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Manganese in PDB 7w7a: Heme Exporter in Complex with Mn-Containing Protoporphyrin IX, Mn- Anomalous Data

Protein crystallography data

The structure of Heme Exporter in Complex with Mn-Containing Protoporphyrin IX, Mn- Anomalous Data, PDB code: 7w7a 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) 48.82 / 3.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 82.488, 133.672, 159.838, 111.81, 99.83, 94.43
R / Rfree (%) 26.4 / 30.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Heme Exporter in Complex with Mn-Containing Protoporphyrin IX, Mn- Anomalous Data (pdb code 7w7a). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Heme Exporter in Complex with Mn-Containing Protoporphyrin IX, Mn- Anomalous Data, PDB code: 7w7a:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 7w7a

Go back to Manganese Binding Sites List in 7w7a
Manganese binding site 1 out of 2 in the Heme Exporter in Complex with Mn-Containing Protoporphyrin IX, Mn- Anomalous Data


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Heme Exporter in Complex with Mn-Containing Protoporphyrin IX, Mn- Anomalous Data within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:240.4
occ:1.00
MN D:MNR401 0.0 240.4 1.0
OE2 B:GLU219 1.9 124.7 1.0
OE2 D:GLU219 1.9 144.7 1.0
NB D:MNR401 2.1 239.6 1.0
ND D:MNR401 2.1 241.4 1.0
NC D:MNR401 2.1 239.8 1.0
NA D:MNR401 2.1 241.1 1.0
C4C D:MNR401 3.1 240.0 1.0
C1D D:MNR401 3.1 241.4 1.0
C1A D:MNR401 3.1 241.9 1.0
C4D D:MNR401 3.1 242.1 1.0
C4A D:MNR401 3.1 241.0 1.0
C1C D:MNR401 3.1 239.1 1.0
CD B:GLU219 3.2 124.4 1.0
C1B D:MNR401 3.2 239.6 1.0
C4B D:MNR401 3.2 238.8 1.0
CD D:GLU219 3.2 146.1 1.0
CHD D:MNR401 3.4 240.8 1.0
CHA D:MNR401 3.5 242.3 1.0
CHB D:MNR401 3.5 240.2 1.0
CHC D:MNR401 3.5 238.6 1.0
OE1 B:GLU219 3.9 124.8 1.0
OE1 D:GLU219 4.0 148.7 1.0
CG D:GLU219 4.1 144.6 1.0
CG B:GLU219 4.2 123.4 1.0
C3C D:MNR401 4.4 239.4 1.0
C2A D:MNR401 4.4 242.2 1.0
C3D D:MNR401 4.4 242.6 1.0
C2D D:MNR401 4.4 242.2 1.0
C3A D:MNR401 4.4 241.6 1.0
C2C D:MNR401 4.4 238.8 1.0
C3B D:MNR401 4.5 238.4 1.0
C2B D:MNR401 4.5 238.9 1.0
NE2 D:HIS163 4.6 154.1 1.0
CB D:GLU219 4.8 145.1 1.0
CB B:GLU219 4.8 123.8 1.0
CD1 D:LEU39 4.8 183.1 1.0
CE1 D:HIS163 4.8 153.5 1.0
CE1 B:HIS163 4.9 119.3 1.0
NE2 B:HIS163 5.0 119.6 1.0

Manganese binding site 2 out of 2 in 7w7a

Go back to Manganese Binding Sites List in 7w7a
Manganese binding site 2 out of 2 in the Heme Exporter in Complex with Mn-Containing Protoporphyrin IX, Mn- Anomalous Data


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Heme Exporter in Complex with Mn-Containing Protoporphyrin IX, Mn- Anomalous Data within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn401

b:482.5
occ:1.00
MN H:MNR401 0.0 482.5 1.0
OE2 F:GLU219 1.9 149.9 1.0
OE2 H:GLU219 1.9 161.3 1.0
NB H:MNR401 2.1 483.2 1.0
ND H:MNR401 2.1 481.7 1.0
NA H:MNR401 2.1 482.1 1.0
NC H:MNR401 2.1 482.9 1.0
C4C H:MNR401 3.1 482.9 1.0
C1A H:MNR401 3.1 481.4 1.0
C1D H:MNR401 3.1 481.9 1.0
C4D H:MNR401 3.1 481.1 1.0
C4A H:MNR401 3.1 482.6 1.0
C1C H:MNR401 3.1 483.3 1.0
C4B H:MNR401 3.1 483.7 1.0
C1B H:MNR401 3.2 483.6 1.0
CD H:GLU219 3.2 160.5 1.0
CD F:GLU219 3.2 148.0 1.0
CHA H:MNR401 3.4 480.8 1.0
CHD H:MNR401 3.4 482.5 1.0
CHC H:MNR401 3.5 483.6 1.0
CHB H:MNR401 3.5 483.4 1.0
OE1 F:GLU219 4.0 148.4 1.0
OE1 H:GLU219 4.0 161.4 1.0
CG H:GLU219 4.1 158.6 1.0
CG F:GLU219 4.2 145.0 1.0
C3C H:MNR401 4.4 483.3 1.0
C2D H:MNR401 4.4 481.3 1.0
C2A H:MNR401 4.4 481.4 1.0
C3D H:MNR401 4.4 480.7 1.0
C3A H:MNR401 4.4 482.2 1.0
C3B H:MNR401 4.4 484.4 1.0
C2C H:MNR401 4.4 483.6 1.0
C2B H:MNR401 4.4 484.3 1.0
NE2 F:HIS163 4.6 133.7 1.0
NE2 H:HIS163 4.7 172.5 1.0
CE1 H:HIS163 4.7 175.0 1.0
CB F:GLU219 4.9 145.1 1.0
CB H:GLU219 4.9 158.5 1.0
CE1 F:HIS163 4.9 133.6 1.0

Reference:

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
Page generated: Sun Oct 6 10:59:15 2024

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