Iron in PDB 5m3l: Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin

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Binding sites:

The binding sites of Iron atom in the Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin (pdb code 5m3l). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin, PDB code: 5m3l:
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 Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:0.9 occ:1.00 FE A:HEM201 0.0 0.9 1.0 ND A:HEM201 1.9 0.5 1.0 NA A:HEM201 2.0 0.6 1.0 NB A:HEM201 2.1 94.4 1.0 NC A:HEM201 2.1 96.5 1.0 NE2 A:HIS101 2.5 0.6 1.0 CE1 A:HIS101 2.8 0.4 1.0 C4D A:HEM201 2.9 0.5 1.0 C1D A:HEM201 2.9 0.7 1.0 C1A A:HEM201 3.0 0.5 1.0 C4A A:HEM201 3.1 0.7 1.0 C1B A:HEM201 3.1 93.6 1.0 C4B A:HEM201 3.1 88.0 1.0 C4C A:HEM201 3.1 90.3 1.0 C1C A:HEM201 3.1 95.3 1.0 CHA A:HEM201 3.3 0.8 1.0 CHD A:HEM201 3.4 90.4 1.0 CHB A:HEM201 3.4 96.3 1.0 CHC A:HEM201 3.4 91.5 1.0 CD2 A:HIS101 3.8 0.7 1.0 ND1 A:HIS101 4.1 0.8 1.0 C3D A:HEM201 4.1 0.1 1.0 C2D A:HEM201 4.1 0.7 1.0 C2A A:HEM201 4.2 0.7 1.0 C3A A:HEM201 4.2 0.2 1.0 C2B A:HEM201 4.3 92.6 1.0 C3C A:HEM201 4.3 93.5 1.0 C2C A:HEM201 4.3 98.0 1.0 C3B A:HEM201 4.3 85.5 1.0 CG A:HIS101 4.6 0.3 1.0

Iron binding site 2 out of 12 in the Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:78.7 occ:1.00 FE B:HEM201 0.0 78.7 1.0 ND B:HEM201 1.9 71.3 1.0 NA B:HEM201 2.0 69.5 1.0 NC B:HEM201 2.1 65.3 1.0 NB B:HEM201 2.1 61.2 1.0 NE2 B:HIS96 2.3 86.4 1.0 C1D B:HEM201 2.9 66.9 1.0 C4D B:HEM201 2.9 73.0 1.0 C1A B:HEM201 3.0 68.7 1.0 C4C B:HEM201 3.0 63.4 1.0 C4A B:HEM201 3.0 67.9 1.0 C1B B:HEM201 3.0 62.1 1.0 C4B B:HEM201 3.1 54.9 1.0 C1C B:HEM201 3.1 61.4 1.0 CE1 B:HIS96 3.1 88.3 1.0 CHD B:HEM201 3.3 63.5 1.0 CHA B:HEM201 3.4 69.7 1.0 CD2 B:HIS96 3.4 88.9 1.0 CHB B:HEM201 3.4 64.3 1.0 CHC B:HEM201 3.5 56.4 1.0 C2D B:HEM201 4.1 71.5 1.0 C3D B:HEM201 4.1 78.3 1.0 C3A B:HEM201 4.2 73.3 1.0 C2A B:HEM201 4.2 75.3 1.0 C3C B:HEM201 4.2 63.0 1.0 C2C B:HEM201 4.3 62.2 1.0 C2B B:HEM201 4.3 58.5 1.0 ND1 B:HIS96 4.3 90.9 1.0 C3B B:HEM201 4.3 52.8 1.0 CG B:HIS96 4.5 92.2 1.0 CG2 B:VAL68 4.8 61.3 1.0

Iron binding site 3 out of 12 in the Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:89.1 occ:1.00 FE C:HEM201 0.0 89.1 1.0 ND C:HEM201 1.9 79.3 1.0 NA C:HEM201 2.0 72.8 1.0 NC C:HEM201 2.1 73.0 1.0 NB C:HEM201 2.1 70.5 1.0 NE2 C:HIS102 2.6 97.1 1.0 C4D C:HEM201 2.9 78.2 1.0 C1D C:HEM201 2.9 74.9 1.0 C1A C:HEM201 2.9 73.5 1.0 CE1 C:HIS102 2.9 96.7 1.0 C4A C:HEM201 3.0 67.2 1.0 C1B C:HEM201 3.1 65.6 1.0 C4C C:HEM201 3.1 69.3 1.0 C4B C:HEM201 3.1 67.1 1.0 C1C C:HEM201 3.1 72.3 1.0 CHA C:HEM201 3.3 75.8 1.0 CHD C:HEM201 3.4 68.4 1.0 CHB C:HEM201 3.4 65.4 1.0 CHC C:HEM201 3.5 67.7 1.0 CD2 C:HIS102 3.9 98.6 1.0 C2A C:HEM201 4.1 74.0 1.0 C3D C:HEM201 4.1 79.7 1.0 C2D C:HEM201 4.1 76.8 1.0 C3A C:HEM201 4.1 68.9 1.0 ND1 C:HIS102 4.2 95.2 1.0 CD1 C:ILE74 4.2 1.0 1.0 C3C C:HEM201 4.3 75.5 1.0 C2B C:HEM201 4.3 66.7 1.0 C2C C:HEM201 4.3 77.3 1.0 C3B C:HEM201 4.4 67.7 1.0 CG C:HIS102 4.7 91.6 1.0 CG1 C:ILE74 4.9 0.5 1.0

Iron binding site 4 out of 12 in the Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:92.4 occ:1.00 FE D:HEM201 0.0 92.4 1.0 ND D:HEM201 1.9 78.6 1.0 NA D:HEM201 2.0 85.2 1.0 NC D:HEM201 2.1 72.4 1.0 NB D:HEM201 2.1 74.2 1.0 NE2 D:HIS101 2.4 0.9 1.0 C4D D:HEM201 2.9 83.8 1.0 C1D D:HEM201 2.9 71.6 1.0 C1A D:HEM201 3.0 87.6 1.0 C4C D:HEM201 3.1 66.6 1.0 C4A D:HEM201 3.1 79.0 1.0 C1B D:HEM201 3.1 71.9 1.0 C4B D:HEM201 3.1 68.3 1.0 CE1 D:HIS101 3.1 0.8 1.0 C1C D:HEM201 3.1 69.4 1.0 CHA D:HEM201 3.3 85.7 1.0 CHD D:HEM201 3.4 65.4 1.0 CD2 D:HIS101 3.5 0.1 1.0 CHC D:HEM201 3.5 67.2 1.0 CHB D:HEM201 3.5 71.5 1.0 C3D D:HEM201 4.1 87.5 1.0 C2D D:HEM201 4.1 77.3 1.0 C2A D:HEM201 4.2 91.5 1.0 C3A D:HEM201 4.2 84.8 1.0 C3C D:HEM201 4.3 71.5 1.0 C2C D:HEM201 4.3 69.9 1.0 ND1 D:HIS101 4.3 0.2 1.0 C2B D:HEM201 4.3 71.9 1.0 C3B D:HEM201 4.3 67.8 1.0 CG D:HIS101 4.5 0.4 1.0

Iron binding site 5 out of 12 in the Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe201 b:0.3 occ:1.00 FE E:HEM201 0.0 0.3 1.0 ND E:HEM201 1.9 0.5 1.0 NA E:HEM201 2.0 0.6 1.0 NC E:HEM201 2.1 0.9 1.0 NB E:HEM201 2.1 0.1 1.0 NE2 E:HIS101 2.6 0.9 1.0 C4D E:HEM201 2.8 0.7 1.0 C1D E:HEM201 2.9 0.1 1.0 CE1 E:HIS101 2.9 0.2 1.0 C1A E:HEM201 3.0 0.2 1.0 C4A E:HEM201 3.0 0.1 1.0 C4C E:HEM201 3.1 0.7 1.0 C1B E:HEM201 3.1 0.0 1.0 C4B E:HEM201 3.1 0.3 1.0 C1C E:HEM201 3.1 0.7 1.0 CHA E:HEM201 3.3 0.5 1.0 CHD E:HEM201 3.4 0.7 1.0 CHB E:HEM201 3.5 0.6 1.0 CHC E:HEM201 3.5 0.5 1.0 CD2 E:HIS101 3.9 1.0 1.0 C3D E:HEM201 4.1 0.1 1.0 C2D E:HEM201 4.1 0.2 1.0 C2A E:HEM201 4.2 0.8 1.0 C3A E:HEM201 4.2 0.5 1.0 ND1 E:HIS101 4.2 0.5 1.0 C3C E:HEM201 4.3 0.3 1.0 C2B E:HEM201 4.3 0.1 1.0 C2C E:HEM201 4.3 0.1 1.0 C3B E:HEM201 4.4 0.7 1.0 CG E:HIS101 4.7 0.4 1.0 CG2 E:VAL73 4.9 0.4 1.0

Iron binding site 6 out of 12 in the Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe201 b:72.3 occ:1.00 FE F:HEM201 0.0 72.3 1.0 ND F:HEM201 1.9 59.0 1.0 NA F:HEM201 2.0 62.3 1.0 NC F:HEM201 2.1 60.2 1.0 NB F:HEM201 2.1 54.1 1.0 NE2 F:HIS96 2.3 0.2 1.0 C1D F:HEM201 2.9 59.1 1.0 C4D F:HEM201 2.9 61.8 1.0 C1A F:HEM201 3.0 60.2 1.0 C4C F:HEM201 3.0 57.2 1.0 C4A F:HEM201 3.0 57.9 1.0 C1B F:HEM201 3.1 52.0 1.0 C4B F:HEM201 3.1 49.2 1.0 CE1 F:HIS96 3.1 0.6 1.0 C1C F:HEM201 3.2 55.5 1.0 CHD F:HEM201 3.3 54.5 1.0 CHA F:HEM201 3.3 56.5 1.0 CD2 F:HIS96 3.4 0.9 1.0 CHB F:HEM201 3.4 51.9 1.0 CHC F:HEM201 3.6 47.4 1.0 C2D F:HEM201 4.1 68.2 1.0 C3D F:HEM201 4.1 74.9 1.0 C2A F:HEM201 4.2 67.6 1.0 C3A F:HEM201 4.2 61.3 1.0 C3C F:HEM201 4.2 61.4 1.0 C2C F:HEM201 4.3 60.2 1.0 ND1 F:HIS96 4.3 0.0 1.0 C2B F:HEM201 4.3 53.8 1.0 C3B F:HEM201 4.4 52.4 1.0 CG F:HIS96 4.5 0.5 1.0 CG2 F:VAL68 4.8 73.6 1.0

Iron binding site 7 out of 12 in the Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe201 b:1.0 occ:1.00 FE G:HEM201 0.0 1.0 1.0 ND G:HEM201 1.9 0.7 1.0 NA G:HEM201 2.0 0.6 1.0 NC G:HEM201 2.1 0.4 1.0 NB G:HEM201 2.1 0.2 1.0 NE2 G:HIS102 2.5 0.7 1.0 C4D G:HEM201 2.9 0.7 1.0 CE1 G:HIS102 2.9 0.3 1.0 C1D G:HEM201 2.9 1.0 1.0 C1A G:HEM201 2.9 0.7 1.0 C4A G:HEM201 3.0 0.9 1.0 C4C G:HEM201 3.1 0.8 1.0 C1B G:HEM201 3.1 0.3 1.0 C4B G:HEM201 3.1 0.7 1.0 C1C G:HEM201 3.2 0.8 1.0 CHA G:HEM201 3.3 0.9 1.0 CHD G:HEM201 3.4 0.7 1.0 CHB G:HEM201 3.5 0.6 1.0 CHC G:HEM201 3.5 0.7 1.0 CD2 G:HIS102 3.8 0.3 1.0 C2A G:HEM201 4.1 0.2 1.0 C2D G:HEM201 4.1 0.4 1.0 C3D G:HEM201 4.1 0.0 1.0 C3A G:HEM201 4.2 0.6 1.0 ND1 G:HIS102 4.2 0.1 1.0 CD1 G:ILE74 4.2 0.2 1.0 C3C G:HEM201 4.3 0.2 1.0 C2B G:HEM201 4.3 0.8 1.0 C2C G:HEM201 4.3 0.8 1.0 C3B G:HEM201 4.4 0.4 1.0 CG G:HIS102 4.6 1.0 1.0 CG1 G:ILE74 4.8 0.3 1.0

Iron binding site 8 out of 12 in the Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe201 b:1.0 occ:1.00 FE H:HEM201 0.0 1.0 1.0 ND H:HEM201 1.9 0.5 1.0 NA H:HEM201 2.0 0.4 1.0 NC H:HEM201 2.1 0.4 1.0 NB H:HEM201 2.1 97.2 1.0 NE2 H:HIS101 2.5 0.5 1.0 C4D H:HEM201 2.9 0.6 1.0 C1D H:HEM201 2.9 0.8 1.0 C1A H:HEM201 3.0 0.1 1.0 C4A H:HEM201 3.1 1.0 1.0 C4C H:HEM201 3.1 0.5 1.0 C1B H:HEM201 3.1 94.2 1.0 C4B H:HEM201 3.1 89.6 1.0 C1C H:HEM201 3.1 96.6 1.0 CE1 H:HIS101 3.2 0.1 1.0 CHA H:HEM201 3.3 0.3 1.0 CHD H:HEM201 3.4 0.7 1.0 CHB H:HEM201 3.5 96.3 1.0 CHC H:HEM201 3.5 90.0 1.0 CD2 H:HIS101 3.7 0.2 1.0 C3D H:HEM201 4.1 0.4 1.0 C2D H:HEM201 4.2 0.3 1.0 C2A H:HEM201 4.2 0.7 1.0 C3A H:HEM201 4.2 0.3 1.0 C3C H:HEM201 4.3 0.9 1.0 C2C H:HEM201 4.3 0.3 1.0 C2B H:HEM201 4.3 92.3 1.0 C3B H:HEM201 4.4 91.1 1.0 ND1 H:HIS101 4.4 0.5 1.0 CG H:HIS101 4.7 0.0 1.0 CG2 H:VAL73 5.0 0.6 1.0 CE1 H:HIS69 5.0 0.5 1.0

Iron binding site 9 out of 12 in the Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe201 b:0.7 occ:1.00 FE I:HEM201 0.0 0.7 1.0 ND I:HEM201 1.9 0.5 1.0 NA I:HEM201 2.0 0.3 1.0 NC I:HEM201 2.1 0.1 1.0 NB I:HEM201 2.1 0.1 1.0 NE2 I:HIS101 2.6 0.9 1.0 C4D I:HEM201 2.8 0.6 1.0 C1D I:HEM201 2.9 0.5 1.0 CE1 I:HIS101 2.9 0.2 1.0 C1A I:HEM201 3.0 0.7 1.0 C4A I:HEM201 3.0 0.4 1.0 C1B I:HEM201 3.1 0.2 1.0 C4C I:HEM201 3.1 0.4 1.0 C4B I:HEM201 3.1 0.0 1.0 C1C I:HEM201 3.1 0.2 1.0 CHA I:HEM201 3.3 1.0 1.0 CHD I:HEM201 3.4 0.3 1.0 CHB I:HEM201 3.4 0.7 1.0 CHC I:HEM201 3.5 0.5 1.0 CD2 I:HIS101 3.9 0.0 1.0 C3D I:HEM201 4.1 1.0 1.0 C2D I:HEM201 4.1 0.6 1.0 C2A I:HEM201 4.2 0.7 1.0 C3A I:HEM201 4.2 0.3 1.0 ND1 I:HIS101 4.2 0.7 1.0 C2B I:HEM201 4.3 0.1 1.0 C3C I:HEM201 4.3 0.4 1.0 C2C I:HEM201 4.3 0.5 1.0 C3B I:HEM201 4.3 0.0 1.0 CG I:HIS101 4.7 0.6 1.0 CG2 I:VAL73 4.9 0.7 1.0

Iron binding site 10 out of 12 in the Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe201 b:80.3 occ:1.00 FE J:HEM201 0.0 80.3 1.0 ND J:HEM201 1.9 77.1 1.0 NA J:HEM201 2.0 71.5 1.0 NC J:HEM201 2.1 66.7 1.0 NB J:HEM201 2.1 71.8 1.0 NE2 J:HIS96 2.4 0.5 1.0 C4D J:HEM201 2.9 79.4 1.0 C1D J:HEM201 2.9 74.7 1.0 C1A J:HEM201 3.0 75.3 1.0 C4A J:HEM201 3.0 69.1 1.0 C4C J:HEM201 3.1 67.5 1.0 C1B J:HEM201 3.1 70.5 1.0 C4B J:HEM201 3.1 66.9 1.0 C1C J:HEM201 3.2 59.4 1.0 CE1 J:HIS96 3.2 0.7 1.0 CHA J:HEM201 3.4 74.9 1.0 CHD J:HEM201 3.4 69.9 1.0 CHB J:HEM201 3.4 67.5 1.0 CD2 J:HIS96 3.5 0.9 1.0 CHC J:HEM201 3.6 58.7 1.0 C2D J:HEM201 4.1 80.0 1.0 C3D J:HEM201 4.2 89.6 1.0 C3A J:HEM201 4.2 74.4 1.0 C2A J:HEM201 4.2 80.9 1.0 C3C J:HEM201 4.3 67.2 1.0 C2C J:HEM201 4.3 61.7 1.0 C2B J:HEM201 4.3 71.2 1.0 C3B J:HEM201 4.4 70.8 1.0 ND1 J:HIS96 4.4 0.4 1.0 CG J:HIS96 4.6 0.6 1.0 CG2 J:VAL68 4.7 0.5 1.0

P.Afanasyev, C.Seer-Linnemayr, R.B.G.Ravelli, R.Matadeen, S.De Carlo, B.Alewijnse, R.V.Portugal, N.S.Pannu, M.Schatz, M.Van Heel. Single-Particle Cryo-Em Using Alignment By Classification (Abc): the Structure of Lumbricus Terrestris Haemoglobin. Iucrj V. 4 678 2017.
ISSN: ESSN 2052-2525
PubMed: 28989723
DOI: 10.1107/S2052252517010922