Manganese in PDB 7w79: Heme Exporter Hrtba in Complex with Mn-Amppnp

The structure of Heme Exporter Hrtba in Complex with Mn-Amppnp, PDB code: 7w79 was solved by T.Hisano, H.Nakamura, M.M.Rahman, T.Tosha, M.Shirouzu, Y.Shiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.54 / 3.10
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	169.369, 169.369, 95.053, 90, 90, 90
R / Rfree (%)	22 / 26.1

The binding sites of Manganese atom in the Heme Exporter Hrtba in Complex with Mn-Amppnp (pdb code 7w79). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Heme Exporter Hrtba in Complex with Mn-Amppnp, PDB code: 7w79:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the Heme Exporter Hrtba in Complex with Mn-Amppnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Heme Exporter Hrtba in Complex with Mn-Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:105.0 occ:0.53 OE1 A:GLU32 2.7 93.7 1.0 OG A:SER8 3.3 98.1 1.0 CB A:SER8 3.6 97.5 1.0 CG2 A:THR10 3.9 97.6 1.0 CD A:GLU32 4.0 91.2 1.0 CG A:GLU32 4.7 87.8 1.0 NE2 A:HIS70 4.9 110.6 1.0 OE2 A:GLU32 4.9 86.2 1.0 CA A:SER8 5.0 88.9 1.0

Manganese binding site 2 out of 5 in the Heme Exporter Hrtba in Complex with Mn-Amppnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Heme Exporter Hrtba in Complex with Mn-Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:113.0 occ:0.60 OD1 A:ASP214 3.9 89.6 1.0 CG A:ASP214 4.3 91.5 1.0 CB A:ASP214 4.7 81.8 1.0 OD2 A:ASP214 4.8 103.8 1.0

Manganese binding site 3 out of 5 in the Heme Exporter Hrtba in Complex with Mn-Amppnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Heme Exporter Hrtba in Complex with Mn-Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn304 b:63.6 occ:1.00 OG A:SER50 2.1 72.8 1.0 OE1 A:GLN90 2.2 81.6 1.0 O2G A:ATP301 2.5 72.6 1.0 O2B A:ATP301 2.7 72.6 1.0 O3B A:ATP301 2.9 72.6 1.0 CD A:GLN90 3.1 73.0 1.0 CB A:SER50 3.2 66.4 1.0 NE2 A:GLN90 3.2 73.0 1.0 PG A:ATP301 3.3 72.6 1.0 PB A:ATP301 3.3 72.6 1.0 O1A A:ATP301 3.5 72.6 1.0 O3G A:ATP301 3.9 72.6 1.0 N A:SER50 4.0 70.0 1.0 OE2 A:GLU165 4.1 82.8 1.0 CA A:SER50 4.2 65.9 1.0 OD1 A:ASP164 4.2 75.9 1.0 O3A A:ATP301 4.3 72.6 1.0 PA A:ATP301 4.4 72.6 1.0 CG A:GLN90 4.5 68.3 1.0 OD2 A:ASP164 4.5 70.7 1.0 O1B A:ATP301 4.5 72.6 1.0 O1G A:ATP301 4.6 72.6 1.0 MN A:MN305 4.8 73.5 1.0 CG A:ASP164 4.8 72.4 1.0 O2A A:ATP301 5.0 72.6 1.0

Manganese binding site 4 out of 5 in the Heme Exporter Hrtba in Complex with Mn-Amppnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Heme Exporter Hrtba in Complex with Mn-Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn305 b:73.5 occ:1.00 OE2 A:GLU165 2.3 82.8 1.0 CE1 A:HIS198 2.4 70.4 1.0 O3G A:ATP301 2.8 72.6 1.0 OE1 A:GLU165 2.9 74.1 1.0 CD A:GLU165 2.9 72.1 1.0 O2G A:ATP301 3.0 72.6 1.0 NE2 A:HIS198 3.2 75.0 1.0 ND1 A:HIS198 3.3 70.3 1.0 PG A:ATP301 3.3 72.6 1.0 O1G A:ATP301 3.9 72.6 1.0 CD2 A:HIS198 4.2 68.4 1.0 CE A:LYS49 4.2 66.5 1.0 CG A:HIS198 4.3 68.8 1.0 CG A:GLU165 4.4 66.4 1.0 NZ A:LYS49 4.7 71.7 1.0 O3B A:ATP301 4.8 72.6 1.0 MN A:MN304 4.8 63.6 1.0 CA A:SER45 5.0 72.9 1.0

Manganese binding site 5 out of 5 in the Heme Exporter Hrtba in Complex with Mn-Amppnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Heme Exporter Hrtba in Complex with Mn-Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:90.6 occ:0.30 OE1 B:GLN175 4.6 74.7 1.0

H.Nakamura, T.Hisano, M.M.Rahman, T.Tosha, M.Shirouzu, Y.Shiro. Structural Basis For Heme Detoxification By An Atp-Binding Cassette-Type Efflux Pump in Gram-Positive Pathogenic Bacteria. Proc.Natl.Acad.Sci.Usa V. 119 85119 2022.
ISSN: ESSN 1091-6490
PubMed: 35767641
DOI: 10.1073/PNAS.2123385119