Iron in PDB 8yrd: Cryo-Em Structure of Hydroxylase in Soluble Methane Monooxygenase From Methylosinus Sporium 5

The binding sites of Iron atom in the Cryo-Em Structure of Hydroxylase in Soluble Methane Monooxygenase From Methylosinus Sporium 5 (pdb code 8yrd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of Hydroxylase in Soluble Methane Monooxygenase From Methylosinus Sporium 5, PDB code: 8yrd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryo-Em Structure of Hydroxylase in Soluble Methane Monooxygenase From Methylosinus Sporium 5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Hydroxylase in Soluble Methane Monooxygenase From Methylosinus Sporium 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:43.9 occ:1.00 OE1 A:GLU144 2.0 32.6 1.0 O A:HOH706 2.1 50.0 1.0 ND1 A:HIS147 2.2 31.1 1.0 OE1 A:GLU114 2.2 32.9 1.0 CD A:GLU144 2.9 32.6 1.0 CE1 A:HIS147 3.0 31.1 1.0 OE2 A:GLU144 3.1 32.6 1.0 FE A:FE602 3.1 52.1 1.0 CD A:GLU114 3.2 32.9 1.0 CG A:HIS147 3.3 31.1 1.0 OE2 A:GLU114 3.4 32.9 1.0 OE1 A:GLU243 3.5 43.2 1.0 CB A:HIS147 3.8 31.1 1.0 O A:HOH713 3.9 37.1 1.0 OE2 A:GLU243 3.9 43.2 1.0 CD A:GLU243 4.1 43.2 1.0 NE2 A:HIS147 4.2 31.1 1.0 CG A:GLU144 4.3 32.6 1.0 CD2 A:HIS147 4.4 31.1 1.0 CE1 A:HIS246 4.4 42.0 1.0 CG A:GLU114 4.5 32.9 1.0 ND1 A:HIS246 4.6 42.0 1.0 OE2 A:GLU209 4.6 46.7 1.0 CA A:GLU144 4.7 32.6 1.0 CB A:GLU144 4.8 32.6 1.0 CB A:GLU114 4.9 32.9 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Hydroxylase in Soluble Methane Monooxygenase From Methylosinus Sporium 5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Hydroxylase in Soluble Methane Monooxygenase From Methylosinus Sporium 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:52.1 occ:1.00 OE1 A:GLU243 1.9 43.2 1.0 OE2 A:GLU209 2.0 46.7 1.0 OE2 A:GLU144 2.2 32.6 1.0 ND1 A:HIS246 2.3 42.0 1.0 CD A:GLU209 2.8 46.7 1.0 CE1 A:HIS246 3.1 42.0 1.0 CD A:GLU243 3.1 43.2 1.0 FE A:FE601 3.1 43.9 1.0 CD A:GLU144 3.2 32.6 1.0 OE1 A:GLU209 3.3 46.7 1.0 CG A:HIS246 3.4 42.0 1.0 OE1 A:GLU144 3.6 32.6 1.0 CG A:GLU209 3.8 46.7 1.0 OE2 A:GLU243 3.8 43.2 1.0 O A:HOH706 3.9 50.0 1.0 CB A:HIS246 3.9 42.0 1.0 O A:HOH713 4.1 37.1 1.0 CG A:GLU243 4.1 43.2 1.0 NE2 A:HIS246 4.3 42.0 1.0 OE1 A:GLN140 4.4 35.3 1.0 CD2 A:HIS246 4.5 42.0 1.0 CG A:GLU144 4.5 32.6 1.0 ND1 A:HIS147 4.7 31.1 1.0 CE1 A:HIS147 4.7 31.1 1.0 CB A:GLU209 4.9 46.7 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Hydroxylase in Soluble Methane Monooxygenase From Methylosinus Sporium 5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Hydroxylase in Soluble Methane Monooxygenase From Methylosinus Sporium 5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe601 b:43.9 occ:1.00 OE1 D:GLU144 2.0 32.6 1.0 O D:HOH703 2.0 50.0 1.0 ND1 D:HIS147 2.2 31.1 1.0 OE1 D:GLU114 2.2 32.9 1.0 CD D:GLU144 2.9 32.6 1.0 CE1 D:HIS147 3.0 31.1 1.0 OE2 D:GLU144 3.1 32.6 1.0 FE D:FE602 3.1 52.1 1.0 CD D:GLU114 3.2 32.9 1.0 CG D:HIS147 3.3 31.1 1.0 OE2 D:GLU114 3.4 32.9 1.0 OE1 D:GLU243 3.5 43.2 1.0 CB D:HIS147 3.8 31.1 1.0 O D:HOH711 3.9 50.0 1.0 OE2 D:GLU243 3.9 43.2 1.0 CD D:GLU243 4.1 43.2 1.0 NE2 D:HIS147 4.2 31.1 1.0 CG D:GLU144 4.3 32.6 1.0 CD2 D:HIS147 4.4 31.1 1.0 CE1 D:HIS246 4.4 42.0 1.0 CG D:GLU114 4.5 32.9 1.0 ND1 D:HIS246 4.6 42.0 1.0 OE2 D:GLU209 4.6 46.7 1.0 CA D:GLU144 4.7 32.6 1.0 CB D:GLU144 4.8 32.6 1.0 CB D:GLU114 4.9 32.9 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Hydroxylase in Soluble Methane Monooxygenase From Methylosinus Sporium 5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Hydroxylase in Soluble Methane Monooxygenase From Methylosinus Sporium 5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe602 b:52.1 occ:1.00 OE1 D:GLU243 1.9 43.2 1.0 OE2 D:GLU209 2.0 46.7 1.0 OE2 D:GLU144 2.2 32.6 1.0 ND1 D:HIS246 2.3 42.0 1.0 CD D:GLU209 2.8 46.7 1.0 CE1 D:HIS246 3.1 42.0 1.0 CD D:GLU243 3.1 43.2 1.0 FE D:FE601 3.1 43.9 1.0 CD D:GLU144 3.2 32.6 1.0 OE1 D:GLU209 3.3 46.7 1.0 CG D:HIS246 3.4 42.0 1.0 OE1 D:GLU144 3.6 32.6 1.0 CG D:GLU209 3.8 46.7 1.0 OE2 D:GLU243 3.8 43.2 1.0 O D:HOH703 3.9 50.0 1.0 CB D:HIS246 3.9 42.0 1.0 O D:HOH711 4.1 50.0 1.0 CG D:GLU243 4.1 43.2 1.0 NE2 D:HIS246 4.3 42.0 1.0 OE1 D:GLN140 4.4 35.3 1.0 CD2 D:HIS246 4.5 42.0 1.0 CG D:GLU144 4.5 32.6 1.0 ND1 D:HIS147 4.7 31.1 1.0 CE1 D:HIS147 4.7 31.1 1.0 CB D:GLU209 4.9 46.7 1.0

Y.Hwang, B.Ryu, D.H.Lee, H.J.Hong, J.G.Na, C.G.Song, H.G.Kang, E.Pozharski, S.J.Lee. Heartbeat-Like Dynamics Drives Oxygen Activation in Methane Monooxygenase Biorxiv 2025.
ISSN: ISSN 2692-8205
DOI: 10.1101/2025.01.28.635075