Calcium 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:

Magnesium

(Mg)

14 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 44;

Binding sites:

The binding sites of Calcium atom in the Pore-Forming Cel-III (pdb code 3w9t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 44 binding sites of Calcium where determined in the Pore-Forming Cel-III, PDB code: 3w9t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 44 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:70.0 occ:1.00 O13 A:W9T1001 2.2 81.7 1.0 OD1 A:ASP23 2.3 68.9 1.0 O A:GLY26 2.4 69.9 1.0 OD2 A:ASP43 2.5 74.5 1.0 O A:ILE24 2.6 68.9 1.0 O14 A:W9T1001 3.0 79.9 1.0 CG A:ASP23 3.3 69.3 1.0 CG A:ASP43 3.3 77.0 1.0 OD1 A:ASP43 3.4 84.9 1.0 C13 A:W9T1001 3.4 81.6 1.0 OD2 A:ASP23 3.6 71.1 1.0 C A:GLY26 3.7 66.9 1.0 C14 A:W9T1001 3.8 82.9 1.0 C A:ILE24 3.8 68.5 1.0 C12 A:W9T1001 3.9 82.2 1.0 OD2 A:ASP39 4.0 87.2 1.0 N A:GLY26 4.2 64.6 1.0 NE2 A:GLN44 4.3 67.1 1.0 N A:ILE24 4.4 68.2 1.0 C A:VAL25 4.5 65.3 1.0 CA A:GLY26 4.6 67.0 1.0 CA A:ASN27 4.6 68.5 1.0 N A:ASN27 4.6 63.9 1.0 O12 A:W9T1001 4.6 83.9 1.0 CB A:ASP23 4.6 70.8 1.0 CA A:ILE24 4.6 67.0 1.0 OD1 A:ASP39 4.7 81.5 1.0 N A:VAL25 4.7 68.7 1.0 CB A:ASP43 4.7 72.3 1.0 CG A:ASP39 4.8 84.2 1.0 CA A:VAL25 4.8 68.0 1.0 O A:VAL25 4.9 66.5 1.0 CG A:GLN44 5.0 70.0 1.0

Calcium binding site 2 out of 44 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:92.4 occ:1.00 O A:GLY124 1.9 0.9 1.0 O A:ILE122 2.2 0.8 1.0 OD1 A:ASP121 2.5 95.6 1.0 OD2 A:ASP141 2.7 0.4 1.0 O13 A:W9T1002 2.8 0.5 1.0 C A:GLY124 3.0 0.1 1.0 N A:GLY124 3.2 0.1 1.0 C A:ILE122 3.4 99.4 1.0 CG A:ASP121 3.4 90.9 1.0 CA A:GLY124 3.6 0.8 1.0 O14 A:W9T1002 3.6 0.9 1.0 CG A:ASP141 3.7 0.3 1.0 OD2 A:ASP121 3.7 88.3 1.0 C A:GLU123 3.7 0.4 1.0 OD1 A:ASP141 3.9 0.6 1.0 C13 A:W9T1002 4.0 0.2 1.0 N A:SER125 4.2 0.3 1.0 CA A:GLU123 4.2 0.8 1.0 N A:GLU123 4.2 0.4 1.0 N A:ILE122 4.3 87.7 1.0 C14 A:W9T1002 4.3 0.4 1.0 O A:GLU123 4.4 0.8 1.0 CA A:ILE122 4.5 91.5 1.0 C12 A:W9T1002 4.6 0.1 1.0 CA A:SER125 4.6 0.0 1.0 CB A:ASP121 4.8 85.4 1.0 O12 A:W9T1002 5.0 0.7 1.0

Calcium binding site 3 out of 44 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1007 b:67.4 occ:1.00 OD1 A:ASP256 2.4 64.6 1.0 OD2 A:ASP276 2.5 71.1 1.0 O13 A:W9T1012 2.7 73.9 1.0 O A:GLY259 2.7 70.7 1.0 O A:VAL257 2.8 65.5 1.0 O14 A:W9T1012 3.0 73.2 1.0 CG A:ASP276 3.4 68.3 1.0 OD1 A:ASP276 3.5 68.3 1.0 CG A:ASP256 3.6 64.9 1.0 C13 A:W9T1012 3.7 73.8 1.0 C14 A:W9T1012 3.8 74.0 1.0 C A:GLY259 3.9 72.0 1.0 C A:VAL257 4.0 63.8 1.0 C12 A:W9T1012 4.0 76.1 1.0 OD2 A:ASP272 4.0 82.4 1.0 OD2 A:ASP256 4.2 64.5 1.0 NE2 A:GLN277 4.3 63.1 1.0 N A:VAL257 4.5 57.8 1.0 N A:GLY259 4.5 69.9 1.0 O12 A:W9T1012 4.6 75.2 1.0 CG A:GLN277 4.7 63.3 1.0 C A:SER258 4.7 68.7 1.0 CB A:ASP276 4.8 65.7 1.0 CB A:ASP256 4.8 62.5 1.0 CA A:VAL257 4.8 61.0 1.0 CA A:GLY259 4.8 70.8 1.0 N A:ASP260 4.9 72.9 1.0 CA A:ASP260 4.9 74.0 1.0 CA A:SER258 4.9 69.7 1.0 N A:SER258 4.9 66.1 1.0 CD A:GLN277 5.0 64.3 1.0

Calcium binding site 4 out of 44 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1008 b:66.2 occ:1.00 O13 A:W9T1004 2.2 67.7 1.0 OD1 A:ASP168 2.5 69.7 1.0 O A:GLY171 2.5 75.7 1.0 OD2 A:ASP188 2.5 58.3 1.0 O A:VAL169 2.6 68.7 1.0 O14 A:W9T1004 2.9 70.5 1.0 C13 A:W9T1004 3.3 74.7 1.0 CG A:ASP188 3.3 57.7 1.0 OD1 A:ASP188 3.4 57.9 1.0 CG A:ASP168 3.4 67.6 1.0 C14 A:W9T1004 3.6 73.7 1.0 OD2 A:ASP168 3.6 71.4 1.0 C A:GLY171 3.7 80.5 1.0 C12 A:W9T1004 3.8 77.9 1.0 C A:VAL169 3.8 65.2 1.0 OE2 A:GLU184 4.0 75.8 1.0 NE2 A:GLN189 4.2 62.1 1.0 N A:GLY171 4.3 77.4 1.0 N A:VAL169 4.4 61.4 1.0 O12 A:W9T1004 4.4 78.8 1.0 C A:GLU170 4.5 78.6 1.0 CA A:GLY171 4.6 77.7 1.0 N A:SER172 4.6 78.6 1.0 CA A:SER172 4.6 78.8 1.0 CA A:VAL169 4.7 61.6 1.0 N A:GLU170 4.7 65.8 1.0 CA A:GLU170 4.7 74.0 1.0 CB A:ASP188 4.8 57.3 1.0 CB A:ASP168 4.8 66.2 1.0 CG A:GLN189 4.9 57.0 1.0 C15 A:W9T1004 5.0 75.4 1.0

Calcium binding site 5 out of 44 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1009 b:68.1 occ:1.00 OD1 A:ASP209 2.4 72.0 1.0 OD2 A:ASP229 2.4 76.9 1.0 O13 A:W9T1003 2.4 80.2 1.0 O A:GLY212 2.8 74.6 1.0 O A:VAL210 2.9 79.1 1.0 OD1 A:ASP229 3.0 67.9 1.0 O14 A:W9T1003 3.0 73.2 1.0 CG A:ASP229 3.1 71.2 1.0 C13 A:W9T1003 3.5 78.5 1.0 CG A:ASP209 3.6 74.4 1.0 C14 A:W9T1003 3.8 78.5 1.0 C A:GLY212 4.0 82.1 1.0 C12 A:W9T1003 4.1 83.1 1.0 C A:VAL210 4.1 75.9 1.0 NE2 A:GLN230 4.2 69.6 1.0 CG A:GLN230 4.3 70.5 1.0 OD2 A:ASP209 4.3 72.1 1.0 N A:VAL210 4.5 73.2 1.0 CB A:ASP229 4.6 72.2 1.0 CB A:ASP209 4.6 72.5 1.0 CD A:GLN230 4.6 72.5 1.0 N A:GLY212 4.7 86.1 1.0 O12 A:W9T1003 4.7 85.4 1.0 CA A:SER213 4.7 82.2 1.0 N A:SER213 4.8 85.8 1.0 C A:GLU211 4.9 87.1 1.0 CA A:VAL210 4.9 71.9 1.0 CA A:GLY212 4.9 84.0 1.0

Calcium binding site 6 out of 44 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1013 b:96.3 occ:1.00 OD1 A:ASP373 2.8 80.1 1.0 NZ A:LYS420 3.6 75.0 1.0 O A:ILE432 3.7 91.0 1.0 CG A:ASP373 3.7 80.2 1.0 OD2 A:ASP373 3.9 81.4 1.0 O A:ASP371 4.4 62.8 1.0 NH1 G:ARG378 4.6 70.8 1.0 CE A:LYS420 4.6 65.8 1.0 C A:ILE432 4.9 90.6 1.0 CB A:ASP373 5.0 75.6 1.0 CG1 A:ILE432 5.0 96.0 1.0

Calcium binding site 7 out of 44 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1006 b:66.0 occ:1.00 OD2 C:ASP276 2.3 83.1 1.0 OD1 C:ASP256 2.4 69.4 1.0 O14 C:W9T1003 2.6 75.0 1.0 O C:GLY259 2.6 78.2 1.0 O C:VAL257 2.7 71.7 1.0 O13 C:W9T1003 2.9 79.1 1.0 CG C:ASP276 3.2 82.2 1.0 OD1 C:ASP276 3.4 81.8 1.0 CG C:ASP256 3.7 70.4 1.0 C14 C:W9T1003 3.7 79.1 1.0 C13 C:W9T1003 3.7 80.2 1.0 C C:GLY259 3.9 82.9 1.0 C C:VAL257 4.0 71.1 1.0 OD2 C:ASP272 4.1 99.0 1.0 C12 C:W9T1003 4.1 83.6 1.0 OD2 C:ASP256 4.3 69.2 1.0 NE2 C:GLN277 4.4 81.3 1.0 N C:VAL257 4.5 68.8 1.0 N C:GLY259 4.5 80.0 1.0 C C:SER258 4.6 76.7 1.0 CB C:ASP276 4.6 83.9 1.0 CG C:GLN277 4.7 73.8 1.0 N C:ASP260 4.8 81.5 1.0 CA C:GLY259 4.8 82.5 1.0 CA C:ASP260 4.8 80.5 1.0 CB C:ASP256 4.8 70.7 1.0 CA C:VAL257 4.8 70.4 1.0 CA C:SER258 4.9 76.2 1.0 N C:SER258 4.9 71.1 1.0 O C:SER258 5.0 71.3 1.0 C15 C:W9T1003 5.0 81.2 1.0

Calcium binding site 8 out of 44 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1007 b:64.6 occ:1.00 O13 C:W9T1002 2.4 79.8 1.0 OD1 C:ASP168 2.4 60.5 1.0 O C:GLY171 2.6 83.2 1.0 O C:VAL169 2.6 85.3 1.0 OD2 C:ASP188 2.7 73.2 1.0 O14 C:W9T1002 2.9 73.2 1.0 CG C:ASP168 3.3 59.6 1.0 C13 C:W9T1002 3.4 77.2 1.0 OD2 C:ASP168 3.5 58.7 1.0 OD1 C:ASP188 3.5 70.2 1.0 CG C:ASP188 3.5 72.2 1.0 C14 C:W9T1002 3.7 77.4 1.0 C12 C:W9T1002 3.7 77.7 1.0 C C:GLY171 3.7 86.4 1.0 C C:VAL169 3.8 82.9 1.0 OE2 C:GLU184 3.8 82.1 1.0 NE2 C:GLN189 4.1 66.2 1.0 N C:GLY171 4.3 84.8 1.0 O12 C:W9T1002 4.3 73.2 1.0 N C:VAL169 4.5 73.4 1.0 C C:GLU170 4.5 87.9 1.0 CA C:GLY171 4.6 85.4 1.0 N C:SER172 4.7 90.8 1.0 CA C:VAL169 4.7 78.3 1.0 N C:GLU170 4.7 86.7 1.0 CA C:GLU170 4.7 88.8 1.0 CA C:SER172 4.8 92.9 1.0 CB C:ASP168 4.8 62.1 1.0 CG C:GLN189 4.9 64.7 1.0 CB C:ASP188 5.0 69.8 1.0

Calcium binding site 9 out of 44 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1008 b:69.6 occ:1.00 OD1 C:ASP23 2.4 80.5 1.0 O C:GLY26 2.5 85.2 1.0 OD2 C:ASP43 2.5 86.6 1.0 O16 C:W9T1001 2.6 85.1 1.0 O C:ILE24 2.8 79.9 1.0 O14 C:W9T1001 3.2 98.8 1.0 OD1 C:ASP43 3.2 80.3 1.0 CG C:ASP43 3.2 81.4 1.0 CG C:ASP23 3.4 78.6 1.0 O13 C:W9T1001 3.5 91.3 1.0 C C:GLY26 3.7 84.2 1.0 OD2 C:ASP23 3.8 79.6 1.0 OD2 C:ASP39 3.8 93.5 1.0 C16 C:W9T1001 3.9 90.5 1.0 C C:ILE24 4.0 83.6 1.0 C14 C:W9T1001 4.2 0.4 1.0 NE2 C:GLN44 4.3 69.0 1.0 C13 C:W9T1001 4.4 96.5 1.0 N C:GLY26 4.4 85.6 1.0 OD1 C:ASP39 4.4 97.6 1.0 N C:ILE24 4.5 78.9 1.0 CA C:ASN27 4.5 86.6 1.0 CG C:ASP39 4.6 93.8 1.0 N C:ASN27 4.6 85.2 1.0 C15 C:W9T1001 4.6 97.8 1.0 C C:VAL25 4.7 85.9 1.0 CA C:GLY26 4.7 83.0 1.0 CB C:ASP43 4.7 76.7 1.0 CB C:ASP23 4.7 80.1 1.0 CA C:ILE24 4.9 78.6 1.0 CG C:GLN44 4.9 68.8 1.0 CD C:GLN44 4.9 70.1 1.0 C12 C:W9T1001 4.9 98.4 1.0 N C:VAL25 4.9 84.5 1.0

Calcium binding site 10 out of 44 in the Pore-Forming Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Pore-Forming Cel-III within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1009 b:75.3 occ:1.00 O C:GLY124 2.1 0.7 1.0 O16 C:W9T1004 2.4 1.0 1.0 OD1 C:ASP121 2.5 82.0 1.0 O C:ILE122 2.5 77.9 1.0 OD2 C:ASP141 2.9 91.6 1.0 O14 C:W9T1004 2.9 0.5 1.0 OD1 C:ASP141 3.1 88.8 1.0 C C:GLY124 3.2 0.0 1.0 CG C:ASP141 3.4 93.8 1.0 CG C:ASP121 3.5 82.6 1.0 N C:GLY124 3.7 0.7 1.0 C16 C:W9T1004 3.7 0.1 1.0 C C:ILE122 3.8 78.8 1.0 O13 C:W9T1004 3.8 0.8 1.0 OD2 C:ASP121 3.9 85.3 1.0 CA C:GLY124 4.0 0.0 1.0 C14 C:W9T1004 4.0 0.1 1.0 NE2 C:GLN137 4.0 0.8 1.0 C C:GLU123 4.2 0.8 1.0 N C:SER125 4.3 0.4 1.0 C13 C:W9T1004 4.4 0.3 1.0 N C:ILE122 4.4 71.9 1.0 C15 C:W9T1004 4.5 0.4 1.0 CG C:GLN142 4.5 80.0 1.0 NE2 C:GLN142 4.5 83.6 1.0 CA C:SER125 4.6 0.8 1.0 C12 C:W9T1004 4.6 0.6 1.0 CA C:ILE122 4.7 74.9 1.0 N C:GLU123 4.7 85.2 1.0 CA C:GLU123 4.7 94.8 1.0 CB C:ASP121 4.7 78.7 1.0 O C:GLU123 4.8 0.8 1.0 CD1 C:LEU139 4.8 0.4 1.0 CB C:ASP141 4.9 96.2 1.0 CD C:GLN137 4.9 0.4 1.0 CD C:GLN142 4.9 82.6 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