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
|