Calcium in PDB 4wqq: Structure of Epnh Mutant of Cel-I

The structure of Structure of Epnh Mutant of Cel-I, PDB code: 4wqq was solved by H.Unno, T.Hatakeyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.290, 61.060, 80.700, 90.00, 109.39, 90.00
R / Rfree (%)	15.2 / 19

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Structure of Epnh Mutant of Cel-I (pdb code 4wqq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Structure of Epnh Mutant of Cel-I, PDB code: 4wqq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Structure of Epnh Mutant of Cel-I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Epnh Mutant of Cel-I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:12.8 occ:1.00 O A:HOH388 2.3 12.0 1.0 O A:GLU109 2.4 13.0 1.0 OD1 A:ASP110 2.4 13.6 1.0 OD2 A:ASP77 2.5 13.1 1.0 OE2 A:GLU81 2.5 13.4 1.0 OD1 A:ASP77 2.5 13.2 1.0 OE1 A:GLU81 2.6 13.8 1.0 OD1 A:ASN104 2.6 16.5 1.0 CD A:GLU81 2.8 13.2 1.0 CG A:ASP77 2.9 14.1 1.0 C A:GLU109 3.3 13.1 1.0 CG A:ASN104 3.4 18.0 1.0 CG A:ASP110 3.5 12.6 1.0 CA A:ASP110 3.7 12.7 1.0 N A:ASP110 3.9 12.0 1.0 O A:HOH312 3.9 23.6 1.0 CA A:CA203 3.9 14.6 1.0 CB A:ASN104 4.0 17.4 1.0 CB A:ASP110 4.1 12.7 1.0 ND2 A:ASN104 4.3 19.8 1.0 CG A:GLU81 4.3 13.3 1.0 CZ A:PHE84 4.3 15.1 1.0 CB A:ASP77 4.4 13.8 1.0 CA A:GLU109 4.5 14.3 1.0 N A:GLU109 4.5 15.5 1.0 OD2 A:ASP110 4.5 13.7 1.0 CA A:ASN104 4.5 17.8 1.0 OD2 A:ASP124 4.6 14.2 1.0 O A:HOH356 4.6 22.1 1.0 O A:HOH428 4.7 20.9 1.0 N A:GLY82 4.7 13.4 1.0 O A:ASP77 4.7 13.3 1.0 O A:HOH327 4.8 12.2 1.0 CE1 A:PHE84 4.9 14.2 1.0 C A:ASP110 4.9 12.5 1.0 CA A:GLU81 5.0 12.7 1.0 CB A:GLU81 5.0 12.1 1.0

Calcium binding site 2 out of 12 in the Structure of Epnh Mutant of Cel-I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Epnh Mutant of Cel-I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:13.1 occ:1.00 OD1 A:ASP124 2.3 12.4 1.0 OD1 A:ASN123 2.4 10.9 1.0 OD1 A:ASN103 2.4 15.4 1.0 OE1 A:GLU109 2.4 13.2 1.0 O A:ASP124 2.5 10.8 1.0 OE1 A:GLU101 2.5 12.7 1.0 O3 A:MAN204 2.5 15.4 1.0 O4 A:MAN204 2.6 13.3 1.0 CG A:ASP124 3.4 12.9 1.0 C3 A:MAN204 3.4 15.3 1.0 CD A:GLU101 3.4 13.8 1.0 CD A:GLU109 3.4 15.2 1.0 CG A:ASN123 3.4 10.7 1.0 CG A:ASN103 3.4 17.6 1.0 C4 A:MAN204 3.4 16.3 1.0 C A:ASP124 3.5 12.2 1.0 OE2 A:GLU101 3.7 14.1 1.0 OE2 A:GLU109 3.7 14.1 1.0 N A:ASP124 3.8 11.5 1.0 ND2 A:ASN123 3.8 11.1 1.0 ND2 A:ASN103 3.9 17.3 1.0 CA A:ASP124 4.0 12.4 1.0 OD2 A:ASP124 4.1 14.2 1.0 N A:ASN103 4.2 17.4 1.0 CB A:ASP124 4.3 11.7 1.0 CB A:ASN103 4.6 17.9 1.0 CG A:GLU101 4.7 13.6 1.0 CG A:GLU109 4.7 14.4 1.0 CB A:ASN123 4.7 11.2 1.0 N A:ASN125 4.7 11.9 1.0 C A:ASN123 4.7 11.9 1.0 CB A:HIS105 4.7 19.6 1.0 C2 A:MAN204 4.7 19.6 1.0 N A:ASN104 4.7 17.0 1.0 N A:HIS105 4.8 15.1 1.0 CB A:GLU109 4.8 14.4 1.0 CA A:ASN103 4.8 17.1 1.0 C5 A:MAN204 4.8 19.1 1.0 CA A:ASN123 4.9 11.3 1.0 O2 A:MAN204 4.9 21.8 1.0

Calcium binding site 3 out of 12 in the Structure of Epnh Mutant of Cel-I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Epnh Mutant of Cel-I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:14.6 occ:1.00 O A:HOH327 2.3 12.2 1.0 OD1 A:ASP110 2.4 13.6 1.0 OE2 A:GLU81 2.4 13.4 1.0 O A:HOH312 2.5 23.6 1.0 OD2 A:ASP110 2.5 13.7 1.0 CG A:ASP110 2.8 12.6 1.0 CD A:GLU81 3.6 13.2 1.0 CA A:CA201 3.9 12.8 1.0 OD1 A:ASN104 4.2 16.5 1.0 CG A:GLU81 4.3 13.3 1.0 CB A:GLU81 4.3 12.1 1.0 CB A:ASP110 4.4 12.7 1.0 O A:HOH326 4.4 24.5 1.0 O A:ASP77 4.4 13.3 1.0 OE1 A:GLU81 4.6 13.8 1.0 O A:HOH461 4.7 28.3 1.0 OD1 A:ASP77 4.7 13.2 1.0 O A:ASN107 4.9 18.8 1.0 CA A:GLU81 5.0 12.7 1.0

Calcium binding site 4 out of 12 in the Structure of Epnh Mutant of Cel-I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Epnh Mutant of Cel-I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:12.7 occ:1.00 OD1 B:ASP110 2.4 11.7 1.0 O B:HOH368 2.4 12.3 1.0 O B:GLU109 2.4 14.8 1.0 OE2 B:GLU81 2.4 14.0 1.0 OD2 B:ASP77 2.5 12.4 1.0 OE1 B:GLU81 2.5 14.9 1.0 OD1 B:ASN104 2.6 15.9 1.0 OD1 B:ASP77 2.6 11.5 1.0 CD B:GLU81 2.8 14.4 1.0 CG B:ASP77 2.9 12.9 1.0 CG B:ASN104 3.4 14.8 1.0 C B:GLU109 3.4 12.8 1.0 CG B:ASP110 3.4 13.6 1.0 CA B:ASP110 3.7 12.3 1.0 O B:HOH404 3.8 19.9 1.0 CA B:CA203 3.9 22.7 1.0 CB B:ASN104 4.0 13.5 1.0 N B:ASP110 4.0 12.1 1.0 CB B:ASP110 4.1 12.1 1.0 ND2 B:ASN104 4.3 15.7 1.0 CG B:GLU81 4.3 13.6 1.0 CZ B:PHE84 4.3 11.9 1.0 CB B:ASP77 4.4 10.2 1.0 CA B:ASN104 4.4 13.9 1.0 OD2 B:ASP110 4.5 15.6 1.0 N B:GLU109 4.5 14.3 1.0 CA B:GLU109 4.5 12.5 1.0 N B:GLY82 4.6 12.5 1.0 OD2 B:ASP124 4.6 11.0 1.0 O B:HOH384 4.7 11.6 1.0 CE1 B:PHE84 4.7 11.1 1.0 O B:HOH386 4.7 13.2 1.0 CA B:GLU81 4.9 12.4 1.0 O B:HOH366 4.9 14.0 1.0 O B:ASP77 4.9 11.2 1.0 C B:ASP110 5.0 12.4 1.0

Calcium binding site 5 out of 12 in the Structure of Epnh Mutant of Cel-I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Epnh Mutant of Cel-I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:13.4 occ:1.00 OD1 B:ASP124 2.4 10.2 1.0 OD1 B:ASN103 2.4 14.8 1.0 OD1 B:ASN123 2.4 14.0 1.0 OE1 B:GLU109 2.5 12.7 1.0 O B:ASP124 2.5 13.2 1.0 O4 B:MAN204 2.5 15.8 1.0 OE1 B:GLU101 2.5 13.5 1.0 O3 B:MAN204 2.7 14.7 1.0 C4 B:MAN204 3.4 21.0 1.0 CG B:ASP124 3.4 11.1 1.0 C3 B:MAN204 3.4 19.4 1.0 CG B:ASN103 3.4 13.8 1.0 CD B:GLU109 3.4 13.3 1.0 CD B:GLU101 3.4 15.8 1.0 CG B:ASN123 3.4 13.9 1.0 C B:ASP124 3.6 12.9 1.0 OE2 B:GLU101 3.7 16.4 1.0 OE2 B:GLU109 3.8 13.7 1.0 N B:ASP124 3.8 12.8 1.0 ND2 B:ASN123 3.8 16.2 1.0 ND2 B:ASN103 3.9 15.4 1.0 CA B:ASP124 4.1 11.6 1.0 OD2 B:ASP124 4.1 11.0 1.0 N B:ASN103 4.2 12.2 1.0 CB B:ASP124 4.3 12.2 1.0 CB B:ASN103 4.6 14.1 1.0 CG B:GLU109 4.6 12.8 1.0 CG B:GLU101 4.7 15.0 1.0 CB B:GLU109 4.7 13.5 1.0 N B:ASN125 4.7 12.1 1.0 C B:ASN123 4.7 13.4 1.0 C5 B:MAN204 4.7 26.4 1.0 N B:ASN104 4.7 14.0 1.0 CB B:ASN123 4.7 13.4 1.0 CA B:ASN103 4.8 13.2 1.0 C2 B:MAN204 4.8 23.3 1.0 CB B:HIS105 4.8 17.3 1.0 N B:HIS105 4.9 13.9 1.0 CA B:ASN123 4.9 13.3 1.0

Calcium binding site 6 out of 12 in the Structure of Epnh Mutant of Cel-I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Epnh Mutant of Cel-I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:22.7 occ:1.00 O B:HOH396 2.2 29.3 1.0 O B:HOH384 2.3 11.6 1.0 O B:HOH426 2.3 21.8 1.0 O B:HOH404 2.3 19.9 1.0 OE2 B:GLU81 2.5 14.0 1.0 OD1 B:ASP110 2.5 11.7 1.0 OD2 B:ASP110 2.6 15.6 1.0 CG B:ASP110 2.9 13.6 1.0 CD B:GLU81 3.6 14.4 1.0 CA B:CA201 3.9 12.7 1.0 OD1 B:ASN104 4.3 15.9 1.0 CB B:GLU81 4.3 12.9 1.0 CG B:GLU81 4.4 13.6 1.0 CB B:ASP110 4.4 12.1 1.0 OE1 B:GLU81 4.6 14.9 1.0 O B:ASP77 4.6 11.2 1.0 OD1 B:ASN107 4.7 37.3 1.0 OD1 B:ASP77 4.7 11.5 1.0 O B:HOH464 4.8 23.2 1.0 CA B:GLU81 4.8 12.4 1.0 O B:LYS78 4.9 13.0 1.0 O B:ASN107 5.0 22.3 1.0

Calcium binding site 7 out of 12 in the Structure of Epnh Mutant of Cel-I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Epnh Mutant of Cel-I within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:13.3 occ:1.00 OE2 C:GLU81 2.3 14.3 1.0 OD1 C:ASP110 2.3 13.9 1.0 O C:HOH375 2.4 14.1 1.0 O C:GLU109 2.4 12.1 1.0 OD2 C:ASP77 2.6 12.7 1.0 OE1 C:GLU81 2.6 12.4 1.0 OD1 C:ASN104 2.6 14.8 1.0 OD1 C:ASP77 2.7 13.9 1.0 CD C:GLU81 2.8 14.3 1.0 CG C:ASP77 3.0 11.6 1.0 CG C:ASP110 3.4 13.8 1.0 CG C:ASN104 3.4 17.1 1.0 C C:GLU109 3.4 12.1 1.0 CA C:ASP110 3.7 12.2 1.0 O C:HOH305 3.9 25.8 1.0 CA C:CA203 4.0 13.5 1.0 N C:ASP110 4.0 12.1 1.0 CB C:ASN104 4.1 17.6 1.0 CB C:ASP110 4.1 13.1 1.0 CG C:GLU81 4.3 13.9 1.0 ND2 C:ASN104 4.3 20.8 1.0 OD2 C:ASP110 4.4 14.2 1.0 CZ C:PHE84 4.5 12.3 1.0 CB C:ASP77 4.5 11.6 1.0 N C:GLU109 4.5 13.7 1.0 CA C:ASN104 4.6 17.6 1.0 CA C:GLU109 4.6 13.6 1.0 N C:GLY82 4.6 11.9 1.0 OD2 C:ASP124 4.6 13.0 1.0 O C:HOH387 4.7 16.3 1.0 O C:HOH381 4.7 17.6 1.0 O C:ASP77 4.8 12.1 1.0 O C:HOH330 4.8 33.0 1.0 O C:HOH312 4.8 12.4 1.0 CA C:GLU81 4.9 11.6 1.0 C C:ASP110 4.9 13.6 1.0 CB C:GLU81 5.0 12.8 1.0

Calcium binding site 8 out of 12 in the Structure of Epnh Mutant of Cel-I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Epnh Mutant of Cel-I within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:15.8 occ:1.00 OD1 C:ASP124 2.4 14.9 1.0 OD1 C:ASN123 2.4 14.1 1.0 O3 C:MAN204 2.5 17.8 1.0 OE1 C:GLU109 2.5 15.7 1.0 O C:ASP124 2.5 12.7 1.0 OD1 C:ASN103 2.5 17.1 1.0 O4 C:MAN204 2.5 17.5 1.0 OE1 C:GLU101 2.6 17.5 1.0 C4 C:MAN204 3.3 20.8 1.0 C3 C:MAN204 3.4 20.7 1.0 CD C:GLU109 3.4 14.2 1.0 CD C:GLU101 3.4 18.7 1.0 CG C:ASP124 3.4 15.7 1.0 CG C:ASN103 3.4 18.7 1.0 CG C:ASN123 3.5 14.8 1.0 C C:ASP124 3.5 13.9 1.0 OE2 C:GLU101 3.7 21.0 1.0 OE2 C:GLU109 3.7 15.0 1.0 N C:ASP124 3.8 13.8 1.0 ND2 C:ASN123 3.9 15.5 1.0 ND2 C:ASN103 3.9 19.1 1.0 CA C:ASP124 4.0 13.5 1.0 OD2 C:ASP124 4.2 13.0 1.0 N C:ASN103 4.2 19.2 1.0 CB C:ASP124 4.3 13.4 1.0 CB C:ASN103 4.6 19.1 1.0 CG C:GLU101 4.6 18.1 1.0 N C:ASN125 4.7 12.7 1.0 CG C:GLU109 4.7 15.2 1.0 N C:ASN104 4.7 18.9 1.0 C C:ASN123 4.7 13.5 1.0 C5 C:MAN204 4.7 23.6 1.0 CB C:ASN123 4.8 15.5 1.0 C2 C:MAN204 4.8 22.8 1.0 CB C:HIS105 4.8 22.7 1.0 CA C:ASN103 4.8 19.2 1.0 CB C:GLU109 4.8 14.7 1.0 N C:HIS105 4.8 19.1 1.0 CA C:ASN123 4.9 13.8 1.0

Calcium binding site 9 out of 12 in the Structure of Epnh Mutant of Cel-I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Epnh Mutant of Cel-I within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:13.5 occ:1.00 O C:HOH330 2.3 33.0 1.0 O C:HOH312 2.3 12.4 1.0 OE2 C:GLU81 2.4 14.3 1.0 OD2 C:ASP110 2.5 14.2 1.0 OD1 C:ASP110 2.5 13.9 1.0 O C:HOH305 2.5 25.8 1.0 CG C:ASP110 2.9 13.8 1.0 CD C:GLU81 3.6 14.3 1.0 CA C:CA201 4.0 13.3 1.0 O C:HOH337 4.1 39.8 1.0 CG C:GLU81 4.2 13.9 1.0 CB C:GLU81 4.3 12.8 1.0 OD1 C:ASN104 4.4 14.8 1.0 CB C:ASP110 4.4 13.1 1.0 O C:ASP77 4.4 12.1 1.0 O C:HOH315 4.4 16.5 1.0 OE1 C:GLU81 4.6 12.4 1.0 O C:HOH327 4.6 26.1 1.0 O C:HOH481 4.7 33.8 1.0 OD1 C:ASP77 4.8 13.9 1.0 O C:ASN107 4.8 17.7 1.0 CA C:GLU81 4.9 11.6 1.0

Calcium binding site 10 out of 12 in the Structure of Epnh Mutant of Cel-I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Epnh Mutant of Cel-I within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:11.4 occ:1.00 OD1 D:ASP110 2.4 11.3 1.0 O D:HOH355 2.4 10.6 1.0 OE1 D:GLU81 2.4 11.5 1.0 O D:GLU109 2.4 12.0 1.0 OE2 D:GLU81 2.5 11.2 1.0 OD2 D:ASP77 2.5 11.2 1.0 OD1 D:ASP77 2.6 11.4 1.0 OD1 D:ASN104 2.6 11.8 1.0 CD D:GLU81 2.8 10.3 1.0 CG D:ASP77 2.9 10.8 1.0 C D:GLU109 3.4 11.7 1.0 CG D:ASN104 3.4 13.1 1.0 CG D:ASP110 3.5 10.9 1.0 CA D:ASP110 3.8 10.2 1.0 O D:HOH419 3.9 20.4 1.0 CA D:CA203 4.0 14.7 1.0 N D:ASP110 4.0 10.8 1.0 CB D:ASN104 4.1 11.9 1.0 CB D:ASP110 4.1 10.8 1.0 ND2 D:ASN104 4.2 15.9 1.0 CZ D:PHE84 4.2 11.2 1.0 CG D:GLU81 4.3 10.6 1.0 CB D:ASP77 4.4 9.9 1.0 OD2 D:ASP110 4.4 14.5 1.0 CA D:GLU109 4.5 11.8 1.0 N D:GLU109 4.5 13.9 1.0 CA D:ASN104 4.5 11.8 1.0 OD2 D:ASP124 4.6 11.6 1.0 CE2 D:PHE84 4.6 9.5 1.0 O D:HOH362 4.7 12.9 1.0 N D:GLY82 4.7 11.5 1.0 O D:HOH384 4.8 14.6 1.0 O D:HOH357 4.8 14.3 1.0 CA D:GLU81 4.9 10.5 1.0 O D:ASP77 4.9 10.8 1.0 C D:ASP110 5.0 11.2 1.0 CB D:GLU81 5.0 11.2 1.0

H.Moriuchi, H.Unno, S.Goda, H.Tateno, J.Hirabayashi, T.Hatakeyama. Mannose-Recognition Mutant of the Galactose/N-Acetylgalactosamine-Specific C-Type Lectin Cel-I Engineered By Site-Directed Mutagenesis. Biochim.Biophys.Acta V.1850 1457 2015.
ISSN: ISSN 0006-3002
PubMed: 25869490
DOI: 10.1016/J.BBAGEN.2015.04.004