Iron in PDB 7dz9: Mbnabc Complex

The structure of Mbnabc Complex, PDB code: 7dz9 was solved by D.Chao, Z.Dan, G.Yijun, C.Wei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.64 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.915, 69.065, 82.573, 90, 93.59, 90
R / Rfree (%)	17.3 / 21.9

The binding sites of Iron atom in the Mbnabc Complex (pdb code 7dz9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Mbnabc Complex, PDB code: 7dz9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Mbnabc Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Mbnabc Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:19.7 occ:1.00 OE2 A:GLU135 2.0 19.2 1.0 O A:HOH510 2.0 15.9 1.0 OD2 A:ASP165 2.0 18.7 1.0 O A:HOH507 2.2 20.1 1.0 OE1 A:GLU238 2.2 22.4 1.0 ND1 A:HIS194 2.3 15.9 1.0 CD A:GLU135 3.0 18.7 1.0 CD A:GLU238 3.0 19.1 1.0 CG A:ASP165 3.2 19.3 1.0 OE2 A:GLU238 3.2 19.4 1.0 CE1 A:HIS194 3.3 17.9 1.0 CG A:HIS194 3.3 16.2 1.0 OE1 A:GLU135 3.4 18.3 1.0 CB A:HIS194 3.6 17.6 1.0 FE A:FE403 3.6 19.8 1.0 FE A:FE402 3.7 21.0 1.0 O A:HOH535 3.8 20.9 1.0 CB A:ASP165 3.9 18.5 1.0 O A:HOH560 4.0 23.3 1.0 ND2 A:ASN168 4.1 16.3 1.0 CE1 A:HIS211 4.1 21.1 1.0 OD1 A:ASP165 4.2 20.4 1.0 NE2 A:HIS211 4.3 20.9 1.0 CG A:GLU135 4.3 19.6 1.0 CG A:GLU238 4.4 20.4 1.0 NE2 A:HIS194 4.4 20.2 1.0 CD2 A:HIS194 4.5 16.5 1.0 OD1 A:ASN168 4.5 19.5 1.0 CG A:ASN168 4.6 18.1 1.0 NE2 A:HIS55 4.8 19.4 1.0

Iron binding site 2 out of 6 in the Mbnabc Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Mbnabc Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:21.0 occ:1.00 NE2 A:HIS211 2.1 20.9 1.0 OD2 A:ASP209 2.2 18.6 1.0 O A:HOH535 2.2 20.9 1.0 OD1 A:ASN168 2.2 19.5 1.0 O A:HOH510 2.2 15.9 1.0 OD1 A:ASP209 2.4 20.3 1.0 CG A:ASP209 2.6 17.5 1.0 CE1 A:HIS211 3.1 21.1 1.0 CD2 A:HIS211 3.2 16.7 1.0 CG A:ASN168 3.2 18.1 1.0 OD2 A:ASP165 3.3 18.7 1.0 ND2 A:ASN168 3.5 16.3 1.0 FE A:FE401 3.7 19.7 1.0 OE1 A:GLU238 3.7 22.4 1.0 CG A:ASP165 3.9 19.3 1.0 OD1 A:ASP165 3.9 20.4 1.0 O A:HOH531 4.1 21.9 1.0 CB A:ASP209 4.1 18.1 1.0 ND1 A:HIS211 4.2 21.0 1.0 CG A:HIS211 4.3 21.7 1.0 O A:HOH560 4.5 23.3 1.0 OE2 A:GLU135 4.5 19.2 1.0 OG A:SER167 4.6 23.1 1.0 CB A:ASN168 4.6 17.1 1.0 O A:ASP209 4.7 18.9 1.0 N A:ASN168 4.8 18.6 1.0 CD A:GLU238 4.8 19.1 1.0 O A:HOH507 4.8 20.1 1.0 CB A:ALA196 4.9 16.7 1.0 CA A:ASN168 4.9 17.8 1.0

Iron binding site 3 out of 6 in the Mbnabc Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Mbnabc Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:19.8 occ:1.00 O A:HOH507 2.0 20.1 1.0 OE1 A:GLU135 2.2 18.3 1.0 NE2 A:HIS91 2.3 21.5 1.0 NE2 A:HIS55 2.3 19.4 1.0 O A:HOH560 2.5 23.3 1.0 SG F:CYS18 2.5 37.1 1.0 CD A:GLU135 3.2 18.7 1.0 CE1 A:HIS55 3.2 18.7 1.0 CE1 A:HIS91 3.2 21.2 1.0 CD2 A:HIS91 3.2 20.4 1.0 CD2 A:HIS55 3.3 18.1 1.0 OE2 A:GLU135 3.5 19.2 1.0 CB F:CYS18 3.6 27.5 1.0 FE A:FE401 3.6 19.7 1.0 O A:HOH510 3.7 15.9 1.0 CE1 A:HIS194 4.2 17.9 1.0 ND1 A:HIS91 4.3 19.0 1.0 CG A:HIS91 4.3 20.4 1.0 ND1 A:HIS55 4.3 20.8 1.0 O A:HOH562 4.4 25.4 1.0 ND1 A:HIS194 4.4 15.9 1.0 CG A:HIS55 4.4 19.0 1.0 OE2 A:GLU238 4.5 19.4 1.0 CG A:GLU135 4.5 19.6 1.0 CA F:CYS18 4.8 30.1 1.0 CB A:GLU135 4.8 14.8 1.0 CE A:MET57 5.0 25.4 1.0

Iron binding site 4 out of 6 in the Mbnabc Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Mbnabc Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:19.4 occ:1.00 O B:HOH432 1.9 16.8 1.0 OE1 B:GLU135 2.2 22.8 1.0 NE2 B:HIS91 2.2 22.1 1.0 NE2 B:HIS55 2.2 18.2 1.0 O B:HOH464 2.3 22.2 1.0 SG E:CYS18 2.5 32.7 1.0 CE1 B:HIS91 3.1 20.7 1.0 CD B:GLU135 3.1 18.4 1.0 CE1 B:HIS55 3.2 17.4 1.0 CD2 B:HIS91 3.2 21.2 1.0 CD2 B:HIS55 3.2 16.6 1.0 OE2 B:GLU135 3.4 20.7 1.0 CB E:CYS18 3.6 27.5 1.0 FE B:FE302 3.6 19.2 1.0 O B:HOH417 3.7 14.4 1.0 ND1 B:HIS91 4.2 20.8 1.0 CE1 B:HIS194 4.3 18.4 1.0 CG B:HIS91 4.3 19.4 1.0 O B:HOH473 4.3 24.3 1.0 ND1 B:HIS55 4.3 19.1 1.0 CG B:HIS55 4.4 18.3 1.0 ND1 B:HIS194 4.5 17.5 1.0 OE2 B:GLU238 4.5 17.8 1.0 CG B:GLU135 4.5 18.4 1.0 CA E:CYS18 4.8 33.8 1.0 CB B:GLU135 4.9 16.6 1.0

Iron binding site 5 out of 6 in the Mbnabc Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Mbnabc Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:19.2 occ:1.00 OE2 B:GLU135 2.0 20.7 1.0 O B:HOH417 2.0 14.4 1.0 O B:HOH432 2.1 16.8 1.0 OD2 B:ASP165 2.1 16.5 1.0 OE1 B:GLU238 2.2 18.2 1.0 ND1 B:HIS194 2.3 17.5 1.0 CD B:GLU238 2.9 17.5 1.0 CD B:GLU135 3.1 18.4 1.0 OE2 B:GLU238 3.1 17.8 1.0 CE1 B:HIS194 3.2 18.4 1.0 CG B:ASP165 3.3 17.0 1.0 CG B:HIS194 3.3 18.6 1.0 OE1 B:GLU135 3.5 22.8 1.0 O B:HOH422 3.6 17.0 1.0 FE B:FE301 3.6 19.4 1.0 CB B:HIS194 3.6 14.3 1.0 FE B:FE303 3.7 18.6 1.0 O B:HOH464 3.9 22.2 1.0 CB B:ASP165 4.0 16.5 1.0 ND2 B:ASN168 4.1 14.4 1.0 CE1 B:HIS211 4.1 20.9 1.0 NE2 B:HIS211 4.2 16.2 1.0 OD1 B:ASP165 4.2 19.6 1.0 CG B:GLU238 4.3 18.7 1.0 CG B:GLU135 4.4 18.4 1.0 NE2 B:HIS194 4.4 16.8 1.0 CD2 B:HIS194 4.5 17.9 1.0 OD1 B:ASN168 4.5 19.2 1.0 CG B:ASN168 4.6 16.6 1.0 NE2 B:HIS55 4.8 18.2 1.0

Iron binding site 6 out of 6 in the Mbnabc Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Mbnabc Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:18.6 occ:1.00 O B:HOH422 2.0 17.0 1.0 NE2 B:HIS211 2.2 16.2 1.0 OD1 B:ASN168 2.2 19.2 1.0 OD2 B:ASP209 2.2 16.5 1.0 O B:HOH417 2.2 14.4 1.0 OD1 B:ASP209 2.4 13.6 1.0 CG B:ASP209 2.6 15.8 1.0 CG B:ASN168 3.1 16.6 1.0 CD2 B:HIS211 3.1 15.8 1.0 CE1 B:HIS211 3.1 20.9 1.0 ND2 B:ASN168 3.4 14.4 1.0 OD2 B:ASP165 3.4 16.5 1.0 OE1 B:GLU238 3.6 18.2 1.0 FE B:FE302 3.7 19.2 1.0 CG B:ASP165 3.9 17.0 1.0 OD1 B:ASP165 4.0 19.6 1.0 O B:HOH426 4.1 17.6 1.0 CB B:ASP209 4.1 13.8 1.0 ND1 B:HIS211 4.3 17.0 1.0 CG B:HIS211 4.3 22.2 1.0 O B:HOH464 4.5 22.2 1.0 OG B:SER167 4.5 20.5 1.0 CB B:ASN168 4.5 15.8 1.0 OE2 B:GLU135 4.7 20.7 1.0 O B:HOH432 4.7 16.8 1.0 CD B:GLU238 4.7 17.5 1.0 N B:ASN168 4.8 16.7 1.0 O B:ASP209 4.9 20.5 1.0 CA B:ASN168 4.9 16.8 1.0 CB B:ALA196 4.9 16.0 1.0

C.Dou, Z.Long, S.Li, D.Zhou, Y.Jin, L.Zhang, X.Zhang, Y.Zheng, L.Li, X.Zhu, Z.Liu, S.He, W.Yan, L.Yang, J.Xiong, X.Fu, S.Qi, H.Ren, S.Chen, L.Dai, B.Wang, W.Cheng. Crystal Structure and Catalytic Mechanism of the Mbnbc Holoenzyme Required For Methanobactin Biosynthesis. Cell Res. V. 32 302 2022.
ISSN: ISSN 1001-0602
PubMed: 35110668
DOI: 10.1038/S41422-022-00620-2