Magnesium in PDB 8ipr: Cryo-Em Structure of Heme Transporter Cyddc From Mycobacterium Smegmatis in the Outward Facing Atp Bound State

All present enzymatic activity of Cryo-Em Structure of Heme Transporter Cyddc From Mycobacterium Smegmatis in the Outward Facing Atp Bound State:
3.6.3.25;

The binding sites of Magnesium atom in the Cryo-Em Structure of Heme Transporter Cyddc From Mycobacterium Smegmatis in the Outward Facing Atp Bound State (pdb code 8ipr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of Heme Transporter Cyddc From Mycobacterium Smegmatis in the Outward Facing Atp Bound State, PDB code: 8ipr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Heme Transporter Cyddc From Mycobacterium Smegmatis in the Outward Facing Atp Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Heme Transporter Cyddc From Mycobacterium Smegmatis in the Outward Facing Atp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:49.3 occ:1.00 OG1 A:THR351 2.1 45.1 1.0 O2B A:ATP602 2.6 20.0 1.0 O3G A:ATP602 2.7 20.0 1.0 CB A:THR351 3.2 31.5 1.0 OD2 A:ASP457 3.4 40.6 1.0 O1A A:ATP602 3.5 20.0 1.0 CG2 A:THR351 3.9 29.9 1.0 PB A:ATP602 3.9 20.0 1.0 PG A:ATP602 3.9 20.0 1.0 CD1 C:LEU433 4.0 29.5 1.0 O3B A:ATP602 4.1 20.0 1.0 NE2 A:GLN458 4.1 39.1 1.0 CG A:ASP457 4.4 46.1 1.0 O3A A:ATP602 4.4 20.0 1.0 PA A:ATP602 4.4 20.0 1.0 CA A:THR351 4.4 25.5 1.0 N A:THR351 4.5 27.4 1.0 OD1 A:ASP457 4.6 48.7 1.0 CG C:LEU433 4.6 23.8 1.0 N C:LEU433 4.7 24.2 1.0 O2G A:ATP602 4.7 20.0 1.0 CB C:LEU433 4.9 25.5 1.0 CB C:SER432 4.9 19.7 1.0 O1G A:ATP602 5.0 20.0 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Heme Transporter Cyddc From Mycobacterium Smegmatis in the Outward Facing Atp Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Heme Transporter Cyddc From Mycobacterium Smegmatis in the Outward Facing Atp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:23.8 occ:1.00 OG C:SER337 2.0 35.9 1.0 O2B C:ATP602 2.2 20.0 1.0 O1G C:ATP602 2.3 20.0 1.0 NE2 C:HIS378 2.5 21.8 1.0 CD2 C:HIS378 2.9 22.3 1.0 CB C:SER337 3.2 26.9 1.0 PB C:ATP602 3.5 20.0 1.0 O1A C:ATP602 3.6 20.0 1.0 PG C:ATP602 3.6 20.0 1.0 CE1 C:HIS378 3.7 21.1 1.0 O3B C:ATP602 3.8 20.0 1.0 O3A C:ATP602 4.2 20.0 1.0 N C:SER337 4.2 25.6 1.0 CG C:HIS378 4.2 16.6 1.0 N A:ALA435 4.3 19.9 1.0 CA C:SER337 4.3 14.7 1.0 O2G C:ATP602 4.3 20.0 1.0 CB A:ALA435 4.4 22.3 1.0 PA C:ATP602 4.4 20.0 1.0 OD1 C:ASP455 4.5 30.0 1.0 ND1 C:HIS378 4.6 20.9 1.0 O1B C:ATP602 4.7 20.0 1.0 O3G C:ATP602 4.7 20.0 1.0 CG C:ASP455 4.8 30.0 1.0 CB A:SER434 4.8 10.1 1.0 OD2 C:ASP455 4.8 30.0 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Heme Transporter Cyddc From Mycobacterium Smegmatis in the Outward Facing Atp Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Heme Transporter Cyddc From Mycobacterium Smegmatis in the Outward Facing Atp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:49.4 occ:1.00 OG1 D:THR351 2.1 45.6 1.0 O2B D:ATP602 2.6 20.0 1.0 O3G D:ATP602 2.7 20.0 1.0 CB D:THR351 3.2 30.9 1.0 OD2 D:ASP457 3.4 41.2 1.0 O1A D:ATP602 3.5 20.0 1.0 CG2 D:THR351 3.9 29.4 1.0 PB D:ATP602 3.9 20.0 1.0 CD1 E:LEU433 3.9 30.0 1.0 PG D:ATP602 3.9 20.0 1.0 O3B D:ATP602 4.1 20.0 1.0 NE2 D:GLN458 4.1 38.5 1.0 CG D:ASP457 4.4 46.7 1.0 O3A D:ATP602 4.4 20.0 1.0 CA D:THR351 4.4 25.6 1.0 PA D:ATP602 4.4 20.0 1.0 N D:THR351 4.5 27.5 1.0 OD1 D:ASP457 4.6 49.1 1.0 CG E:LEU433 4.6 25.2 1.0 CB E:LEU433 4.7 25.2 1.0 O2G D:ATP602 4.7 20.0 1.0 N E:LEU433 4.8 24.0 1.0 O1G D:ATP602 5.0 20.0 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Heme Transporter Cyddc From Mycobacterium Smegmatis in the Outward Facing Atp Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Heme Transporter Cyddc From Mycobacterium Smegmatis in the Outward Facing Atp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:24.6 occ:1.00 OG E:SER337 2.0 36.3 1.0 O2B E:ATP602 2.2 20.0 1.0 O1G E:ATP602 2.3 20.0 1.0 NE2 E:HIS378 2.5 22.6 1.0 CD2 E:HIS378 2.9 22.4 1.0 CB E:SER337 3.2 27.2 1.0 PB E:ATP602 3.5 20.0 1.0 O1A E:ATP602 3.6 20.0 1.0 PG E:ATP602 3.6 20.0 1.0 CE1 E:HIS378 3.7 21.0 1.0 O3B E:ATP602 3.8 20.0 1.0 OD1 E:ASP455 4.1 30.7 1.0 O3A E:ATP602 4.2 20.0 1.0 N E:SER337 4.2 26.8 1.0 CG E:HIS378 4.2 17.3 1.0 N D:ALA435 4.3 21.0 1.0 O2G E:ATP602 4.3 20.0 1.0 CA E:SER337 4.3 15.5 1.0 OD2 E:ASP455 4.3 36.4 1.0 CB D:ALA435 4.4 24.2 1.0 PA E:ATP602 4.4 20.0 1.0 CG E:ASP455 4.5 30.6 1.0 ND1 E:HIS378 4.6 21.0 1.0 O1B E:ATP602 4.7 20.0 1.0 O3G E:ATP602 4.7 20.0 1.0 CB D:SER434 4.8 10.1 1.0

C.Zhu, Y.Shi, J.Yu, W.Zhao, L.Li, L.Jingxi, X.Yang, B.Zhang, Y.Zhao, Y.Gao, X.Chen, X.Yang, L.Zhang, L.W.Guddat, L.Liu, H.Yang, Z.Rao, J.Li. Cryo-Em Structures of A Prokaryotic Heme Transporter Cyddc. Protein Cell 2023.
ISSN: ESSN 1674-8018
PubMed: 37144855
DOI: 10.1093/PROCEL/PWAD022