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Calcium in PDB 3ef2: Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium.

Protein crystallography data

The structure of Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium., PDB code: 3ef2 was solved by E.M.Grahn, I.J.Goldstein, U.Krengel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 121.279, 121.279, 100.124, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 18.9

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium. (pdb code 3ef2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium., PDB code: 3ef2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 3ef2

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Calcium binding site 1 out of 16 in the Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:8.8
occ:1.00
 OD1 A:ASP214 2.3 8.7 1.0
OD2 A:ASP216 2.4 11.1 1.0
OD2 A:ASP217 2.4 9.3 1.0
O A:HOH323 2.4 7.7 1.0
O A:GLN211 2.4 8.2 1.0
OD2 B:ASP183 2.4 8.1 1.0
OD1 B:ASP183 2.5 9.0 1.0
OD1 A:ASP216 2.5 12.6 1.0
CG B:ASP183 2.8 8.4 1.0
CG A:ASP216 2.8 7.3 1.0
CG A:ASP217 3.3 7.8 1.0
CG A:ASP214 3.5 8.2 1.0
C A:GLN211 3.5 8.1 1.0
OD1 A:ASP217 3.7 9.3 1.0
CA A:CA304 3.8 11.3 1.0
OD2 A:ASP214 4.0 10.6 1.0
CA A:GLN211 4.1 8.6 1.0
O B:HOH757 4.2 19.1 1.0
N A:ASP214 4.3 7.8 1.0
CB B:ASP183 4.3 7.7 1.0
CB A:ASP216 4.4 8.4 1.0
CB B:ALA240 4.4 8.1 1.0
N A:ASP217 4.5 7.2 1.0
O A:HOH446 4.6 21.6 1.0
N A:ILE212 4.6 7.3 1.0
CB A:ASP217 4.6 7.1 1.0
CB A:ASP214 4.7 7.4 1.0
O B:LEU182 4.8 9.5 1.0
C A:ILE212 4.8 7.5 1.0
CA A:ASP214 4.9 7.7 1.0
O B:HOH517 4.9 8.2 1.0
CB A:GLN211 4.9 8.2 1.0
N A:TYR213 5.0 8.4 1.0
CA A:ILE212 5.0 7.7 1.0

Calcium binding site 2 out of 16 in 3ef2

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Calcium binding site 2 out of 16 in the Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:11.3
occ:1.00
 O B:LEU182 2.3 9.5 1.0
O A:HOH539 2.3 12.2 0.5
O B:HOH651 2.3 15.0 1.0
OD1 B:ASP183 2.3 9.0 1.0
OD2 A:ASP214 2.3 10.6 1.0
OD1 A:ASP216 2.4 12.6 1.0
CG A:ASP214 3.1 8.2 1.0
OD1 A:ASP214 3.1 8.7 1.0
CG B:ASP183 3.3 8.4 1.0
C B:LEU182 3.5 8.6 1.0
CG A:ASP216 3.6 7.3 1.0
CA A:CA303 3.8 8.8 1.0
CA B:ASP183 4.0 8.4 1.0
OD2 B:ASP183 4.1 8.1 1.0
N B:ASP183 4.2 8.7 1.0
CH3 A:ACT306 4.2 22.5 1.0
CB B:ASP183 4.2 7.7 1.0
OD2 A:ASP216 4.4 11.1 1.0
CB A:ASP216 4.5 8.4 1.0
CB A:ASP214 4.5 7.4 1.0
O A:HOH358 4.5 12.4 1.0
CA B:LEU182 4.6 8.2 1.0
O A:HOH629 4.7 32.2 1.0
N A:ASP216 4.8 7.4 1.0
CA A:GLN211 4.8 8.6 1.0
CB B:LEU182 4.8 8.1 1.0
O B:HOH765 5.0 29.7 1.0
OD3 A:OCS215 5.0 5.3 0.5

Calcium binding site 3 out of 16 in 3ef2

Go back to Calcium Binding Sites List in 3ef2
Calcium binding site 3 out of 16 in the Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:10.7
occ:1.00
 O A:HOH426 2.3 14.6 1.0
O A:LEU182 2.3 9.1 1.0
O B:HOH722 2.3 12.1 0.5
OD1 A:ASP183 2.3 8.1 1.0
OD2 B:ASP214 2.3 10.4 1.0
OD1 B:ASP216 2.4 12.5 1.0
CG B:ASP214 3.1 8.3 1.0
OD1 B:ASP214 3.1 9.3 1.0
CG A:ASP183 3.3 9.2 1.0
C A:LEU182 3.5 8.6 1.0
CG B:ASP216 3.6 8.1 1.0
CA B:CA303 3.8 8.7 1.0
CA A:ASP183 4.0 9.0 1.0
OD2 A:ASP183 4.1 7.5 1.0
N A:ASP183 4.2 8.9 1.0
CB A:ASP183 4.2 8.6 1.0
CH3 A:ACT309 4.3 23.6 1.0
OD2 B:ASP216 4.4 11.9 1.0
CB B:ASP216 4.5 8.5 1.0
CB B:ASP214 4.5 8.0 1.0
CA A:LEU182 4.6 8.1 1.0
O B:HOH559 4.6 11.9 1.0
O A:HOH637 4.6 29.4 1.0
N B:ASP216 4.8 7.4 1.0
CA B:GLN211 4.8 8.3 1.0
CB A:LEU182 4.8 8.3 1.0

Calcium binding site 4 out of 16 in 3ef2

Go back to Calcium Binding Sites List in 3ef2
Calcium binding site 4 out of 16 in the Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca307

b:52.5
occ:1.00
 O A:SER201 3.6 15.9 1.0
O A:HOH432 4.1 13.8 1.0
OH A:TYR213 4.1 12.2 1.0
CE B:LYS228 4.2 18.6 1.0
C A:GLY202 4.3 15.4 1.0
OG A:SER206 4.3 22.5 1.0
CA A:GLY202 4.4 15.2 1.0
O A:GLY202 4.4 16.1 1.0
CG B:LYS228 4.5 11.2 1.0
CD B:LYS228 4.6 14.2 1.0
NZ B:LYS228 4.6 20.1 1.0
N A:LEU203 4.6 15.4 1.0
O A:HOH479 4.7 20.3 1.0
C A:SER201 4.7 15.3 1.0
O A:HOH385 4.8 11.9 1.0
CD2 A:LEU203 4.8 12.7 1.0
CZ A:TYR213 5.0 11.1 1.0

Calcium binding site 5 out of 16 in 3ef2

Go back to Calcium Binding Sites List in 3ef2
Calcium binding site 5 out of 16 in the Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca308

b:58.2
occ:1.00
 C A:VAL15 3.7 9.6 1.0
N A:PRO16 3.8 10.0 1.0
O A:GLY14 3.9 9.9 1.0
N A:VAL15 3.9 9.0 1.0
CA A:VAL15 3.9 9.6 1.0
C A:GLY14 3.9 9.7 1.0
O A:ALA13 4.0 10.7 1.0
O A:VAL15 4.1 9.4 1.0
CD A:PRO16 4.1 10.5 1.0
CA A:PRO16 4.3 9.7 1.0
O A:ASN12 4.3 8.7 1.0
OE2 A:GLU11 4.3 12.9 0.5
C A:ALA13 4.4 10.3 1.0
CB A:PRO16 4.5 10.0 1.0
O A:HOH632 4.5 34.3 1.0
O A:HOH620 4.6 31.3 1.0
CA A:GLY14 4.7 9.7 1.0
N A:GLY14 4.7 9.9 1.0
CG A:PRO16 4.8 11.1 1.0

Calcium binding site 6 out of 16 in 3ef2

Go back to Calcium Binding Sites List in 3ef2
Calcium binding site 6 out of 16 in the Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:8.7
occ:1.00
 OD1 B:ASP214 2.3 9.3 1.0
OD2 B:ASP216 2.4 11.9 1.0
O B:HOH525 2.4 8.8 1.0
OD2 A:ASP183 2.4 7.5 1.0
OD2 B:ASP217 2.4 8.6 1.0
O B:GLN211 2.4 8.2 1.0
OD1 A:ASP183 2.5 8.1 1.0
OD1 B:ASP216 2.5 12.5 1.0
CG A:ASP183 2.8 9.2 1.0
CG B:ASP216 2.8 8.1 1.0
CG B:ASP217 3.3 8.7 1.0
CG B:ASP214 3.5 8.3 1.0
C B:GLN211 3.5 7.7 1.0
OD1 B:ASP217 3.6 10.0 1.0
CA A:CA305 3.8 10.7 1.0
OD2 B:ASP214 4.0 10.4 1.0
CA B:GLN211 4.1 8.3 1.0
O A:HOH406 4.1 21.4 1.0
N B:ASP214 4.3 8.5 1.0
CB A:ASP183 4.3 8.6 1.0
CB B:ASP216 4.4 8.5 1.0
CB A:ALA240 4.4 7.7 1.0
O B:HOH667 4.5 19.8 1.0
N B:ASP217 4.5 7.7 1.0
N B:ILE212 4.6 6.2 1.0
CB B:ASP217 4.6 7.7 1.0
CB B:ASP214 4.7 8.0 1.0
O A:LEU182 4.8 9.1 1.0
C B:ILE212 4.9 6.7 1.0
CA B:ASP214 4.9 8.1 1.0
O A:HOH326 4.9 9.3 1.0
N B:TYR213 4.9 7.3 1.0
CB B:GLN211 5.0 8.3 1.0

Calcium binding site 7 out of 16 in 3ef2

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Calcium binding site 7 out of 16 in the Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:55.7
occ:1.00
 O B:SER201 3.6 15.1 1.0
OH B:TYR213 4.1 12.9 1.0
O B:HOH632 4.1 13.1 1.0
C B:GLY202 4.2 14.7 1.0
OG B:SER206 4.2 23.3 1.0
O B:GLY202 4.3 14.8 1.0
CA B:GLY202 4.3 14.4 1.0
CE A:LYS228 4.4 18.0 1.0
CD A:LYS228 4.5 12.3 1.0
N B:LEU203 4.6 14.6 1.0
CG A:LYS228 4.7 11.5 1.0
O B:HOH678 4.7 22.8 1.0
C B:SER201 4.7 14.5 1.0
CD2 B:LEU203 4.7 12.8 1.0
O B:HOH573 4.8 12.5 1.0
CZ B:TYR213 5.0 11.5 1.0

Calcium binding site 8 out of 16 in 3ef2

Go back to Calcium Binding Sites List in 3ef2
Calcium binding site 8 out of 16 in the Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:57.7
occ:1.00
 C B:VAL15 3.6 9.7 1.0
N B:PRO16 3.6 10.2 1.0
CA B:VAL15 3.8 9.4 1.0
N B:VAL15 3.9 8.7 1.0
C B:GLY14 3.9 9.2 1.0
O B:GLY14 3.9 9.0 1.0
O B:VAL15 4.0 9.7 1.0
CD B:PRO16 4.0 10.6 1.0
O B:ALA13 4.0 10.4 1.0
CA B:PRO16 4.1 9.8 1.0
O B:ASN12 4.2 8.4 1.0
OE2 B:GLU11 4.2 10.8 0.5
CB B:PRO16 4.4 9.9 1.0
C B:ALA13 4.4 9.8 1.0
O B:HOH782 4.6 26.9 1.0
O B:HOH779 4.7 32.0 1.0
CA B:GLY14 4.7 9.3 1.0
N B:GLY14 4.7 9.2 1.0
CG B:PRO16 4.8 11.3 1.0

Calcium binding site 9 out of 16 in 3ef2

Go back to Calcium Binding Sites List in 3ef2
Calcium binding site 9 out of 16 in the Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:11.3
occ:1.00
 O D:LEU182 2.3 9.6 1.0
O C:HOH889 2.3 14.4 1.0
O C:HOH794 2.3 12.0 0.5
OD1 D:ASP183 2.3 9.8 1.0
OD1 C:ASP216 2.3 12.1 1.0
OD2 C:ASP214 2.4 10.9 1.0
CG C:ASP214 3.1 8.0 1.0
OD1 C:ASP214 3.1 9.1 1.0
CG D:ASP183 3.3 9.1 1.0
C D:LEU182 3.5 9.4 1.0
CG C:ASP216 3.6 8.3 1.0
CA C:CA304 3.8 9.2 1.0
CA D:ASP183 4.0 8.9 1.0
OD2 D:ASP183 4.1 8.9 1.0
N D:ASP183 4.2 9.4 1.0
CH3 C:ACT306 4.2 21.3 1.0
CB D:ASP183 4.2 8.9 1.0
OD2 C:ASP216 4.4 12.1 1.0
CB C:ASP216 4.5 7.9 1.0
CB C:ASP214 4.5 7.3 1.0
O C:HOH632 4.5 13.4 1.0
CA D:LEU182 4.6 8.9 1.0
O C:HOH848 4.7 28.2 1.0
N C:ASP216 4.8 7.2 1.0
CA C:GLN211 4.8 8.5 1.0
CB D:LEU182 4.8 9.5 1.0
O D:HOH555 4.8 27.8 1.0
OD3 C:OCS215 5.0 7.5 0.5

Calcium binding site 10 out of 16 in 3ef2

Go back to Calcium Binding Sites List in 3ef2
Calcium binding site 10 out of 16 in the Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of the Marasmius Oreades Mushroom Lectin (Moa) in Complex with Galalpha(1,3)[Fucalpha(1,2)]Gal and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca304

b:9.2
occ:1.00
 OD1 C:ASP214 2.3 9.1 1.0
OD2 C:ASP217 2.4 8.4 1.0
OD2 C:ASP216 2.4 12.1 1.0
OD2 D:ASP183 2.4 8.9 1.0
O C:GLN211 2.4 8.2 1.0
O C:HOH600 2.4 8.6 1.0
OD1 D:ASP183 2.4 9.8 1.0
OD1 C:ASP216 2.5 12.1 1.0
CG D:ASP183 2.8 9.1 1.0
CG C:ASP216 2.8 8.3 1.0
CG C:ASP217 3.3 8.5 1.0
CG C:ASP214 3.5 8.0 1.0
C C:GLN211 3.5 7.9 1.0
OD1 C:ASP217 3.6 8.9 1.0
CA C:CA303 3.8 11.3 1.0
OD2 C:ASP214 4.0 10.9 1.0
CA C:GLN211 4.1 8.5 1.0
O D:HOH420 4.1 20.1 1.0
N C:ASP214 4.3 7.7 1.0
CB D:ASP183 4.3 8.9 1.0
CB C:ASP216 4.4 7.9 1.0
CB D:ALA240 4.5 7.3 1.0
N C:ASP217 4.5 7.3 1.0
O C:HOH736 4.6 18.7 1.0
N C:ILE212 4.6 7.2 1.0
CB C:ASP217 4.6 7.3 1.0
CB C:ASP214 4.7 7.3 1.0
O D:LEU182 4.8 9.6 1.0
C C:ILE212 4.8 7.3 1.0
CA C:ASP214 4.9 7.6 1.0
O D:HOH321 4.9 8.6 1.0
N C:TYR213 4.9 7.4 1.0
CA C:ILE212 5.0 7.2 1.0
CB C:GLN211 5.0 8.9 1.0

Reference:

E.M.Grahn, H.C.Winter, H.Tateno, I.J.Goldstein, U.Krengel. Structural Characterization of A Lectin From the Mushroom Marasmius Oreades in Complex with the Blood Group B Trisaccharide and Calcium. J.Mol.Biol. V. 390 457 2009.
ISSN: ISSN 0022-2836
PubMed: 19426740
DOI: 10.1016/J.JMB.2009.04.074
Page generated: Sat Dec 12 04:10:05 2020

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