Iron in PDB 7bok: Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis

All present enzymatic activity of Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis:
1.11.1.7;

The binding sites of Iron atom in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis (pdb code 7bok). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis, PDB code: 7bok:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis


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 the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:79.3 occ:1.00 FE A:HEM401 0.0 79.3 1.0 ND A:HEM401 1.9 79.3 1.0 NA A:HEM401 2.0 79.3 1.0 NC A:HEM401 2.1 79.3 1.0 NB A:HEM401 2.1 79.3 1.0 NE2 A:HIS220 2.8 86.6 1.0 C4D A:HEM401 2.8 79.3 1.0 C1D A:HEM401 2.9 79.3 1.0 C1A A:HEM401 2.9 79.3 1.0 C4C A:HEM401 3.0 79.3 1.0 C4A A:HEM401 3.0 79.3 1.0 C1B A:HEM401 3.1 79.3 1.0 C4B A:HEM401 3.1 79.3 1.0 C1C A:HEM401 3.1 79.3 1.0 CD2 A:HIS220 3.2 86.6 1.0 CHA A:HEM401 3.3 79.3 1.0 CHD A:HEM401 3.3 79.3 1.0 CHB A:HEM401 3.4 79.3 1.0 CHC A:HEM401 3.5 79.3 1.0 ND2 A:ASN224 3.9 85.9 1.0 NE A:ARG238 4.0 73.4 1.0 CE1 A:HIS220 4.0 86.6 1.0 C2D A:HEM401 4.1 79.3 1.0 C3D A:HEM401 4.1 79.3 1.0 C2A A:HEM401 4.1 79.3 1.0 C3A A:HEM401 4.2 79.3 1.0 C3C A:HEM401 4.2 79.3 1.0 C2C A:HEM401 4.3 79.3 1.0 C2B A:HEM401 4.3 79.3 1.0 C3B A:HEM401 4.3 79.3 1.0 ND2 A:ASN240 4.4 71.4 1.0 CG A:HIS220 4.5 86.6 1.0 CD A:ARG238 4.5 73.4 1.0 CZ A:ARG238 4.8 73.4 1.0 ND1 A:HIS220 4.9 86.6 1.0 NH2 A:ARG238 4.9 73.4 1.0

Iron binding site 2 out of 6 in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis


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 the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:77.1 occ:1.00 FE B:HEM401 0.0 77.1 1.0 ND B:HEM401 1.9 77.1 1.0 NA B:HEM401 2.0 77.1 1.0 NC B:HEM401 2.1 77.1 1.0 NB B:HEM401 2.1 77.1 1.0 NE2 B:HIS220 2.8 80.3 1.0 C4D B:HEM401 2.9 77.1 1.0 C1D B:HEM401 2.9 77.1 1.0 C1A B:HEM401 2.9 77.1 1.0 C4C B:HEM401 3.0 77.1 1.0 C4A B:HEM401 3.0 77.1 1.0 C1B B:HEM401 3.1 77.1 1.0 C4B B:HEM401 3.1 77.1 1.0 C1C B:HEM401 3.1 77.1 1.0 CD2 B:HIS220 3.2 80.3 1.0 CHA B:HEM401 3.3 77.1 1.0 CHD B:HEM401 3.3 77.1 1.0 CHB B:HEM401 3.4 77.1 1.0 CHC B:HEM401 3.5 77.1 1.0 ND2 B:ASN224 3.9 80.4 1.0 NE B:ARG238 4.0 72.5 1.0 CE1 B:HIS220 4.0 80.3 1.0 C2D B:HEM401 4.1 77.1 1.0 C3D B:HEM401 4.1 77.1 1.0 C2A B:HEM401 4.1 77.1 1.0 C3A B:HEM401 4.2 77.1 1.0 C3C B:HEM401 4.2 77.1 1.0 C2C B:HEM401 4.3 77.1 1.0 C2B B:HEM401 4.3 77.1 1.0 C3B B:HEM401 4.3 77.1 1.0 ND2 B:ASN240 4.4 73.1 1.0 CG B:HIS220 4.5 80.3 1.0 CD B:ARG238 4.5 72.5 1.0 CZ B:ARG238 4.8 72.5 1.0 ND1 B:HIS220 4.9 80.3 1.0 NH2 B:ARG238 4.9 72.5 1.0

Iron binding site 3 out of 6 in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis


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 the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:64.0 occ:1.00 FE C:HEM401 0.0 64.0 1.0 ND C:HEM401 1.9 64.0 1.0 NA C:HEM401 2.0 64.0 1.0 NC C:HEM401 2.1 64.0 1.0 NB C:HEM401 2.1 64.0 1.0 NE2 C:HIS220 2.8 67.9 1.0 C4D C:HEM401 2.9 64.0 1.0 C1D C:HEM401 2.9 64.0 1.0 C1A C:HEM401 2.9 64.0 1.0 C4C C:HEM401 3.0 64.0 1.0 C4A C:HEM401 3.0 64.0 1.0 C1B C:HEM401 3.1 64.0 1.0 C4B C:HEM401 3.1 64.0 1.0 C1C C:HEM401 3.1 64.0 1.0 CD2 C:HIS220 3.2 67.9 1.0 CHA C:HEM401 3.3 64.0 1.0 CHD C:HEM401 3.3 64.0 1.0 CHB C:HEM401 3.4 64.0 1.0 CHC C:HEM401 3.5 64.0 1.0 ND2 C:ASN224 3.9 68.6 1.0 NE C:ARG238 4.0 59.5 1.0 CE1 C:HIS220 4.0 67.9 1.0 C2D C:HEM401 4.1 64.0 1.0 C3D C:HEM401 4.1 64.0 1.0 C2A C:HEM401 4.1 64.0 1.0 C3A C:HEM401 4.2 64.0 1.0 C3C C:HEM401 4.2 64.0 1.0 C2C C:HEM401 4.3 64.0 1.0 C2B C:HEM401 4.3 64.0 1.0 C3B C:HEM401 4.3 64.0 1.0 ND2 C:ASN240 4.4 61.9 1.0 CG C:HIS220 4.5 67.9 1.0 CD C:ARG238 4.5 59.5 1.0 CZ C:ARG238 4.8 59.5 1.0 ND1 C:HIS220 4.9 67.9 1.0 NH2 C:ARG238 4.9 59.5 1.0

Iron binding site 4 out of 6 in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis


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 the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:78.5 occ:1.00 FE D:HEM401 0.0 78.5 1.0 ND D:HEM401 1.9 78.5 1.0 NA D:HEM401 2.0 78.5 1.0 NC D:HEM401 2.1 78.5 1.0 NB D:HEM401 2.1 78.5 1.0 NE2 D:HIS220 2.8 81.5 1.0 C4D D:HEM401 2.9 78.5 1.0 C1D D:HEM401 2.9 78.5 1.0 C1A D:HEM401 2.9 78.5 1.0 C4C D:HEM401 3.0 78.5 1.0 C4A D:HEM401 3.0 78.5 1.0 C1B D:HEM401 3.1 78.5 1.0 C4B D:HEM401 3.1 78.5 1.0 C1C D:HEM401 3.1 78.5 1.0 CD2 D:HIS220 3.2 81.5 1.0 CHA D:HEM401 3.3 78.5 1.0 CHD D:HEM401 3.3 78.5 1.0 CHB D:HEM401 3.4 78.5 1.0 CHC D:HEM401 3.5 78.5 1.0 ND2 D:ASN224 3.9 83.5 1.0 NE D:ARG238 4.0 70.2 1.0 CE1 D:HIS220 4.0 81.5 1.0 C2D D:HEM401 4.1 78.5 1.0 C3D D:HEM401 4.1 78.5 1.0 C2A D:HEM401 4.1 78.5 1.0 C3A D:HEM401 4.2 78.5 1.0 C3C D:HEM401 4.2 78.5 1.0 C2C D:HEM401 4.3 78.5 1.0 C2B D:HEM401 4.3 78.5 1.0 C3B D:HEM401 4.3 78.5 1.0 ND2 D:ASN240 4.4 69.1 1.0 CG D:HIS220 4.5 81.5 1.0 CD D:ARG238 4.5 70.2 1.0 CZ D:ARG238 4.8 70.2 1.0 ND1 D:HIS220 4.9 81.5 1.0 NH2 D:ARG238 4.9 70.2 1.0

Iron binding site 5 out of 6 in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe401 b:76.8 occ:1.00 FE E:HEM401 0.0 76.8 1.0 ND E:HEM401 1.9 76.8 1.0 NA E:HEM401 2.0 76.8 1.0 NC E:HEM401 2.1 76.8 1.0 NB E:HEM401 2.1 76.8 1.0 NE2 E:HIS220 2.8 80.2 1.0 C4D E:HEM401 2.8 76.8 1.0 C1D E:HEM401 2.9 76.8 1.0 C1A E:HEM401 2.9 76.8 1.0 C4C E:HEM401 3.0 76.8 1.0 C4A E:HEM401 3.0 76.8 1.0 C1B E:HEM401 3.1 76.8 1.0 C4B E:HEM401 3.1 76.8 1.0 C1C E:HEM401 3.1 76.8 1.0 CD2 E:HIS220 3.2 80.2 1.0 CHA E:HEM401 3.3 76.8 1.0 CHD E:HEM401 3.3 76.8 1.0 CHB E:HEM401 3.4 76.8 1.0 CHC E:HEM401 3.5 76.8 1.0 ND2 E:ASN224 3.9 78.0 1.0 NE E:ARG238 4.0 71.6 1.0 CE1 E:HIS220 4.0 80.2 1.0 C2D E:HEM401 4.1 76.8 1.0 C3D E:HEM401 4.1 76.8 1.0 C2A E:HEM401 4.1 76.8 1.0 C3A E:HEM401 4.2 76.8 1.0 C3C E:HEM401 4.2 76.8 1.0 C2C E:HEM401 4.3 76.8 1.0 C2B E:HEM401 4.3 76.8 1.0 C3B E:HEM401 4.3 76.8 1.0 ND2 E:ASN240 4.4 67.8 1.0 CG E:HIS220 4.5 80.2 1.0 CD E:ARG238 4.5 71.6 1.0 CZ E:ARG238 4.8 71.6 1.0 ND1 E:HIS220 4.9 80.2 1.0 NH2 E:ARG238 4.9 71.6 1.0

Iron binding site 6 out of 6 in the Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of the Encapsulated Dyp-Type Peroxidase From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe401 b:68.8 occ:1.00 FE F:HEM401 0.0 68.8 1.0 ND F:HEM401 1.9 68.8 1.0 NA F:HEM401 2.0 68.8 1.0 NC F:HEM401 2.1 68.8 1.0 NB F:HEM401 2.1 68.8 1.0 NE2 F:HIS220 2.8 77.6 1.0 C4D F:HEM401 2.9 68.8 1.0 C1D F:HEM401 2.9 68.8 1.0 C1A F:HEM401 2.9 68.8 1.0 C4C F:HEM401 3.0 68.8 1.0 C4A F:HEM401 3.0 68.8 1.0 C1B F:HEM401 3.1 68.8 1.0 C4B F:HEM401 3.1 68.8 1.0 C1C F:HEM401 3.1 68.8 1.0 CD2 F:HIS220 3.2 77.6 1.0 CHA F:HEM401 3.3 68.8 1.0 CHD F:HEM401 3.3 68.8 1.0 CHB F:HEM401 3.4 68.8 1.0 CHC F:HEM401 3.5 68.8 1.0 ND2 F:ASN224 3.9 79.8 1.0 NE F:ARG238 4.0 65.6 1.0 CE1 F:HIS220 4.0 77.6 1.0 C2D F:HEM401 4.1 68.8 1.0 C3D F:HEM401 4.1 68.8 1.0 C2A F:HEM401 4.1 68.8 1.0 C3A F:HEM401 4.2 68.8 1.0 C3C F:HEM401 4.2 68.8 1.0 C2C F:HEM401 4.3 68.8 1.0 C2B F:HEM401 4.3 68.8 1.0 C3B F:HEM401 4.3 68.8 1.0 ND2 F:ASN240 4.4 62.3 1.0 CG F:HIS220 4.5 77.6 1.0 CD F:ARG238 4.5 65.6 1.0 CZ F:ARG238 4.8 65.6 1.0 ND1 F:HIS220 4.9 77.6 1.0 NH2 F:ARG238 4.9 65.6 1.0

Y.T.Tang, A.Mu, W.W.Wang, S.Zhou, Y.Y.Zhang, X.T.Zhou, F.J.Liu, X.N.Yang, H.R.Gong, Q.Wang, Z.H.Rao. Cryo-Em Structure of A Native Cargo-Loaded Encapsulin From Mycobacterium Smegmatis To Be Published.