2 D:ASP540 3.8 69.8 1.0 CG D:ASP541 4.6 77.7 1.0 CB D:ASP540 4.6 69.8 1.0 O D:ASP540 4.7 67.9 1.0 CB D:ASP605 4.7 58.0 1.0 C D:ASP540 4.9 64.3 1.0

Magnesium binding site 8 out of 8 in the Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Receptor-Binding Protein of Clostridium Difficile Phage Cdhs-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:63.1 occ:1.00 OD1 D:ASP540 2.3 73.6 1.0 O D:GLY606 2.4 68.7 1.0 OD1 D:ASP605 2.5 77.4 1.0 O D:ASP540 2.7 67.9 1.0 OE1 D:GLN602 2.9 57.3 1.0 CG D:ASP605 3.1 67.9 1.0 N D:GLY606 3.3 72.0 1.0 C D:GLY606 3.4 62.5 1.0 NE2 D:GLN602 3.4 72.4 1.0 C D:ASP605 3.4 70.6 1.0 CG D:ASP540 3.4 73.5 1.0 MG D:MG700 3.5 56.9 1.0 CD D:GLN602 3.5 58.3 1.0 CA D:ASP605 3.5 67.5 1.0 C D:ASP540 3.6 64.3 1.0 OD2 D:ASP605 3.6 75.7 1.0 CB D:ASP605 3.9 58.0 1.0 CA D:GLY606 3.9 56.2 1.0 CA D:ASP540 4.1 60.5 1.0 O D:ASP605 4.1 70.1 1.0 OD2 D:ASP540 4.2 69.8 1.0 CB D:ASP540 4.3 69.8 1.0 N D:TYR607 4.6 49.3 1.0 OD1 D:ASP541 4.6 76.5 1.0 N D:ASP541 4.6 63.4 1.0 CB D:TYR560 4.8 58.4 1.0 O D:GLY604 4.9 72.4 1.0 N D:ASP605 4.9 68.7 1.0 CG D:GLN602 4.9 69.2 1.0 CA D:TYR607 5.0 52.3 1.0

A.Dowah, R.Wallis, M.R.J.Clokie. The Structurome of A Clostridium Difficile Phage and the Remarkable Accurate Prediction of Its Novel Phage Receptor-Binding Protein To Be Published.