Iron in PDB 3v83: The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin

The structure of The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin, PDB code: 3v83 was solved by N.Noinaj, A.Steere, A.B.Mason, S.K.Buchanan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.95 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	254.531, 173.004, 150.151, 90.00, 123.26, 90.00
R / Rfree (%)	18 / 23

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

Binding sites:

The binding sites of Iron atom in the The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin (pdb code 3v83). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin, PDB code: 3v83:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:19.5 occ:1.00 OH A:TYR95 2.1 17.0 1.0 OH A:TYR188 2.2 18.4 1.0 OD1 A:ASP63 2.2 19.0 1.0 O1 A:BCT701 2.3 16.0 1.0 O2 A:BCT701 2.3 19.8 1.0 NE2 A:HIS249 2.4 14.1 1.0 C A:BCT701 2.6 14.2 1.0 CD2 A:HIS249 3.1 13.6 1.0 CZ A:TYR95 3.2 20.7 1.0 CG A:ASP63 3.2 16.5 1.0 CZ A:TYR188 3.3 19.1 1.0 CE1 A:HIS249 3.5 19.3 1.0 CB A:ASP63 3.7 18.1 1.0 CE1 A:TYR95 3.7 20.1 1.0 O A:HOH801 3.8 13.5 1.0 CE1 A:TYR188 3.9 13.2 1.0 O3 A:BCT701 4.0 14.4 1.0 CE2 A:TYR188 4.2 17.9 1.0 CE2 A:TYR95 4.2 14.9 1.0 NZ A:LYS296 4.3 19.9 1.0 OD2 A:ASP63 4.3 19.4 1.0 NH1 A:ARG124 4.4 19.0 1.0 CG A:HIS249 4.4 14.2 1.0 CA A:ASP63 4.4 15.2 1.0 CB A:SER125 4.4 19.9 1.0 ND1 A:HIS249 4.5 17.6 1.0 N A:SER125 4.7 17.9 1.0 N A:ALA126 4.7 16.4 1.0 NE A:ARG124 4.7 19.0 1.0 OG A:SER125 4.8 19.1 1.0

Iron binding site 2 out of 12 in the The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe704 b:34.2 occ:1.00 OH A:TYR426 2.2 34.4 1.0 OH A:TYR517 2.3 36.4 1.0 OD1 A:ASP392 2.3 31.4 1.0 O2 A:BCT702 2.4 34.7 1.0 NE2 A:HIS585 2.4 31.5 1.0 O1 A:BCT702 2.4 28.9 1.0 C A:BCT702 2.7 31.1 1.0 CZ A:TYR426 3.3 43.6 1.0 CZ A:TYR517 3.3 33.7 1.0 CD2 A:HIS585 3.3 31.8 1.0 CE1 A:HIS585 3.3 33.1 1.0 CG A:ASP392 3.4 30.2 1.0 CE1 A:TYR517 3.7 36.5 1.0 CE2 A:TYR426 3.8 41.9 1.0 CB A:ASP392 3.9 34.0 1.0 O A:HOH1040 3.9 40.4 1.0 O3 A:BCT702 4.1 38.6 1.0 CE1 A:TYR426 4.3 47.0 1.0 CE2 A:TYR517 4.3 33.4 1.0 OD2 A:ASP392 4.4 37.1 1.0 ND1 A:HIS585 4.4 30.4 1.0 NH1 A:ARG632 4.4 36.6 1.0 CG A:HIS585 4.4 31.0 1.0 NH2 A:ARG456 4.5 33.5 1.0 CB A:THR457 4.6 34.5 1.0 CA A:ASP392 4.7 34.1 1.0 NE A:ARG456 4.7 29.8 1.0 N A:ALA458 4.7 43.3 1.0 N A:THR457 4.8 37.6 1.0 OG1 A:THR457 4.9 33.4 1.0

Iron binding site 3 out of 12 in the The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe703 b:29.1 occ:1.00 OH B:TYR517 2.2 27.4 1.0 OH B:TYR426 2.2 33.2 1.0 OD1 B:ASP392 2.3 27.6 1.0 O1 B:BCT702 2.3 27.7 1.0 NE2 B:HIS585 2.4 31.5 1.0 O2 B:BCT702 2.4 31.6 1.0 C B:BCT702 2.7 28.9 1.0 CZ B:TYR517 3.2 28.0 1.0 CZ B:TYR426 3.3 33.3 1.0 CD2 B:HIS585 3.3 19.9 1.0 CE1 B:HIS585 3.3 31.2 1.0 CG B:ASP392 3.3 29.7 1.0 CB B:ASP392 3.8 23.8 1.0 CE2 B:TYR426 3.8 30.9 1.0 CE1 B:TYR517 3.8 30.0 1.0 O B:HOH1063 3.9 28.4 1.0 O3 B:BCT702 4.0 27.7 1.0 CE2 B:TYR517 4.2 26.5 1.0 CE1 B:TYR426 4.3 28.5 1.0 NH2 B:ARG456 4.3 27.2 1.0 NH1 B:ARG632 4.4 40.6 1.0 OD2 B:ASP392 4.4 39.3 1.0 ND1 B:HIS585 4.4 32.5 1.0 CG B:HIS585 4.5 33.1 1.0 CB B:THR457 4.5 24.9 1.0 CA B:ASP392 4.6 23.1 1.0 N B:ALA458 4.7 26.4 1.0 N B:THR457 4.7 27.5 1.0 NE B:ARG456 4.8 32.2 1.0 OG1 B:THR457 4.8 30.4 1.0 N B:GLY393 5.0 23.8 1.0

Iron binding site 4 out of 12 in the The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe704 b:15.9 occ:1.00 OH B:TYR95 2.1 12.6 1.0 O2 B:BCT701 2.2 16.1 1.0 O1 B:BCT701 2.2 13.3 1.0 OH B:TYR188 2.3 13.7 1.0 OD1 B:ASP63 2.3 16.2 1.0 NE2 B:HIS249 2.3 14.5 1.0 C B:BCT701 2.5 14.1 1.0 CZ B:TYR95 3.1 18.0 1.0 CD2 B:HIS249 3.2 13.9 1.0 CZ B:TYR188 3.3 11.9 1.0 CG B:ASP63 3.4 15.2 1.0 CE1 B:HIS249 3.4 20.1 1.0 CE1 B:TYR95 3.7 17.3 1.0 O B:HOH801 3.8 14.8 1.0 CB B:ASP63 3.9 12.4 1.0 O3 B:BCT701 3.9 15.2 1.0 CE1 B:TYR188 4.0 12.0 1.0 CE2 B:TYR95 4.1 12.9 1.0 CE2 B:TYR188 4.1 14.3 1.0 NZ B:LYS296 4.3 16.9 1.0 CB B:SER125 4.3 13.4 1.0 NH1 B:ARG124 4.4 11.7 1.0 CG B:HIS249 4.4 14.3 1.0 OD2 B:ASP63 4.4 18.1 1.0 ND1 B:HIS249 4.4 18.6 1.0 CA B:ASP63 4.4 12.5 1.0 N B:SER125 4.7 17.5 1.0 NE B:ARG124 4.7 15.1 1.0 OG B:SER125 4.7 17.4 1.0 N B:ALA126 4.7 13.1 1.0 CD1 B:TYR95 5.0 18.8 1.0

Iron binding site 5 out of 12 in the The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe703 b:38.9 occ:1.00 O2 C:BCT702 2.4 32.5 1.0 OH C:TYR426 2.4 64.4 1.0 OH C:TYR517 2.4 59.3 1.0 NE2 C:HIS585 2.4 58.2 1.0 O1 C:BCT702 2.5 44.7 1.0 C C:BCT702 2.8 38.7 1.0 CE1 C:HIS585 3.0 60.5 1.0 OD2 C:ASP392 3.0 83.3 1.0 CZ C:TYR517 3.2 58.5 1.0 CG C:ASP392 3.3 73.5 1.0 CE1 C:TYR517 3.3 60.4 1.0 CZ C:TYR426 3.4 67.9 1.0 CD2 C:HIS585 3.7 58.6 1.0 OD1 C:ASP392 3.7 70.3 1.0 CE2 C:TYR426 3.8 68.3 1.0 CB C:ASP392 3.9 64.2 1.0 NH2 C:ARG456 4.0 52.6 1.0 O3 C:BCT702 4.1 36.6 1.0 ND1 C:HIS585 4.2 53.4 1.0 CE2 C:TYR517 4.3 56.0 1.0 NE C:ARG456 4.3 61.0 1.0 NH1 C:ARG632 4.4 59.1 1.0 N C:ALA458 4.6 76.0 1.0 CE1 C:TYR426 4.6 66.6 1.0 O C:HOH904 4.6 42.6 1.0 CG C:HIS585 4.6 63.2 1.0 CB C:THR457 4.6 84.1 1.0 CD1 C:TYR517 4.6 67.3 1.0 CZ C:ARG456 4.6 62.1 1.0 N C:THR457 4.7 78.8 1.0 CA C:ASP392 4.9 55.3 1.0 OG1 C:THR457 4.9 68.1 1.0 CB C:ALA458 4.9 78.8 1.0

Iron binding site 6 out of 12 in the The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe704 b:16.5 occ:1.00 OH C:TYR95 2.1 16.6 1.0 OH C:TYR188 2.2 13.7 1.0 O2 C:BCT701 2.3 16.0 1.0 O1 C:BCT701 2.3 18.0 1.0 OD1 C:ASP63 2.3 15.6 1.0 NE2 C:HIS249 2.3 13.5 1.0 C C:BCT701 2.6 15.2 1.0 CZ C:TYR95 3.1 14.8 1.0 CD2 C:HIS249 3.2 11.3 1.0 CZ C:TYR188 3.2 19.8 1.0 CG C:ASP63 3.3 17.5 1.0 CE1 C:HIS249 3.4 14.9 1.0 CE1 C:TYR95 3.6 21.0 1.0 CB C:ASP63 3.7 17.8 1.0 O C:HOH806 3.8 14.3 1.0 CE1 C:TYR188 3.9 15.9 1.0 O3 C:BCT701 3.9 14.2 1.0 CE2 C:TYR188 4.1 12.5 1.0 CE2 C:TYR95 4.2 12.6 1.0 NZ C:LYS296 4.3 21.5 1.0 CA C:ASP63 4.4 19.1 1.0 CG C:HIS249 4.4 13.5 1.0 NH1 C:ARG124 4.4 17.4 1.0 CB C:SER125 4.4 14.5 1.0 OD2 C:ASP63 4.5 20.6 1.0 ND1 C:HIS249 4.5 12.5 1.0 N C:SER125 4.6 15.6 1.0 N C:ALA126 4.7 11.1 1.0 NE C:ARG124 4.7 17.1 1.0 OG C:SER125 4.8 16.5 1.0 CD1 C:TYR95 4.9 16.5 1.0

Iron binding site 7 out of 12 in the The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe703 b:26.4 occ:1.00 OH D:TYR517 2.1 24.1 1.0 O2 D:BCT702 2.3 29.7 1.0 OH D:TYR426 2.3 27.2 1.0 NE2 D:HIS585 2.3 25.3 1.0 OD1 D:ASP392 2.3 21.8 1.0 O1 D:BCT702 2.4 32.4 1.0 C D:BCT702 2.7 26.9 1.0 CZ D:TYR517 3.2 24.4 1.0 CD2 D:HIS585 3.2 22.5 1.0 CZ D:TYR426 3.3 26.0 1.0 CE1 D:HIS585 3.3 21.9 1.0 CG D:ASP392 3.4 26.2 1.0 CE2 D:TYR426 3.7 27.5 1.0 O D:HOH809 3.8 24.2 1.0 CE1 D:TYR517 3.8 23.0 1.0 CB D:ASP392 4.0 23.4 1.0 O3 D:BCT702 4.1 23.9 1.0 CE2 D:TYR517 4.2 21.7 1.0 CE1 D:TYR426 4.3 24.1 1.0 NH1 D:ARG632 4.4 29.8 1.0 NH2 D:ARG456 4.4 23.6 1.0 CG D:HIS585 4.4 23.4 1.0 ND1 D:HIS585 4.4 26.9 1.0 OD2 D:ASP392 4.5 35.1 1.0 CB D:THR457 4.5 28.4 1.0 CA D:ASP392 4.6 21.4 1.0 NE D:ARG456 4.8 21.5 1.0 OG1 D:THR457 4.8 27.1 1.0 N D:ALA458 4.8 27.9 1.0 N D:THR457 4.8 31.8 1.0

Iron binding site 8 out of 12 in the The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe704 b:20.2 occ:1.00 OH D:TYR95 2.1 17.6 1.0 OH D:TYR188 2.2 18.1 1.0 OD1 D:ASP63 2.2 15.3 1.0 O1 D:BCT701 2.3 24.1 1.0 NE2 D:HIS249 2.3 20.7 1.0 O2 D:BCT701 2.3 17.6 1.0 C D:BCT701 2.7 15.9 1.0 CZ D:TYR95 3.1 18.7 1.0 CD2 D:HIS249 3.2 14.0 1.0 CZ D:TYR188 3.3 19.2 1.0 CG D:ASP63 3.3 13.2 1.0 CE1 D:HIS249 3.3 18.7 1.0 CE1 D:TYR95 3.7 17.8 1.0 O D:HOH801 3.8 15.9 1.0 CB D:ASP63 3.8 14.9 1.0 CE1 D:TYR188 4.0 14.2 1.0 O3 D:BCT701 4.0 21.1 1.0 CE2 D:TYR188 4.1 16.9 1.0 CE2 D:TYR95 4.2 16.8 1.0 NZ D:LYS296 4.2 24.7 1.0 NH1 D:ARG124 4.3 18.6 1.0 OD2 D:ASP63 4.4 19.2 1.0 CG D:HIS249 4.4 26.3 1.0 ND1 D:HIS249 4.4 16.2 1.0 CA D:ASP63 4.5 13.3 1.0 CB D:SER125 4.5 14.2 1.0 NE D:ARG124 4.6 19.1 1.0 N D:SER125 4.7 23.9 1.0 N D:ALA126 4.7 15.5 1.0 OG D:SER125 4.9 19.0 1.0 CZ D:ARG124 4.9 19.0 1.0 CD1 D:TYR95 5.0 20.0 1.0

Iron binding site 9 out of 12 in the The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe703 b:19.8 occ:1.00 OH E:TYR95 2.1 15.1 1.0 O2 E:BCT701 2.2 14.6 1.0 O1 E:BCT701 2.2 17.2 1.0 OH E:TYR188 2.3 17.2 1.0 OD1 E:ASP63 2.3 18.3 1.0 NE2 E:HIS249 2.3 14.4 1.0 C E:BCT701 2.6 17.6 1.0 CZ E:TYR95 3.1 13.5 1.0 CD2 E:HIS249 3.2 12.3 1.0 CG E:ASP63 3.3 14.8 1.0 CZ E:TYR188 3.3 20.6 1.0 CE1 E:HIS249 3.4 16.6 1.0 CE1 E:TYR95 3.7 16.6 1.0 CB E:ASP63 3.7 17.9 1.0 O E:HOH801 3.7 13.2 1.0 O3 E:BCT701 3.9 18.4 1.0 CE1 E:TYR188 4.1 20.2 1.0 CE2 E:TYR95 4.1 14.2 1.0 CE2 E:TYR188 4.2 14.7 1.0 NZ E:LYS296 4.4 16.5 1.0 CB E:SER125 4.4 23.6 1.0 CG E:HIS249 4.4 17.4 1.0 OD2 E:ASP63 4.4 20.8 1.0 CA E:ASP63 4.4 13.0 1.0 NH1 E:ARG124 4.4 13.5 1.0 ND1 E:HIS249 4.4 16.4 1.0 N E:SER125 4.6 20.9 1.0 N E:ALA126 4.7 15.8 1.0 NE E:ARG124 4.7 16.7 1.0 OG E:SER125 4.8 22.9 1.0 CD1 E:TYR95 5.0 17.8 1.0

Iron binding site 10 out of 12 in the The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The 2.1 Angstrom Crystal Structure of Diferric Human Transferrin within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe704 b:32.1 occ:1.00 O1 E:BCT702 2.2 26.2 1.0 OH E:TYR517 2.2 46.6 1.0 OH E:TYR426 2.3 39.8 1.0 NE2 E:HIS585 2.3 27.9 1.0 O2 E:BCT702 2.4 30.4 1.0 OD1 E:ASP392 2.4 27.5 1.0 C E:BCT702 2.6 29.9 1.0 CZ E:TYR517 3.2 39.2 1.0 CD2 E:HIS585 3.2 29.9 1.0 CZ E:TYR426 3.3 38.9 1.0 CE1 E:HIS585 3.4 25.6 1.0 CG E:ASP392 3.5 34.6 1.0 CE1 E:TYR517 3.7 39.9 1.0 O E:HOH816 3.7 20.6 1.0 CE2 E:TYR426 3.8 39.6 1.0 O3 E:BCT702 4.0 28.7 1.0 CB E:ASP392 4.0 32.3 1.0 NH1 E:ARG632 4.2 42.6 1.0 CE2 E:TYR517 4.3 41.3 1.0 NH2 E:ARG456 4.3 37.2 1.0 CE1 E:TYR426 4.4 34.7 1.0 CG E:HIS585 4.4 31.8 1.0 ND1 E:HIS585 4.5 27.7 1.0 CB E:THR457 4.5 27.0 1.0 CA E:ASP392 4.6 28.7 1.0 OD2 E:ASP392 4.6 37.4 1.0 N E:ALA458 4.8 29.6 1.0 NE E:ARG456 4.8 37.3 1.0 N E:THR457 4.9 29.0 1.0 OG1 E:THR457 4.9 28.6 1.0 N E:GLY393 4.9 23.0 1.0 CD1 E:TYR517 5.0 37.6 1.0

N.Noinaj, N.C.Easley, M.Oke, N.Mizuno, J.Gumbart, E.Boura, A.N.Steere, O.Zak, P.Aisen, E.Tajkhorshid, R.W.Evans, A.R.Gorringe, A.B.Mason, A.C.Steven, S.K.Buchanan. Structural Basis For Iron Piracy By Pathogenic Neisseria. Nature V. 483 53 2012.
ISSN: ISSN 0028-0836
PubMed: 22327295
DOI: 10.1038/NATURE10823