Magnesium in PDB 3w9t: Pore-Forming Cel-III

The structure of Pore-Forming Cel-III, PDB code: 3w9t was solved by H.Unno, S.Goda, T.Hatakeyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.20 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	219.800, 228.650, 133.020, 90.00, 127.13, 90.00
R / Rfree (%)	23.9 / 27.3

The structure of Pore-Forming Cel-III also contains other interesting chemical elements:

Calcium

(Ca)

44 atoms

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Pore-Forming Cel-III (pdb code 3w9t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Pore-Forming Cel-III, PDB code: 3w9t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1010 b:59.5 occ:1.00 OD1 A:ASN177 2.3 73.0 1.0 O A:VAL219 2.3 63.3 1.0 O A:VAL178 2.6 62.4 1.0 O A:VAL266 2.6 58.9 1.0 OD1 A:ASP265 2.7 65.7 1.0 OD1 A:ASN218 2.7 69.7 1.0 ND2 A:ASN218 3.0 70.8 1.0 CG A:ASN218 3.0 68.0 1.0 CG A:ASN177 3.3 67.6 1.0 N A:VAL219 3.4 66.4 1.0 C A:VAL219 3.4 61.1 1.0 N A:VAL178 3.5 63.5 1.0 C A:VAL178 3.6 62.2 1.0 CG A:ASP265 3.7 66.3 1.0 ND2 A:ASN177 3.7 70.8 1.0 C A:VAL266 3.7 61.8 1.0 CA A:VAL219 3.9 60.4 1.0 N A:VAL266 3.9 65.2 1.0 OD2 A:ASP265 4.0 64.2 1.0 CA A:VAL178 4.1 59.9 1.0 CA A:VAL266 4.2 62.1 1.0 CB A:ASN218 4.3 66.8 1.0 C A:ASN218 4.3 69.2 1.0 CB A:VAL219 4.4 58.4 1.0 CB A:VAL178 4.5 59.8 1.0 CB A:VAL266 4.5 62.9 1.0 CA A:ASN218 4.5 70.3 1.0 CB A:ASN177 4.5 65.5 1.0 C A:ASN177 4.5 65.5 1.0 N A:GLY220 4.6 57.9 1.0 CA A:ASN177 4.6 66.7 1.0 N A:LEU179 4.8 62.3 1.0 N A:GLY267 4.8 64.8 1.0 CB A:ASP265 5.0 65.8 1.0 C A:ASP265 5.0 67.5 1.0 CA A:GLY220 5.0 59.2 1.0

Magnesium binding site 2 out of 14 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1011 b:72.9 occ:1.00 OD1 A:ASN72 2.0 86.4 1.0 O A:ILE33 2.5 88.5 1.0 O A:ILE131 2.7 85.5 1.0 O A:VAL73 2.9 78.5 1.0 ND2 A:ASN32 3.1 83.9 1.0 CG A:ASN72 3.2 81.5 1.0 OD1 A:ASP130 3.2 0.3 1.0 N A:ILE131 3.3 90.5 1.0 OD1 A:ASN32 3.4 83.9 1.0 N A:VAL73 3.5 76.9 1.0 CG A:ASP130 3.5 0.2 1.0 OD2 A:ASP130 3.5 0.8 1.0 CG A:ASN32 3.6 79.7 1.0 C A:ILE131 3.6 82.8 1.0 C A:ILE33 3.6 80.7 1.0 C A:VAL73 3.7 80.2 1.0 N A:ILE33 3.8 75.2 1.0 CA A:ILE131 3.9 82.8 1.0 ND2 A:ASN72 3.9 84.6 1.0 CA A:VAL73 4.1 79.8 1.0 CA A:ILE33 4.2 77.9 1.0 CB A:ILE131 4.2 82.5 1.0 C A:ASP130 4.3 98.0 1.0 CB A:ASN72 4.3 80.1 1.0 C A:ASN72 4.4 81.5 1.0 CA A:ASP130 4.4 96.8 1.0 CA A:ASN72 4.5 83.7 1.0 CB A:ILE33 4.5 75.9 1.0 CB A:VAL73 4.6 79.0 1.0 CB A:ASP130 4.6 0.2 1.0 N A:ALA34 4.8 79.2 1.0 C A:ASN32 4.8 74.2 1.0 N A:GLY132 4.9 83.2 1.0 N A:MET74 4.9 81.3 1.0 CB A:ASN32 4.9 76.9 1.0

Magnesium binding site 3 out of 14 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1011 b:86.8 occ:1.00 O C:VAL178 2.2 73.5 1.0 OD1 C:ASP265 2.3 80.8 1.0 OD1 C:ASN177 2.5 75.5 1.0 O C:VAL266 2.5 77.3 1.0 O C:VAL219 2.7 69.7 1.0 OD1 C:ASN218 2.9 75.7 1.0 CG C:ASN177 3.3 74.8 1.0 C C:VAL178 3.3 72.6 1.0 CG C:ASP265 3.4 80.1 1.0 CG C:ASN218 3.4 74.8 1.0 ND2 C:ASN218 3.4 73.0 1.0 N C:VAL266 3.5 75.7 1.0 C C:VAL266 3.5 77.7 1.0 N C:VAL178 3.5 74.2 1.0 ND2 C:ASN177 3.6 79.7 1.0 N C:VAL219 3.7 77.0 1.0 C C:VAL219 3.7 73.0 1.0 OD2 C:ASP265 3.8 84.1 1.0 CA C:VAL266 3.9 75.3 1.0 CA C:VAL178 3.9 71.5 1.0 CB C:VAL266 4.2 74.2 1.0 CA C:VAL219 4.2 73.0 1.0 CB C:VAL178 4.4 71.8 1.0 N C:LEU179 4.4 72.1 1.0 C C:ASN177 4.5 75.0 1.0 C C:ASP265 4.6 73.9 1.0 CB C:VAL219 4.6 71.4 1.0 CB C:ASN177 4.6 72.8 1.0 CB C:ASP265 4.6 74.8 1.0 CB C:ASN218 4.7 76.1 1.0 C C:ASN218 4.7 79.7 1.0 N C:GLY267 4.7 77.1 1.0 CA C:ASN177 4.8 75.5 1.0 CA C:LEU179 4.8 71.1 1.0 CA C:ASP265 4.8 73.5 1.0 CA C:ASN218 4.9 79.5 1.0 N C:GLY220 4.9 72.1 1.0

Magnesium binding site 4 out of 14 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1012 b:67.2 occ:1.00 OD1 C:ASN72 2.1 85.0 1.0 O C:ILE33 2.4 73.0 1.0 O C:ILE131 2.5 67.5 1.0 O C:VAL73 2.7 91.8 1.0 ND2 C:ASN32 2.7 87.1 1.0 OD1 C:ASN32 3.1 87.7 1.0 CG C:ASN32 3.2 84.9 1.0 CG C:ASN72 3.2 81.2 1.0 N C:ILE33 3.4 76.5 1.0 C C:ILE33 3.4 73.5 1.0 OD2 C:ASP130 3.4 93.0 1.0 OD1 C:ASP130 3.6 88.8 1.0 C C:ILE131 3.6 68.8 1.0 C C:VAL73 3.6 85.6 1.0 N C:VAL73 3.7 78.0 1.0 ND2 C:ASN72 3.7 79.4 1.0 CG C:ASP130 3.7 89.6 1.0 N C:ILE131 3.8 74.9 1.0 CA C:ILE33 3.8 73.5 1.0 CA C:VAL73 4.1 80.2 1.0 CA C:ILE131 4.2 68.5 1.0 CB C:ILE33 4.3 73.9 1.0 C C:ASN32 4.4 79.7 1.0 CB C:ASN32 4.5 82.0 1.0 CB C:ASN72 4.5 81.7 1.0 C C:ASN72 4.6 80.6 1.0 N C:ALA34 4.6 74.2 1.0 CA C:ASN32 4.6 81.0 1.0 CB C:ILE131 4.6 65.2 1.0 N C:MET74 4.7 85.5 1.0 C C:ASP130 4.7 79.2 1.0 CB C:VAL73 4.7 79.2 1.0 CA C:ASN72 4.8 83.0 1.0 N C:GLY132 4.8 69.5 1.0 CB C:ASP130 4.9 88.8 1.0 CA C:ASP130 5.0 86.1 1.0

Magnesium binding site 5 out of 14 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg511 b:74.1 occ:1.00 OD1 G:ASP265 2.1 86.3 1.0 O G:VAL178 2.4 67.4 1.0 OD1 G:ASN177 2.5 78.8 1.0 O G:VAL266 2.6 82.6 1.0 OD1 G:ASN218 2.7 88.0 1.0 O G:VAL219 2.9 78.7 1.0 CG G:ASP265 3.1 84.2 1.0 CG G:ASN218 3.2 81.7 1.0 CG G:ASN177 3.2 77.7 1.0 ND2 G:ASN218 3.3 80.2 1.0 N G:VAL266 3.4 78.9 1.0 ND2 G:ASN177 3.4 81.0 1.0 C G:VAL178 3.5 66.3 1.0 OD2 G:ASP265 3.5 85.6 1.0 C G:VAL266 3.5 78.7 1.0 N G:VAL178 3.7 71.9 1.0 N G:VAL219 3.8 81.0 1.0 CA G:VAL266 3.9 75.1 1.0 C G:VAL219 3.9 76.0 1.0 CA G:VAL178 4.1 67.9 1.0 CB G:VAL266 4.3 72.0 1.0 CA G:VAL219 4.3 76.3 1.0 CB G:ASP265 4.4 81.8 1.0 C G:ASP265 4.4 79.7 1.0 N G:LEU179 4.6 62.8 1.0 CB G:ASN218 4.6 80.8 1.0 CB G:VAL178 4.6 66.5 1.0 CB G:ASN177 4.6 75.2 1.0 CA G:ASP265 4.7 78.6 1.0 C G:ASN177 4.7 73.5 1.0 N G:GLY267 4.7 78.4 1.0 C G:ASN218 4.7 85.9 1.0 CB G:VAL219 4.7 74.9 1.0 CA G:ASN218 4.8 82.5 1.0 CA G:LEU179 4.9 63.5 1.0 CA G:ASN177 4.9 74.5 1.0

Magnesium binding site 6 out of 14 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg512 b:0.9 occ:1.00 O G:ILE131 2.1 0.9 1.0 OD1 G:ASN72 2.2 0.1 1.0 O G:ILE33 2.4 0.5 1.0 O G:VAL73 2.6 0.5 1.0 C G:ILE131 3.2 0.7 1.0 ND2 G:ASN32 3.2 0.6 1.0 CG G:ASN72 3.3 0.7 1.0 N G:VAL73 3.4 0.9 1.0 C G:ILE33 3.5 0.9 1.0 C G:VAL73 3.5 0.7 1.0 N G:ILE131 3.5 0.1 1.0 OD1 G:ASN32 3.6 0.3 1.0 N G:ILE33 3.6 0.0 1.0 CG G:ASN32 3.7 0.1 1.0 CA G:ILE131 3.7 0.3 1.0 OD2 G:ASP130 3.8 0.7 1.0 CA G:VAL73 3.8 99.9 1.0 CA G:ILE33 3.9 0.0 1.0 ND2 G:ASN72 4.0 0.2 1.0 OD1 G:ASP130 4.0 0.4 1.0 CG G:ASP130 4.1 0.7 1.0 CB G:ILE131 4.1 96.9 1.0 CB G:ILE33 4.2 0.2 1.0 CB G:VAL73 4.3 0.3 1.0 N G:GLY132 4.3 99.3 1.0 C G:ASN72 4.4 0.9 1.0 CB G:ASN72 4.5 0.5 1.0 CA G:ASN72 4.6 0.1 1.0 C G:ASP130 4.6 0.9 1.0 N G:MET74 4.6 0.2 1.0 N G:ALA34 4.6 0.8 1.0 C G:ASN32 4.7 1.0 1.0 CA G:GLY132 4.8 0.2 1.0 CG2 G:ILE33 4.8 0.1 1.0 CG2 G:ILE131 4.9 94.7 1.0 CB G:ASN32 4.9 0.3 1.0

Magnesium binding site 7 out of 14 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg511 b:84.6 occ:1.00 OD1 B:ASN72 2.3 82.4 1.0 O B:ILE131 2.3 74.9 1.0 O B:VAL73 2.3 74.9 1.0 O B:ILE33 2.4 73.6 1.0 ND2 B:ASN32 3.0 81.8 1.0 C B:VAL73 3.3 69.4 1.0 CG B:ASN72 3.3 77.9 1.0 N B:ILE33 3.3 78.8 1.0 C B:ILE131 3.4 71.1 1.0 N B:VAL73 3.4 69.4 1.0 C B:ILE33 3.4 74.9 1.0 OD1 B:ASN32 3.5 82.4 1.0 CG B:ASN32 3.5 79.1 1.0 OD2 B:ASP130 3.7 0.7 1.0 CA B:ILE33 3.7 75.0 1.0 CA B:VAL73 3.8 66.0 1.0 ND2 B:ASN72 3.9 77.9 1.0 N B:ILE131 3.9 78.2 1.0 OD1 B:ASP130 4.0 0.3 1.0 CB B:ILE33 4.0 73.5 1.0 CG B:ASP130 4.0 0.6 1.0 CA B:ILE131 4.1 73.1 1.0 CB B:VAL73 4.3 63.7 1.0 N B:GLY132 4.3 71.2 1.0 C B:ASN72 4.4 74.4 1.0 C B:ASN32 4.4 82.2 1.0 N B:MET74 4.4 69.1 1.0 CB B:ASN72 4.5 74.3 1.0 CB B:ILE131 4.6 71.1 1.0 CA B:GLY132 4.6 76.0 1.0 N B:ALA34 4.6 72.1 1.0 CB B:ASN32 4.7 78.8 1.0 CA B:ASN32 4.7 79.3 1.0 CA B:ASN72 4.7 72.5 1.0 CG2 B:ILE33 4.7 71.7 1.0 CA B:MET74 4.9 67.9 1.0 C B:ASP130 4.9 81.5 1.0 CG1 B:VAL73 5.0 60.1 1.0

Magnesium binding site 8 out of 14 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg512 b:70.3 occ:1.00 O B:VAL219 2.2 80.5 1.0 OD1 B:ASN177 2.5 80.3 1.0 O B:VAL266 2.5 81.2 1.0 O B:VAL178 2.6 76.0 1.0 OD1 B:ASN218 2.7 89.0 1.0 OD1 B:ASP265 2.8 86.7 1.0 CG B:ASN218 3.0 84.6 1.0 ND2 B:ASN218 3.1 84.7 1.0 N B:VAL219 3.2 86.1 1.0 C B:VAL219 3.3 83.8 1.0 CG B:ASN177 3.4 73.4 1.0 N B:VAL178 3.6 72.1 1.0 C B:VAL266 3.6 72.8 1.0 C B:VAL178 3.6 72.3 1.0 CA B:VAL219 3.7 84.1 1.0 CG B:ASP265 3.8 83.6 1.0 ND2 B:ASN177 3.9 72.1 1.0 N B:VAL266 3.9 68.2 1.0 CA B:VAL178 4.0 71.1 1.0 OD2 B:ASP265 4.1 87.9 1.0 CA B:VAL266 4.2 68.3 1.0 CB B:VAL219 4.2 84.2 1.0 C B:ASN218 4.2 86.5 1.0 CB B:ASN218 4.2 83.6 1.0 CB B:VAL178 4.4 71.7 1.0 CB B:VAL266 4.4 66.6 1.0 N B:GLY220 4.4 81.5 1.0 CA B:ASN218 4.5 84.6 1.0 C B:ASN177 4.6 74.5 1.0 CB B:ASN177 4.7 70.8 1.0 CA B:ASN177 4.7 72.7 1.0 N B:GLY267 4.7 72.7 1.0 N B:LEU179 4.8 69.8 1.0 CA B:GLY220 4.9 78.4 1.0

Magnesium binding site 9 out of 14 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg509 b:53.2 occ:1.00 OD1 F:ASN177 2.2 67.9 1.0 O F:VAL178 2.4 56.9 1.0 O F:VAL219 2.5 70.0 1.0 OD1 F:ASP265 2.6 72.1 1.0 O F:VAL266 2.8 59.8 1.0 OD1 F:ASN218 2.9 76.7 1.0 CG F:ASN177 3.1 65.2 1.0 ND2 F:ASN218 3.2 70.6 1.0 CG F:ASN218 3.3 73.3 1.0 N F:VAL178 3.4 60.2 1.0 C F:VAL178 3.4 57.0 1.0 ND2 F:ASN177 3.4 64.7 1.0 C F:VAL219 3.6 66.9 1.0 CG F:ASP265 3.6 70.7 1.0 N F:VAL219 3.6 69.0 1.0 C F:VAL266 3.8 61.9 1.0 N F:VAL266 3.8 64.3 1.0 CA F:VAL178 3.8 57.6 1.0 OD2 F:ASP265 4.0 70.1 1.0 CA F:VAL219 4.1 65.9 1.0 CA F:VAL266 4.2 61.6 1.0 CB F:VAL178 4.3 57.1 1.0 CB F:ASN177 4.3 65.5 1.0 C F:ASN177 4.3 62.3 1.0 CB F:VAL266 4.4 61.3 1.0 CA F:ASN177 4.5 66.1 1.0 CB F:ASN218 4.5 71.8 1.0 N F:LEU179 4.6 58.6 1.0 CB F:VAL219 4.6 64.0 1.0 C F:ASN218 4.6 70.8 1.0 N F:GLY220 4.7 64.3 1.0 CA F:ASN218 4.8 72.5 1.0 C F:ASP265 4.9 67.6 1.0 CB F:ASP265 4.9 68.1 1.0 N F:GLY267 4.9 64.3 1.0

Magnesium binding site 10 out of 14 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg510 b:68.4 occ:1.00 O F:ILE33 2.3 0.4 1.0 OD1 F:ASN72 2.4 81.0 1.0 ND2 F:ASN32 2.6 0.3 1.0 O F:VAL73 2.7 86.3 1.0 OD1 F:ASN32 2.9 92.4 1.0 CG F:ASN32 3.0 97.5 1.0 O F:ILE131 3.0 85.3 1.0 N F:ILE33 3.2 95.8 1.0 C F:ILE33 3.2 0.0 1.0 CG F:ASN72 3.5 80.9 1.0 OD1 F:ASP130 3.5 0.0 1.0 CA F:ILE33 3.6 97.8 1.0 N F:ILE131 3.6 0.6 1.0 OD2 F:ASP130 3.7 0.3 1.0 C F:VAL73 3.7 86.6 1.0 CG F:ASP130 3.8 0.0 1.0 N F:VAL73 3.9 91.5 1.0 ND2 F:ASN72 3.9 81.3 1.0 C F:ILE131 3.9 90.7 1.0 CB F:ILE33 4.1 96.2 1.0 C F:ASN32 4.1 96.6 1.0 CA F:ILE131 4.1 96.0 1.0 CB F:ASN32 4.2 96.8 1.0 CA F:VAL73 4.3 83.7 1.0 N F:ALA34 4.4 0.7 1.0 CA F:ASN32 4.4 97.8 1.0 CB F:ILE131 4.4 97.1 1.0 C F:ASP130 4.6 0.6 1.0 CA F:ASP130 4.7 0.3 1.0 CB F:ASN72 4.7 85.6 1.0 N F:MET74 4.8 90.0 1.0 C F:ASN72 4.8 95.0 1.0 CB F:ASP130 4.8 0.6 1.0 CB F:VAL73 4.9 79.1 1.0 CA F:ALA34 4.9 0.8 1.0 CG2 F:ILE33 4.9 93.2 1.0 CB F:ALA34 4.9 1.0 1.0

H.Unno, S.Goda, T.Hatakeyama. Hemolytic Lectin Cel-III Heptamer Reveals Its Transmembrane Pore-Formation Mechanism J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X