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Calcium in PDB 1vcl: Crystal Structure of Hemolytic Lectin Cel-III

Protein crystallography data

The structure of Crystal Structure of Hemolytic Lectin Cel-III, PDB code: 1vcl was solved by T.Uchida, T.Yamasaki, S.Eto, H.Sugawara, G.Kurisu, A.Nakagawa, M.Kusunoki, T.Hatakeyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.17 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.420, 65.370, 126.020, 90.00, 98.18, 90.00
R / Rfree (%) 16.5 / 20.1

Other elements in 1vcl:

The structure of Crystal Structure of Hemolytic Lectin Cel-III also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 10 in 1vcl

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Calcium binding site 1 out of 10 in the Crystal Structure of Hemolytic Lectin Cel-III


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Hemolytic Lectin Cel-III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:33.8
occ:1.00
 O A:HOH1681 2.2 29.5 1.0
O A:HOH1337 2.2 27.0 1.0
O A:GLY26 2.2 30.8 1.0
OD1 A:ASP23 2.3 27.8 1.0
O A:ILE24 2.3 30.0 1.0
OD2 A:ASP43 2.3 26.5 1.0
O A:HOH1550 2.7 35.1 1.0
CG A:ASP23 3.3 28.9 1.0
CG A:ASP43 3.4 26.9 1.0
C A:GLY26 3.4 33.0 1.0
OD2 A:ASP23 3.5 31.6 1.0
C A:ILE24 3.6 29.9 1.0
OD1 A:ASP43 3.6 27.1 1.0
N A:GLY26 4.0 33.0 1.0
O A:HOH1328 4.0 27.6 1.0
N A:ILE24 4.1 28.1 1.0
C A:VAL25 4.2 32.7 1.0
CA A:GLY26 4.3 33.6 1.0
OD2 A:ASP39 4.3 31.9 1.0
O A:HOH1713 4.4 45.1 1.0
NE2 A:GLN44 4.4 22.4 1.0
N A:ASN27 4.4 33.6 1.0
CA A:ILE24 4.4 28.8 1.0
N A:VAL25 4.5 31.3 1.0
CA A:VAL25 4.5 33.0 1.0
CA A:ASN27 4.6 32.6 1.0
CB A:ASP23 4.6 27.3 1.0
O A:VAL25 4.6 32.4 1.0
CG A:GLN44 4.7 24.4 1.0
CB A:ASP43 4.7 25.4 1.0
C A:ASP23 4.8 28.4 1.0
CA A:ASP23 4.9 26.6 1.0
CD A:GLN44 5.0 21.7 1.0

Calcium binding site 2 out of 10 in 1vcl

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Calcium binding site 2 out of 10 in the Crystal Structure of Hemolytic Lectin Cel-III


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Hemolytic Lectin Cel-III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:44.8
occ:1.00
 OD2 A:ASP141 2.2 38.3 1.0
O A:GLY124 2.3 44.2 1.0
O A:HOH1652 2.4 41.9 1.0
O A:ILE122 2.5 38.4 1.0
OD1 A:ASP121 2.5 38.3 1.0
O A:HOH1559 2.5 42.9 1.0
O A:HOH1664 2.5 42.5 1.0
CG A:ASP141 3.3 38.0 1.0
CG A:ASP121 3.4 36.3 1.0
C A:GLY124 3.5 45.5 1.0
OD2 A:ASP121 3.6 36.2 1.0
C A:ILE122 3.6 37.4 1.0
OD1 A:ASP141 3.7 37.8 1.0
O A:HOH1391 4.0 30.3 1.0
N A:GLY124 4.0 45.4 1.0
N A:ILE122 4.2 33.6 1.0
NE2 A:GLN137 4.2 45.6 1.0
C A:GLU123 4.3 43.1 1.0
CA A:GLY124 4.3 46.4 1.0
N A:SER125 4.5 46.0 1.0
CA A:ILE122 4.5 34.7 1.0
N A:GLU123 4.6 39.5 1.0
CA A:GLU123 4.6 42.5 1.0
NE2 A:GLN142 4.6 32.3 1.0
CB A:ASP141 4.6 34.8 1.0
CA A:SER125 4.7 45.9 1.0
CB A:ASP121 4.7 34.2 1.0
O A:GLU123 4.7 42.6 1.0
CG A:GLN142 4.9 32.2 1.0

Calcium binding site 3 out of 10 in 1vcl

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Calcium binding site 3 out of 10 in the Crystal Structure of Hemolytic Lectin Cel-III


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Hemolytic Lectin Cel-III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:57.8
occ:1.00
 O A:HOH1710 2.0 37.1 1.0
O A:VAL169 2.1 33.7 1.0
O A:GLY171 2.2 46.5 1.0
OD2 A:ASP188 2.2 40.7 1.0
OD1 A:ASP168 2.3 37.1 1.0
O A:HOH1587 2.3 37.4 1.0
CG A:ASP188 3.2 37.3 1.0
CG A:ASP168 3.3 34.5 1.0
C A:VAL169 3.3 34.7 1.0
C A:GLY171 3.4 47.1 1.0
O A:HOH1699 3.5 40.0 1.0
OD1 A:ASP188 3.6 40.2 1.0
OD2 A:ASP168 3.7 36.4 1.0
N A:VAL169 3.7 32.2 1.0
N A:GLY171 4.0 44.5 1.0
CA A:VAL169 4.1 32.5 1.0
C A:GLU170 4.2 41.5 1.0
N A:SER172 4.3 48.6 1.0
CA A:GLY171 4.3 46.7 1.0
N A:GLU170 4.3 36.2 1.0
CA A:SER172 4.3 49.2 1.0
CB A:ASP168 4.4 31.3 1.0
CA A:GLU170 4.5 39.5 1.0
CB A:ASP188 4.6 33.4 1.0
O A:GLU170 4.6 41.0 1.0
C A:ASP168 4.6 30.8 1.0
CB A:VAL169 4.6 32.7 1.0
CA A:ASP168 4.9 30.2 1.0

Calcium binding site 4 out of 10 in 1vcl

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Calcium binding site 4 out of 10 in the Crystal Structure of Hemolytic Lectin Cel-III


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Hemolytic Lectin Cel-III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:31.6
occ:1.00
 O A:HOH1704 2.1 24.1 1.0
OD2 A:ASP229 2.1 21.7 1.0
O A:HOH1709 2.1 23.8 1.0
OD1 A:ASP209 2.1 23.0 1.0
O A:GLY212 2.2 23.5 1.0
O A:VAL210 2.3 22.4 1.0
CG A:ASP209 3.1 23.9 1.0
CG A:ASP229 3.2 22.0 1.0
OD2 A:ASP209 3.4 26.5 1.0
C A:VAL210 3.4 22.0 1.0
C A:GLY212 3.4 24.6 1.0
OD1 A:ASP229 3.5 22.6 1.0
O A:HOH1304 3.9 19.6 1.0
N A:VAL210 3.9 20.9 1.0
N A:GLY212 3.9 25.3 1.0
C A:GLU211 4.1 24.2 1.0
O A:HOH1462 4.2 33.0 1.0
CA A:VAL210 4.2 21.1 1.0
CA A:GLY212 4.3 25.4 1.0
OD2 A:ASP225 4.3 25.7 1.0
N A:SER213 4.4 24.8 1.0
N A:GLU211 4.4 22.6 1.0
CB A:ASP209 4.5 21.8 1.0
CA A:GLU211 4.5 24.7 1.0
CA A:SER213 4.5 24.4 1.0
CB A:ASP229 4.5 20.2 1.0
NE2 A:GLN230 4.5 20.6 1.0
O A:GLU211 4.6 24.1 1.0
O A:HOH1481 4.6 39.1 1.0
CG A:GLN230 4.7 18.9 1.0
C A:ASP209 4.7 21.7 1.0
CB A:VAL210 4.8 20.4 1.0
CA A:ASP209 4.9 20.7 1.0

Calcium binding site 5 out of 10 in 1vcl

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Calcium binding site 5 out of 10 in the Crystal Structure of Hemolytic Lectin Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Hemolytic Lectin Cel-III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:27.1
occ:1.00
 OD1 A:ASP256 2.3 21.7 1.0
O A:GLY259 2.4 31.3 1.0
O A:VAL257 2.4 26.0 1.0
OD2 A:ASP276 2.4 26.8 1.0
O A:HOH1379 2.4 29.0 1.0
O A:HOH1363 2.5 30.0 1.0
O A:HOH1437 2.5 39.5 1.0
CG A:ASP256 3.2 23.1 1.0
CG A:ASP276 3.5 24.8 1.0
OD2 A:ASP256 3.5 23.8 1.0
C A:GLY259 3.5 31.9 1.0
C A:VAL257 3.6 26.6 1.0
OD1 A:ASP276 3.8 23.7 1.0
O A:HOH1344 3.9 25.8 1.0
N A:VAL257 4.0 22.5 1.0
N A:GLY259 4.1 32.7 1.0
C A:SER258 4.2 31.9 1.0
CA A:GLY259 4.3 33.0 1.0
CA A:VAL257 4.4 24.5 1.0
OD2 A:ASP272 4.5 27.3 1.0
NE2 A:GLN277 4.5 20.0 1.0
N A:SER258 4.5 28.7 1.0
N A:ASP260 4.5 32.2 1.0
CB A:ASP256 4.6 21.1 1.0
CA A:SER258 4.6 31.2 1.0
O A:SER258 4.6 31.3 1.0
CA A:ASP260 4.7 31.6 1.0
CG A:GLN277 4.8 20.1 1.0
CB A:ASP276 4.8 23.2 1.0
C A:ASP256 4.9 22.1 1.0
CA A:ASP256 5.0 20.6 1.0

Calcium binding site 6 out of 10 in 1vcl

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Calcium binding site 6 out of 10 in the Crystal Structure of Hemolytic Lectin Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Hemolytic Lectin Cel-III within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:43.1
occ:1.00
 O B:GLY26 2.2 40.5 1.0
O B:ILE24 2.2 36.6 1.0
OD2 B:ASP43 2.2 31.1 1.0
O B:HOH2606 2.2 33.8 1.0
O B:HOH2608 2.3 33.2 1.0
OD1 B:ASP23 2.3 30.1 1.0
CG B:ASP43 3.2 31.4 1.0
CG B:ASP23 3.2 32.0 1.0
C B:GLY26 3.4 42.3 1.0
C B:ILE24 3.4 36.4 1.0
OD1 B:ASP43 3.4 33.5 1.0
OD2 B:ASP23 3.5 32.4 1.0
N B:GLY26 3.9 42.0 1.0
N B:ILE24 3.9 32.8 1.0
O B:HOH2288 4.0 35.1 1.0
C B:VAL25 4.0 40.8 1.0
CA B:GLY26 4.2 43.0 1.0
CA B:ILE24 4.2 34.5 1.0
OD2 B:ASP39 4.3 37.2 1.0
N B:VAL25 4.3 38.3 1.0
N B:ASN27 4.4 43.3 1.0
CA B:VAL25 4.4 40.5 1.0
O B:HOH2547 4.4 40.5 1.0
O B:VAL25 4.4 41.0 1.0
NE2 B:GLN44 4.5 25.6 1.0
CA B:ASN27 4.5 42.9 1.0
CB B:ASP23 4.6 30.9 1.0
CB B:ASP43 4.6 30.7 1.0
CG B:GLN44 4.7 26.8 1.0
C B:ASP23 4.7 32.3 1.0
CB B:ILE24 4.8 33.6 1.0
CA B:ASP23 4.9 30.1 1.0

Calcium binding site 7 out of 10 in 1vcl

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Calcium binding site 7 out of 10 in the Crystal Structure of Hemolytic Lectin Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Hemolytic Lectin Cel-III within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:45.2
occ:1.00
 OD2 B:ASP141 2.2 38.0 1.0
O B:GLY124 2.3 42.8 1.0
O B:HOH2588 2.4 42.4 1.0
OD2 B:ASP121 2.5 35.3 1.0
O B:ILE122 2.5 36.9 1.0
O B:HOH2584 2.5 39.2 1.0
CG B:ASP141 3.3 36.0 1.0
CG B:ASP121 3.4 36.0 1.0
C B:GLY124 3.5 43.3 1.0
OD1 B:ASP141 3.6 36.6 1.0
OD1 B:ASP121 3.6 37.7 1.0
C B:ILE122 3.7 36.3 1.0
N B:GLY124 4.1 43.7 1.0
NE2 B:GLN137 4.1 43.9 1.0
O B:HOH2351 4.1 32.6 1.0
N B:ILE122 4.2 32.7 1.0
CA B:GLY124 4.3 44.4 1.0
C B:GLU123 4.4 41.8 1.0
N B:SER125 4.5 44.0 1.0
CA B:ILE122 4.6 33.9 1.0
CB B:ASP141 4.6 33.4 1.0
NE2 B:GLN142 4.6 35.8 1.0
CA B:SER125 4.6 43.4 1.0
N B:GLU123 4.7 38.8 1.0
CA B:GLU123 4.7 41.3 1.0
CB B:ASP121 4.8 34.0 1.0
CG B:GLN142 4.8 32.6 1.0
O B:GLU123 4.9 40.4 1.0
CD B:GLN137 5.0 43.6 1.0

Calcium binding site 8 out of 10 in 1vcl

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Calcium binding site 8 out of 10 in the Crystal Structure of Hemolytic Lectin Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Hemolytic Lectin Cel-III within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1003

b:44.2
occ:1.00
 O B:HOH2605 2.0 25.1 1.0
O B:VAL169 2.1 28.1 1.0
O B:GLY171 2.1 34.0 1.0
OD1 B:ASP168 2.2 33.9 1.0
O B:HOH2617 2.2 30.8 1.0
OD2 B:ASP188 2.2 30.9 1.0
CG B:ASP188 3.2 30.1 1.0
CG B:ASP168 3.2 29.7 1.0
C B:VAL169 3.3 28.2 1.0
C B:GLY171 3.3 35.0 1.0
OD1 B:ASP188 3.5 33.5 1.0
OD2 B:ASP168 3.6 32.2 1.0
N B:VAL169 3.7 26.2 1.0
O B:HOH2356 3.8 29.4 1.0
N B:GLY171 3.9 33.6 1.0
O B:HOH2483 4.0 38.5 1.0
CA B:VAL169 4.1 26.1 1.0
C B:GLU170 4.1 32.2 1.0
CA B:GLY171 4.2 34.7 1.0
N B:SER172 4.3 35.5 1.0
N B:GLU170 4.3 28.8 1.0
CB B:ASP168 4.4 25.6 1.0
CA B:SER172 4.4 36.4 1.0
CA B:GLU170 4.5 31.4 1.0
O B:GLU170 4.6 32.0 1.0
CB B:ASP188 4.6 26.8 1.0
C B:ASP168 4.6 25.0 1.0
CB B:VAL169 4.6 26.0 1.0
CA B:ASP168 4.8 24.7 1.0

Calcium binding site 9 out of 10 in 1vcl

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Calcium binding site 9 out of 10 in the Crystal Structure of Hemolytic Lectin Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Hemolytic Lectin Cel-III within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1004

b:28.9
occ:1.00
 O B:HOH2604 2.1 20.9 1.0
OD2 B:ASP229 2.1 19.5 1.0
O B:HOH2616 2.1 24.7 1.0
O B:GLY212 2.2 22.0 1.0
OD2 B:ASP209 2.2 20.3 1.0
O B:VAL210 2.2 19.6 1.0
CG B:ASP209 3.1 20.6 1.0
CG B:ASP229 3.2 18.2 1.0
OD1 B:ASP209 3.3 22.1 1.0
C B:GLY212 3.4 22.1 1.0
C B:VAL210 3.4 19.8 1.0
OD1 B:ASP229 3.5 20.2 1.0
O B:HOH2202 3.8 20.2 1.0
N B:VAL210 3.9 19.0 1.0
N B:GLY212 3.9 22.0 1.0
O B:HOH2487 4.0 36.7 1.0
C B:GLU211 4.1 20.8 1.0
CA B:GLY212 4.2 22.6 1.0
CA B:VAL210 4.2 18.9 1.0
OD2 B:ASP225 4.3 24.4 1.0
N B:SER213 4.4 23.4 1.0
N B:GLU211 4.4 19.7 1.0
CA B:GLU211 4.5 20.9 1.0
CA B:SER213 4.5 23.3 1.0
CB B:ASP229 4.5 18.3 1.0
CB B:ASP209 4.5 19.8 1.0
NE2 B:GLN230 4.5 19.2 1.0
O B:HOH2350 4.5 33.6 1.0
O B:GLU211 4.5 20.2 1.0
CG B:GLN230 4.7 17.9 1.0
C B:ASP209 4.7 19.4 1.0
CB B:VAL210 4.8 17.8 1.0
CA B:ASP209 4.9 19.1 1.0

Calcium binding site 10 out of 10 in 1vcl

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Calcium binding site 10 out of 10 in the Crystal Structure of Hemolytic Lectin Cel-III


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Hemolytic Lectin Cel-III within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1005

b:26.2
occ:1.00
 OD2 B:ASP276 2.3 23.4 1.0
O B:GLY259 2.3 28.6 1.0
OD2 B:ASP256 2.3 21.1 1.0
O B:HOH2264 2.3 25.3 1.0
O B:VAL257 2.4 22.6 1.0
O B:HOH2225 2.5 28.2 1.0
O B:HOH2340 2.5 37.1 1.0
CG B:ASP256 3.3 20.6 1.0
CG B:ASP276 3.4 22.7 1.0
OD1 B:ASP256 3.5 21.5 1.0
C B:GLY259 3.5 29.6 1.0
C B:VAL257 3.6 23.4 1.0
OD1 B:ASP276 3.7 23.0 1.0
O B:HOH2241 4.0 24.4 1.0
N B:GLY259 4.0 29.7 1.0
N B:VAL257 4.1 20.7 1.0
C B:SER258 4.2 28.6 1.0
CA B:GLY259 4.4 30.1 1.0
CA B:VAL257 4.5 21.1 1.0
OD2 B:ASP272 4.5 26.9 1.0
NE2 B:GLN277 4.5 19.4 1.0
N B:ASP260 4.5 29.8 1.0
N B:SER258 4.6 25.1 1.0
CA B:SER258 4.6 27.8 1.0
CA B:ASP260 4.6 29.3 1.0
CB B:ASP256 4.7 18.7 1.0
O B:SER258 4.7 28.0 1.0
CG B:GLN277 4.7 20.5 1.0
CB B:ASP276 4.8 22.0 1.0
C B:ASP256 4.9 20.1 1.0

Reference:

T.Uchida, T.Yamasaki, S.Eto, H.Sugawara, G.Kurisu, A.Nakagawa, M.Kusunoki, T.Hatakeyama. Crystal Structure of the Hemolytic Lectin Cel-III Isolated From the Marine Invertebrate Cucumaria Echinata: Implications of Domain Structure For Its Membrane Pore-Formation Mechanism J.Biol.Chem. V. 279 37133 2004.
ISSN: ISSN 0021-9258
PubMed: 15194688
DOI: 10.1074/JBC.M404065200
Page generated: Fri Jul 12 00:02:49 2024

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