Calcium in PDB 4wmo: Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain

Protein crystallography data

The structure of Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain, PDB code: 4wmo was solved by K.Wangkanont, L.L.Kiessling, K.T.Forest, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.09 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 123.654, 111.069, 123.611, 90.00, 119.72, 90.00
R / Rfree (%) 16 / 18.8

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain (pdb code 4wmo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain, PDB code: 4wmo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in 4wmo

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Calcium binding site 1 out of 18 in the Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca401

b:12.8
occ:1.00
 OE1 F:GLU303 2.3 16.7 1.0
O F:HOH556 2.4 13.5 1.0
OD1 F:ASN289 2.4 15.8 1.0
OE2 F:GLU291 2.4 17.6 1.0
O F:HOH527 2.4 13.9 1.0
O F:HOH686 2.5 13.0 1.0
O F:HOH568 2.5 16.2 1.0
CD F:GLU303 3.3 18.9 1.0
CG F:ASN289 3.4 14.5 1.0
OE2 F:GLU303 3.4 25.8 1.0
CD F:GLU291 3.5 14.2 1.0
CB F:ASN289 3.9 11.5 1.0
OE1 F:GLU291 4.0 11.6 1.0
CA F:ASN289 4.3 14.2 1.0
OG F:SER272 4.3 22.5 1.0
NE2 F:HIS292 4.3 11.5 1.0
NE2 F:GLN308 4.4 11.5 1.0
ND2 F:ASN289 4.4 16.2 1.0
OE2 F:GLU273 4.5 23.6 1.0
OE1 F:GLU273 4.5 19.2 1.0
CG F:GLU303 4.7 13.0 1.0
CG F:GLU291 4.8 13.2 1.0
CD F:GLU273 5.0 18.4 1.0

Calcium binding site 2 out of 18 in 4wmo

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Calcium binding site 2 out of 18 in the Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca402

b:6.1
occ:1.00
 O F:HIS115 2.3 7.6 1.0
OD2 F:ASP311 2.3 7.0 1.0
O F:HOH619 2.3 8.4 1.0
O F:GLY126 2.4 6.2 1.0
OD1 F:ASP162 2.4 8.9 1.0
OD2 F:ASP162 2.4 9.1 1.0
O F:HOH687 2.4 4.0 1.0
CG F:ASP162 2.7 7.4 1.0
CG F:ASP311 3.4 8.5 1.0
C F:HIS115 3.5 8.0 1.0
C F:GLY126 3.5 8.5 1.0
CB F:ASP311 4.0 3.9 1.0
N F:ARG128 4.1 7.6 1.0
CA F:ASP127 4.1 5.6 1.0
CB F:ASP162 4.2 7.2 1.0
N F:ASP127 4.2 7.6 1.0
N F:HIS115 4.3 7.9 1.0
CA F:HIS115 4.3 7.6 1.0
OD1 F:ASP311 4.4 7.2 1.0
OD1 F:ASN117 4.4 10.5 1.0
N F:GLU116 4.4 6.4 1.0
CA F:GLU116 4.5 6.3 1.0
CA F:GLY126 4.5 6.0 1.0
CB F:HIS115 4.5 6.1 1.0
N F:ASN117 4.5 5.8 1.0
ND1 F:HIS115 4.6 9.6 1.0
CD1 F:TRP129 4.6 6.8 1.0
C F:ASP127 4.6 7.0 1.0
OD1 F:ASP127 4.6 9.0 1.0
N F:ASP162 4.7 5.3 1.0
NH1 F:ARG128 4.7 11.8 1.0
CA F:ASP162 4.8 6.9 1.0
C F:GLU116 5.0 9.7 1.0
O F:HOH584 5.0 15.4 1.0

Calcium binding site 3 out of 18 in 4wmo

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Calcium binding site 3 out of 18 in the Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca403

b:8.4
occ:1.00
 O F:GLY121 2.3 7.3 1.0
O F:HOH618 2.3 6.4 1.0
OE1 F:GLU116 2.3 9.8 1.0
O F:ASN118 2.4 7.0 1.0
O F:HOH536 2.4 5.0 1.0
OD2 F:ASP127 2.5 5.1 1.0
OD1 F:ASP127 2.6 9.0 1.0
CG F:ASP127 2.9 8.2 1.0
CD F:GLU116 3.3 11.3 1.0
C F:ASN118 3.4 8.5 1.0
C F:GLY121 3.5 7.0 1.0
OE2 F:GLU116 3.6 9.0 1.0
CA F:GLY121 4.1 5.4 1.0
N F:ASN118 4.1 8.3 1.0
CA F:ASN118 4.2 7.4 1.0
O F:HOH687 4.2 4.0 1.0
OD1 F:ASN117 4.2 10.5 1.0
N F:GLY121 4.3 6.8 1.0
OG1 F:THR124 4.3 6.6 1.0
N F:MSE119 4.4 9.3 1.0
CB F:ASP127 4.4 4.4 1.0
CB F:ASN118 4.4 8.0 1.0
N F:CYS123 4.5 6.0 1.0
N F:LYS122 4.6 6.9 1.0
CA F:MSE119 4.6 9.0 1.0
CG F:GLU116 4.6 8.4 1.0
CA F:GLY310 4.6 8.8 1.0
N F:ASP311 4.6 4.3 1.0
C F:MSE119 4.8 12.1 1.0
O F:HOH523 4.9 10.8 1.0
CA F:LYS122 4.9 8.8 1.0
O F:MSE119 4.9 12.3 1.0
N F:THR124 4.9 6.4 1.0

Calcium binding site 4 out of 18 in 4wmo

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Calcium binding site 4 out of 18 in the Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:13.9
occ:1.00
 OE1 C:GLU303 2.3 17.9 1.0
OE2 C:GLU291 2.4 15.8 1.0
O C:HOH565 2.4 15.0 1.0
O C:HOH650 2.4 14.7 1.0
OD1 C:ASN289 2.4 11.2 1.0
O C:HOH557 2.5 15.4 1.0
O C:HOH653 2.5 18.8 1.0
CD C:GLU303 3.3 21.5 1.0
CG C:ASN289 3.4 17.9 1.0
OE2 C:GLU303 3.5 28.4 1.0
CD C:GLU291 3.5 15.7 1.0
OE1 C:GLU291 3.9 14.2 1.0
CB C:ASN289 4.0 13.4 1.0
OG C:SER272 4.2 28.1 1.0
CA C:ASN289 4.3 15.8 1.0
NE2 C:HIS292 4.4 12.2 1.0
OE2 C:GLU273 4.4 21.5 1.0
NE2 C:GLN308 4.4 13.6 1.0
OE1 C:GLU273 4.4 19.2 1.0
ND2 C:ASN289 4.5 15.7 1.0
O C:HOH700 4.6 40.2 1.0
CG C:GLU303 4.7 17.3 1.0
CG C:GLU291 4.7 14.7 1.0
CD C:GLU273 4.9 18.7 1.0

Calcium binding site 5 out of 18 in 4wmo

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Calcium binding site 5 out of 18 in the Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:8.2
occ:1.00
 O C:GLY121 2.2 10.7 1.0
O C:HOH620 2.3 5.5 1.0
OE1 C:GLU116 2.4 8.3 1.0
O C:HOH550 2.4 8.6 1.0
O C:ASN118 2.5 8.9 1.0
OD2 C:ASP127 2.5 6.6 1.0
OD1 C:ASP127 2.5 7.0 1.0
CG C:ASP127 2.9 6.4 1.0
CD C:GLU116 3.3 10.6 1.0
C C:GLY121 3.4 12.0 1.0
C C:ASN118 3.4 11.5 1.0
OE2 C:GLU116 3.6 12.2 1.0
CA C:GLY121 4.0 10.2 1.0
O C:HOH723 4.2 4.1 1.0
N C:ASN118 4.2 8.7 1.0
OG1 C:THR124 4.2 6.4 1.0
CA C:ASN118 4.2 10.0 1.0
N C:GLY121 4.2 9.4 1.0
OD1 C:ASN117 4.3 6.2 1.0
N C:MSE119 4.4 11.2 1.0
CB C:ASP127 4.4 5.7 1.0
CB C:ASN118 4.5 8.4 1.0
N C:LYS122 4.5 8.7 1.0
N C:CYS123 4.5 9.5 1.0
CA C:GLY310 4.6 7.8 1.0
CA C:MSE119 4.6 11.1 1.0
N C:ASP311 4.6 7.2 1.0
CG C:GLU116 4.6 8.7 1.0
C C:MSE119 4.8 12.8 1.0
CA C:LYS122 4.8 9.2 1.0
O C:HOH525 4.8 8.7 1.0
O C:MSE119 4.9 16.0 1.0
N C:THR124 4.9 5.9 1.0

Calcium binding site 6 out of 18 in 4wmo

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Calcium binding site 6 out of 18 in the Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:6.0
occ:1.00
 OD2 C:ASP311 2.3 4.5 1.0
O C:HIS115 2.3 7.7 1.0
O C:GLY126 2.3 5.5 1.0
O C:HOH558 2.3 10.5 1.0
OD2 C:ASP162 2.4 6.7 1.0
O C:HOH723 2.4 4.1 1.0
OD1 C:ASP162 2.4 7.4 1.0
CG C:ASP162 2.7 6.8 1.0
CG C:ASP311 3.4 7.5 1.0
C C:GLY126 3.5 8.6 1.0
C C:HIS115 3.5 7.0 1.0
CB C:ASP311 4.0 3.5 1.0
CA C:ASP127 4.1 7.4 1.0
N C:ARG128 4.1 7.1 1.0
N C:ASP127 4.2 6.6 1.0
CB C:ASP162 4.2 5.6 1.0
N C:HIS115 4.3 6.8 1.0
OD1 C:ASN117 4.3 6.2 1.0
CA C:HIS115 4.3 5.5 1.0
OD1 C:ASP311 4.4 6.0 1.0
N C:GLU116 4.4 6.7 1.0
CA C:GLU116 4.4 7.3 1.0
N C:ASN117 4.5 5.2 1.0
CB C:HIS115 4.5 6.2 1.0
CA C:GLY126 4.5 6.7 1.0
C C:ASP127 4.6 6.8 1.0
OD1 C:ASP127 4.6 7.0 1.0
CD1 C:TRP129 4.7 6.5 1.0
ND1 C:HIS115 4.7 5.8 1.0
N C:ASP162 4.7 6.0 1.0
NH1 C:ARG128 4.7 10.6 1.0
CA C:ASP162 4.9 7.0 1.0
C C:GLU116 5.0 9.8 1.0
O C:HOH567 5.0 12.3 1.0
CG C:ASN117 5.0 11.2 1.0

Calcium binding site 7 out of 18 in 4wmo

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Calcium binding site 7 out of 18 in the Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:13.1
occ:1.00
 OE1 B:GLU303 2.3 20.2 1.0
OE2 B:GLU291 2.4 14.6 1.0
OD1 B:ASN289 2.4 11.3 1.0
O B:HOH551 2.4 10.9 1.0
O B:HOH504 2.4 11.0 1.0
O B:HOH544 2.5 10.4 1.0
O B:HOH512 3.0 14.4 1.0
CD B:GLU303 3.3 18.6 1.0
CG B:ASN289 3.5 12.1 1.0
OE2 B:GLU303 3.5 25.1 1.0
CD B:GLU291 3.5 11.7 1.0
OE1 B:GLU291 4.0 9.4 1.0
CB B:ASN289 4.0 10.1 1.0
OG B:SER272 4.2 19.6 1.0
CA B:ASN289 4.3 8.2 1.0
NE2 B:GLN308 4.3 9.8 1.0
OE2 B:GLU273 4.4 16.4 1.0
NE2 B:HIS292 4.5 16.1 1.0
OE1 B:GLU273 4.5 14.4 1.0
ND2 B:ASN289 4.6 7.9 1.0
CG B:GLU303 4.7 11.7 1.0
CG B:GLU291 4.7 8.8 1.0
CD B:GLU273 4.9 14.4 1.0

Calcium binding site 8 out of 18 in 4wmo

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Calcium binding site 8 out of 18 in the Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:6.0
occ:1.00
 O B:GLY121 2.3 8.7 1.0
O B:HOH732 2.4 3.5 1.0
O B:ASN118 2.4 7.2 1.0
OE1 B:GLU116 2.4 6.5 1.0
O B:HOH538 2.4 4.4 1.0
OD2 B:ASP127 2.5 6.8 1.0
OD1 B:ASP127 2.5 4.1 1.0
CG B:ASP127 2.9 4.7 1.0
CD B:GLU116 3.3 8.0 1.0
C B:GLY121 3.4 9.9 1.0
OE2 B:GLU116 3.5 5.7 1.0
C B:ASN118 3.5 10.2 1.0
CA B:GLY121 4.1 6.8 1.0
O B:HOH733 4.2 4.3 1.0
OG1 B:THR124 4.2 4.2 1.0
N B:ASN118 4.2 5.1 1.0
N B:GLY121 4.3 12.4 1.0
CA B:ASN118 4.3 9.9 1.0
OD1 B:ASN117 4.4 8.6 1.0
CB B:ASP127 4.4 3.7 1.0
N B:MSE119 4.4 7.4 1.0
N B:LYS122 4.5 8.2 1.0
CB B:ASN118 4.5 5.8 1.0
N B:CYS123 4.5 4.1 1.0
CA B:MSE119 4.6 9.5 1.0
CA B:GLY310 4.6 5.0 1.0
N B:ASP311 4.6 5.2 1.0
CG B:GLU116 4.7 5.6 1.0
C B:MSE119 4.7 11.9 1.0
O B:MSE119 4.8 11.0 1.0
CA B:LYS122 4.8 5.1 1.0
O B:HOH675 4.8 7.3 1.0
N B:THR124 5.0 6.0 1.0

Calcium binding site 9 out of 18 in 4wmo

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Calcium binding site 9 out of 18 in the Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:4.2
occ:1.00
 O B:HIS115 2.2 5.0 1.0
OD2 B:ASP311 2.3 3.1 1.0
O B:GLY126 2.4 4.9 1.0
OD2 B:ASP162 2.4 7.3 1.0
O B:HOH566 2.4 5.9 1.0
OD1 B:ASP162 2.4 6.0 1.0
O B:HOH733 2.5 4.3 1.0
CG B:ASP162 2.7 5.9 1.0
CG B:ASP311 3.4 5.2 1.0
C B:HIS115 3.4 6.2 1.0
C B:GLY126 3.5 6.2 1.0
CB B:ASP311 4.0 5.0 1.0
CA B:ASP127 4.1 4.5 1.0
N B:ARG128 4.2 5.0 1.0
CB B:ASP162 4.2 5.5 1.0
N B:HIS115 4.2 5.2 1.0
N B:ASP127 4.2 4.4 1.0
CA B:HIS115 4.3 5.7 1.0
OD1 B:ASN117 4.3 8.6 1.0
OD1 B:ASP311 4.4 4.7 1.0
N B:GLU116 4.4 5.5 1.0
CA B:GLU116 4.4 5.5 1.0
N B:ASN117 4.5 8.3 1.0
CB B:HIS115 4.5 5.6 1.0
CA B:GLY126 4.5 6.2 1.0
CD1 B:TRP129 4.6 3.4 1.0
ND1 B:HIS115 4.6 7.0 1.0
C B:ASP127 4.6 5.5 1.0
NH1 B:ARG128 4.7 8.1 1.0
N B:ASP162 4.7 4.8 1.0
OD1 B:ASP127 4.7 4.1 1.0
CA B:ASP162 4.9 5.9 1.0
O B:HOH578 4.9 12.9 1.0
C B:GLU116 5.0 7.8 1.0

Calcium binding site 10 out of 18 in 4wmo

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Calcium binding site 10 out of 18 in the Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Selenomethionine Derivative of Xenopus Laevis Embryonic Epidermal Lectin Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:11.3
occ:1.00
 OE2 D:GLU291 2.3 12.5 1.0
OE1 D:GLU303 2.4 15.2 1.0
OD1 D:ASN289 2.4 11.1 1.0
O D:HOH710 2.4 9.8 1.0
O D:HOH680 2.5 13.4 1.0
O D:HOH593 2.5 10.8 1.0
CD D:GLU303 3.3 15.2 1.0
O D:HOH651 3.4 19.6 1.0
OE2 D:GLU303 3.4 21.5 1.0
CG D:ASN289 3.4 11.1 1.0
CD D:GLU291 3.5 9.4 1.0
CB D:ASN289 4.0 10.2 1.0
OE1 D:GLU291 4.0 12.6 1.0
CA D:ASN289 4.3 10.9 1.0
OG D:SER272 4.3 21.7 1.0
NE2 D:GLN308 4.4 9.2 1.0
OE2 D:GLU273 4.5 13.2 1.0
NE2 D:HIS292 4.5 9.8 1.0
OE1 D:GLU273 4.5 13.4 1.0
ND2 D:ASN289 4.6 11.7 1.0
CG D:GLU303 4.7 12.1 1.0
CG D:GLU291 4.7 9.8 1.0
CD D:GLU273 5.0 17.7 1.0

Reference:

K.Wangkanont, D.A.Wesener, J.A.Vidani, L.L.Kiessling, K.T.Forest. Structures of Xenopus Embryonic Epidermal Lectin Reveal A Conserved Mechanism of Microbial Glycan Recognition. J.Biol.Chem. V. 291 5596 2016.
ISSN: ESSN 1083-351X
PubMed: 26755729
DOI: 10.1074/JBC.M115.709212
Page generated: Sat Dec 12 05:11:04 2020

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