Calcium in PDB 3a9q: Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4

All present enzymatic activity of Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4:
1.16.3.1;

The structure of Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4, PDB code: 3a9q was solved by T.Masuda, F.Goto, T.Yoshihara, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.67 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	223.503, 221.816, 122.725, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 18.5

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 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4 (pdb code 3a9q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 130 binding sites of Calcium where determined in the Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4, PDB code: 3a9q:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 130 in the Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca213 b:20.8 occ:1.00 O A:HOH369 2.5 12.0 1.0 O A:HOH1325 2.5 12.9 1.0 O A:HOH1324 2.6 19.0 1.0 O A:HOH1327 2.6 24.4 1.0 O A:HOH2703 2.6 33.4 1.0 O A:HOH2704 2.6 32.4 1.0 O A:HOH1326 2.7 33.1 1.0 NH1 A:ARG38 4.3 9.3 1.0 OE1 A:GLU46 4.3 14.5 1.0 O A:HOH3030 4.4 30.6 1.0 OE2 A:GLU46 4.4 13.4 1.0 O A:HOH413 4.6 17.9 1.0 OXT A:ACY217 4.7 36.0 1.0 CD A:LYS108 4.7 13.1 1.0 CD A:GLU46 4.8 19.0 1.0 O A:HOH3032 4.9 33.5 1.0 OD1 A:ASP43 4.9 13.7 1.0 NZ A:LYS108 5.0 21.7 1.0

Calcium binding site 2 out of 130 in the Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca214 b:17.7 occ:1.00 OE1 A:GLU56 2.4 15.0 1.0 OE2 A:GLU91 2.4 26.1 1.0 O A:HOH437 2.5 18.9 1.0 O A:HOH1328 2.5 17.8 1.0 O A:HOH438 2.6 18.2 1.0 ND1 A:HIS94 2.7 19.4 1.0 OE1 A:GLU91 2.8 25.5 1.0 CD A:GLU91 2.9 28.5 1.0 CE1 A:HIS94 3.4 41.9 1.0 CD A:GLU56 3.4 22.4 1.0 OE2 A:GLU56 3.8 16.4 1.0 CG A:HIS94 3.8 20.0 1.0 CG2 A:THR143 4.0 15.4 1.0 CB A:HIS94 4.2 10.3 1.0 OE1 A:GLN174 4.2 31.0 1.0 CG A:GLU91 4.4 15.4 1.0 OE1 A:GLU140 4.5 19.6 1.0 O A:HOH1426 4.5 25.2 1.0 O A:HOH439 4.6 15.8 1.0 NE2 A:HIS94 4.6 22.8 1.0 CG A:GLU56 4.7 14.0 1.0 CD2 A:HIS94 4.8 19.5 1.0 OE2 A:GLU140 4.8 21.5 1.0 CA A:GLU91 4.9 11.7 1.0 CB A:THR143 4.9 12.7 1.0 CB A:GLU91 4.9 13.0 1.0 CB A:GLU56 5.0 7.2 1.0

Calcium binding site 3 out of 130 in the Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca215 b:49.4 occ:1.00 O A:HOH2552 2.7 35.8 1.0 O A:HOH1359 4.5 33.8 1.0 O A:ASN157 4.8 18.9 1.0 CA A:GLY158 4.8 8.4 1.0

Calcium binding site 4 out of 130 in the Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca216 b:28.3 occ:0.50 CA A:CA216 0.0 28.3 0.5 CA A:CA216 2.2 54.1 0.5 OE2 A:GLU96 2.6 18.7 1.0 OE2 A:GLU93 2.8 67.0 1.0 OE1 A:GLU93 2.9 39.2 1.0 CD A:GLU93 3.2 86.5 1.0 CD A:GLU96 3.7 33.2 1.0 OE1 A:GLU96 4.0 19.8 1.0 OE1 G:GLU89 4.2 51.7 1.0 O A:HOH1391 4.4 26.5 1.0 CE G:LYS85 4.6 29.8 1.0 O A:HOH1390 4.6 52.4 1.0 CG A:GLU93 4.7 28.5 1.0 NH1 A:ARG92 4.9 27.4 1.0 CG A:GLU96 5.0 12.5 1.0 CD G:GLU89 5.0 84.3 1.0 NZ G:LYS85 5.0 27.1 1.0

Calcium binding site 5 out of 130 in the Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca216 b:54.1 occ:0.50 CA A:CA216 0.0 54.1 0.5 CA A:CA216 2.2 28.3 0.5 OE1 A:GLU93 2.9 39.2 1.0 O A:HOH1390 3.2 52.4 1.0 OE2 A:GLU96 3.2 18.7 1.0 CD A:GLU93 3.8 86.5 1.0 OE2 A:GLU93 4.1 67.0 1.0 NZ G:LYS85 4.4 27.1 1.0 CD A:GLU96 4.4 33.2 1.0 CE G:LYS85 4.6 29.8 1.0 OE1 A:GLU100 4.8 34.5 1.0

Calcium binding site 6 out of 130 in the Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca213 b:15.0 occ:1.00 OE1 B:GLU56 2.4 11.2 1.0 O B:HOH444 2.4 13.9 1.0 O B:HOH445 2.5 13.5 1.0 OE2 B:GLU91 2.5 23.7 1.0 ND1 B:HIS94 2.6 21.6 1.0 O B:HOH446 2.6 18.9 1.0 OE1 B:GLU91 2.8 24.8 1.0 CD B:GLU91 3.0 29.1 1.0 CD B:GLU56 3.4 26.6 1.0 CE1 B:HIS94 3.4 22.2 1.0 CG B:HIS94 3.7 16.4 1.0 OE2 B:GLU56 3.8 15.2 1.0 CB B:HIS94 4.0 11.4 1.0 OE1 B:GLN174 4.1 27.4 1.0 CG2 B:THR143 4.3 20.6 1.0 O B:HOH1541 4.4 30.8 1.0 CG B:GLU91 4.4 15.2 1.0 O B:HOH447 4.5 16.2 1.0 OE2 B:GLU140 4.5 24.6 1.0 NE2 B:HIS94 4.6 25.4 1.0 CG B:GLU56 4.7 11.2 1.0 CD2 B:HIS94 4.8 20.1 1.0 CA B:GLU91 4.9 12.4 1.0 CB B:GLU91 4.9 7.5 1.0 CB B:GLU56 5.0 8.6 1.0

Calcium binding site 7 out of 130 in the Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca214 b:52.1 occ:1.00 O B:HOH449 2.6 24.0 1.0 O E:HOH2766 2.6 29.7 1.0 OE1 E:GLU167 2.6 22.9 1.0 O E:HOH1899 2.8 17.3 1.0 OE2 B:GLU167 2.9 22.6 1.0 O V:HOH1313 2.9 33.6 1.0 OE2 E:GLU167 3.0 19.4 1.0 CD E:GLU167 3.1 25.9 1.0 OE1 B:GLU167 3.3 20.3 1.0 CD B:GLU167 3.5 36.0 1.0 CA E:CA213 3.6 28.2 1.0 O B:HOH1554 4.4 16.2 1.0 CA E:ASP164 4.4 10.2 1.0 O V:HOH2657 4.5 32.0 1.0 OD1 E:ASP164 4.6 21.8 1.0 OE1 V:GLU167 4.6 22.7 1.0 CB E:ASP164 4.6 12.6 1.0 N E:ASP164 4.6 7.8 1.0 CG E:GLU167 4.6 10.8 1.0 OD1 V:ASP164 4.7 21.8 1.0 O V:HOH2655 4.7 22.3 1.0 C E:ALA163 4.9 14.7 1.0 CG B:GLU167 4.9 49.7 1.0 CB E:ALA163 5.0 11.2 1.0

Calcium binding site 8 out of 130 in the Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca215 b:25.0 occ:1.00 O B:HOH984 2.5 14.2 1.0 O B:HOH1332 2.6 21.0 1.0 O B:HOH1330 2.6 33.5 1.0 O B:HOH1331 2.7 35.9 1.0 O B:HOH1329 2.7 23.2 1.0 O B:HOH3086 2.8 37.6 1.0 NH1 B:ARG38 4.2 13.7 1.0 O B:HOH792 4.4 14.8 1.0 OE1 B:GLU46 4.4 18.3 1.0 OE2 B:GLU46 4.5 13.8 1.0 O B:HOH1333 4.6 33.7 1.0 CD B:LYS108 4.6 20.6 1.0 CD B:GLU46 4.9 20.1 1.0 NZ B:LYS108 4.9 21.3 1.0

Calcium binding site 9 out of 130 in the Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca216 b:54.1 occ:1.00 O B:HOH3100 2.6 31.4 1.0 O B:HOH3099 2.8 21.8 1.0 O I:HOH1632 4.2 22.7 1.0 O I:HOH1637 4.3 24.7 1.0 OE2 B:GLU183 4.4 14.2 1.0 OE1 B:GLU183 4.5 13.4 1.0 NZ B:LYS179 4.6 9.4 1.0 O B:HOH1631 4.7 19.3 1.0 O I:HOH1633 4.8 13.8 1.0 CD B:GLU183 4.9 16.7 1.0

Calcium binding site 10 out of 130 in the Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure Analysis of E173A Variant of the Soybean Ferritin SFER4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca217 b:20.4 occ:0.50 OE2 B:GLU96 2.6 26.2 1.0 CA B:CA218 2.9 53.1 0.5 OE2 B:GLU93 2.9 43.6 1.0 OE1 B:GLU93 2.9 59.9 1.0 CD B:GLU93 3.3 62.6 1.0 CD B:GLU96 3.6 33.1 1.0 OE1 B:GLU96 4.0 16.5 1.0 O B:HOH2772 4.3 26.9 1.0 CE F:LYS85 4.4 30.8 1.0 OE2 F:GLU89 4.7 68.1 1.0 NH1 B:ARG92 4.7 26.1 1.0 CG B:GLU93 4.8 21.3 1.0 NZ F:LYS85 4.9 27.6 1.0 CG B:GLU96 4.9 14.7 1.0

T.Masuda, F.Goto, T.Yoshihara, B.Mikami. Crystal Structure of Plant Ferritin Reveals A Novel Metal Binding Site That Functions As A Transit Site For Metal Transfer in Ferritin J.Biol.Chem. V. 285 4049 2010.
ISSN: ISSN 0021-9258
PubMed: 20007325
DOI: 10.1074/JBC.M109.059790