Manganese in PDB 5t2k: Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III
Protein crystallography data
The structure of Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III, PDB code: 5t2k
was solved by
G.H.Gauss,
A.I.Celis,
J.L.Dubois,
J.W.Peters,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.40 /
1.80
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.016,
93.458,
132.543,
90.00,
105.31,
90.00
|
R / Rfree (%)
|
15.4 /
17.6
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III
(pdb code 5t2k). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the
Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III, PDB code: 5t2k:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
Manganese binding site 1 out
of 5 in 5t2k
Go back to
Manganese Binding Sites List in 5t2k
Manganese binding site 1 out
of 5 in the Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn301
b:19.2
occ:1.00
|
MN
|
A:76R301
|
0.0
|
19.2
|
1.0
|
NB
|
A:76R301
|
2.1
|
23.6
|
1.0
|
ND
|
A:76R301
|
2.1
|
21.3
|
1.0
|
NA
|
A:76R301
|
2.1
|
20.7
|
1.0
|
NC
|
A:76R301
|
2.1
|
20.8
|
1.0
|
NE2
|
A:HIS171
|
2.3
|
17.9
|
1.0
|
C4B
|
A:76R301
|
3.1
|
18.8
|
1.0
|
C4D
|
A:76R301
|
3.1
|
22.3
|
1.0
|
C1A
|
A:76R301
|
3.1
|
24.4
|
1.0
|
C1C
|
A:76R301
|
3.1
|
17.8
|
1.0
|
C1D
|
A:76R301
|
3.1
|
23.1
|
1.0
|
C4A
|
A:76R301
|
3.1
|
16.6
|
1.0
|
C4C
|
A:76R301
|
3.1
|
18.7
|
1.0
|
C1B
|
A:76R301
|
3.1
|
19.0
|
1.0
|
CD2
|
A:HIS171
|
3.3
|
17.5
|
1.0
|
CE1
|
A:HIS171
|
3.4
|
20.4
|
1.0
|
HD2
|
A:HIS171
|
3.4
|
21.0
|
1.0
|
CHC
|
A:76R301
|
3.5
|
16.6
|
1.0
|
CHA
|
A:76R301
|
3.5
|
21.8
|
1.0
|
CHD
|
A:76R301
|
3.5
|
19.8
|
1.0
|
CHB
|
A:76R301
|
3.5
|
18.4
|
1.0
|
HE1
|
A:HIS171
|
3.5
|
24.4
|
1.0
|
HG13
|
A:ILE186
|
3.7
|
20.0
|
1.0
|
HG3
|
A:GLN184
|
3.8
|
29.1
|
1.0
|
HE1
|
A:MET216
|
4.0
|
22.9
|
1.0
|
HD11
|
A:ILE186
|
4.0
|
25.8
|
1.0
|
C3B
|
A:76R301
|
4.3
|
17.1
|
1.0
|
C2B
|
A:76R301
|
4.4
|
20.3
|
1.0
|
C2D
|
A:76R301
|
4.4
|
33.5
|
1.0
|
C2A
|
A:76R301
|
4.4
|
21.7
|
1.0
|
C3D
|
A:76R301
|
4.4
|
30.4
|
1.0
|
C2C
|
A:76R301
|
4.4
|
18.6
|
1.0
|
C3A
|
A:76R301
|
4.4
|
23.4
|
1.0
|
C3C
|
A:76R301
|
4.4
|
17.8
|
1.0
|
CG
|
A:HIS171
|
4.4
|
16.1
|
1.0
|
ND1
|
A:HIS171
|
4.5
|
16.6
|
1.0
|
HE1
|
A:MET168
|
4.5
|
26.9
|
1.0
|
CG1
|
A:ILE186
|
4.5
|
16.7
|
1.0
|
HHC
|
A:76R301
|
4.5
|
20.0
|
1.0
|
HHA
|
A:76R301
|
4.5
|
26.2
|
1.0
|
HHD
|
A:76R301
|
4.5
|
23.8
|
1.0
|
HHB
|
A:76R301
|
4.6
|
22.1
|
1.0
|
HG12
|
A:ILE186
|
4.6
|
20.0
|
1.0
|
CD1
|
A:ILE186
|
4.6
|
21.5
|
1.0
|
O
|
A:HOH584
|
4.7
|
49.3
|
1.0
|
CG
|
A:GLN184
|
4.8
|
24.2
|
1.0
|
HD12
|
A:ILE186
|
4.8
|
25.8
|
1.0
|
CE
|
A:MET216
|
4.8
|
19.1
|
1.0
|
HE21
|
A:GLN184
|
4.8
|
38.9
|
1.0
|
HE2
|
A:MET216
|
4.9
|
22.9
|
1.0
|
|
Manganese binding site 2 out
of 5 in 5t2k
Go back to
Manganese Binding Sites List in 5t2k
Manganese binding site 2 out
of 5 in the Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn301
b:20.4
occ:1.00
|
MN
|
B:76R301
|
0.0
|
20.4
|
1.0
|
NA
|
B:76R301
|
2.1
|
21.0
|
1.0
|
NB
|
B:76R301
|
2.1
|
20.6
|
1.0
|
ND
|
B:76R301
|
2.1
|
21.5
|
1.0
|
NC
|
B:76R301
|
2.1
|
23.6
|
1.0
|
NE2
|
B:HIS171
|
2.3
|
17.9
|
1.0
|
C1A
|
B:76R301
|
3.0
|
26.1
|
1.0
|
C4A
|
B:76R301
|
3.0
|
21.5
|
1.0
|
C4D
|
B:76R301
|
3.1
|
29.2
|
1.0
|
C4C
|
B:76R301
|
3.1
|
21.2
|
1.0
|
C1C
|
B:76R301
|
3.1
|
18.6
|
1.0
|
C1D
|
B:76R301
|
3.1
|
23.3
|
1.0
|
C4B
|
B:76R301
|
3.1
|
18.7
|
1.0
|
C1B
|
B:76R301
|
3.1
|
20.7
|
1.0
|
CD2
|
B:HIS171
|
3.2
|
17.1
|
1.0
|
CE1
|
B:HIS171
|
3.3
|
17.6
|
1.0
|
HD2
|
B:HIS171
|
3.4
|
20.5
|
1.0
|
CHA
|
B:76R301
|
3.4
|
23.8
|
1.0
|
CHB
|
B:76R301
|
3.5
|
17.9
|
1.0
|
CHD
|
B:76R301
|
3.5
|
21.2
|
1.0
|
HE1
|
B:HIS171
|
3.5
|
21.1
|
1.0
|
CHC
|
B:76R301
|
3.5
|
18.6
|
1.0
|
HG13
|
B:ILE186
|
3.8
|
22.3
|
1.0
|
HG3
|
B:GLN184
|
3.9
|
32.4
|
1.0
|
HE1
|
B:MET216
|
4.0
|
24.1
|
1.0
|
HD11
|
B:ILE186
|
4.1
|
24.6
|
1.0
|
HE1
|
B:MET168
|
4.3
|
25.4
|
1.0
|
C3B
|
B:76R301
|
4.3
|
17.9
|
1.0
|
C2B
|
B:76R301
|
4.3
|
17.1
|
1.0
|
C2A
|
B:76R301
|
4.3
|
24.3
|
1.0
|
C3A
|
B:76R301
|
4.4
|
20.1
|
1.0
|
C3D
|
B:76R301
|
4.4
|
27.6
|
1.0
|
C3C
|
B:76R301
|
4.4
|
18.6
|
1.0
|
C2C
|
B:76R301
|
4.4
|
17.8
|
1.0
|
C2D
|
B:76R301
|
4.4
|
29.7
|
1.0
|
ND1
|
B:HIS171
|
4.4
|
15.7
|
1.0
|
CG
|
B:HIS171
|
4.4
|
15.6
|
1.0
|
O
|
B:HOH593
|
4.5
|
35.5
|
1.0
|
HHA
|
B:76R301
|
4.5
|
28.5
|
1.0
|
HHB
|
B:76R301
|
4.5
|
21.5
|
1.0
|
HHC
|
B:76R301
|
4.5
|
22.3
|
1.0
|
CG1
|
B:ILE186
|
4.5
|
18.6
|
1.0
|
HHD
|
B:76R301
|
4.6
|
25.4
|
1.0
|
HE21
|
B:GLN184
|
4.6
|
41.8
|
1.0
|
HG12
|
B:ILE186
|
4.7
|
22.3
|
1.0
|
CD1
|
B:ILE186
|
4.7
|
20.6
|
1.0
|
CG
|
B:GLN184
|
4.8
|
27.0
|
1.0
|
HD12
|
B:ILE186
|
4.9
|
24.6
|
1.0
|
CE
|
B:MET216
|
4.9
|
20.1
|
1.0
|
HE3
|
B:MET168
|
5.0
|
25.4
|
1.0
|
|
Manganese binding site 3 out
of 5 in 5t2k
Go back to
Manganese Binding Sites List in 5t2k
Manganese binding site 3 out
of 5 in the Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn301
b:29.7
occ:1.00
|
MN
|
C:76R301
|
0.0
|
29.7
|
1.0
|
ND
|
C:76R301
|
2.1
|
36.5
|
1.0
|
NB
|
C:76R301
|
2.1
|
32.6
|
1.0
|
NA
|
C:76R301
|
2.1
|
35.5
|
1.0
|
NC
|
C:76R301
|
2.1
|
32.7
|
1.0
|
NE2
|
C:HIS171
|
2.5
|
26.7
|
1.0
|
C4D
|
C:76R301
|
3.0
|
40.0
|
1.0
|
C1A
|
C:76R301
|
3.1
|
37.9
|
1.0
|
C4B
|
C:76R301
|
3.1
|
26.5
|
1.0
|
C1D
|
C:76R301
|
3.1
|
35.4
|
1.0
|
C4C
|
C:76R301
|
3.1
|
30.8
|
1.0
|
C4A
|
C:76R301
|
3.1
|
34.0
|
1.0
|
C1C
|
C:76R301
|
3.1
|
26.6
|
1.0
|
C1B
|
C:76R301
|
3.2
|
32.7
|
1.0
|
CD2
|
C:HIS171
|
3.3
|
27.6
|
1.0
|
HD2
|
C:HIS171
|
3.3
|
33.1
|
1.0
|
CHA
|
C:76R301
|
3.4
|
35.6
|
1.0
|
CHD
|
C:76R301
|
3.5
|
33.4
|
1.0
|
CHC
|
C:76R301
|
3.5
|
29.6
|
1.0
|
CHB
|
C:76R301
|
3.5
|
31.3
|
1.0
|
CE1
|
C:HIS171
|
3.5
|
23.9
|
1.0
|
HG13
|
C:ILE186
|
3.8
|
27.3
|
1.0
|
HE1
|
C:HIS171
|
3.8
|
28.7
|
1.0
|
HG3
|
C:GLN184
|
4.0
|
39.8
|
1.0
|
HD11
|
C:ILE186
|
4.0
|
30.8
|
1.0
|
HE1
|
C:MET216
|
4.2
|
36.3
|
1.0
|
HE1
|
C:MET168
|
4.2
|
28.0
|
1.0
|
C3B
|
C:76R301
|
4.3
|
30.6
|
1.0
|
C3D
|
C:76R301
|
4.4
|
43.5
|
1.0
|
C2A
|
C:76R301
|
4.4
|
41.9
|
1.0
|
C2B
|
C:76R301
|
4.4
|
29.7
|
1.0
|
C2D
|
C:76R301
|
4.4
|
41.9
|
1.0
|
C3A
|
C:76R301
|
4.4
|
35.0
|
1.0
|
O
|
C:HOH600
|
4.4
|
43.7
|
1.0
|
C3C
|
C:76R301
|
4.4
|
29.6
|
1.0
|
C2C
|
C:76R301
|
4.4
|
30.2
|
1.0
|
CG
|
C:HIS171
|
4.5
|
25.8
|
1.0
|
HHA
|
C:76R301
|
4.5
|
42.7
|
1.0
|
CG1
|
C:ILE186
|
4.5
|
22.7
|
1.0
|
HE21
|
C:GLN184
|
4.5
|
43.2
|
1.0
|
HHC
|
C:76R301
|
4.5
|
35.6
|
1.0
|
HHD
|
C:76R301
|
4.5
|
40.0
|
1.0
|
ND1
|
C:HIS171
|
4.6
|
23.0
|
1.0
|
HHB
|
C:76R301
|
4.6
|
37.5
|
1.0
|
HG12
|
C:ILE186
|
4.6
|
27.3
|
1.0
|
CD1
|
C:ILE186
|
4.6
|
25.6
|
1.0
|
HD12
|
C:ILE186
|
4.8
|
30.8
|
1.0
|
CG
|
C:GLN184
|
4.9
|
33.2
|
1.0
|
HE3
|
C:MET168
|
4.9
|
28.0
|
1.0
|
CE
|
C:MET168
|
4.9
|
23.3
|
1.0
|
NE2
|
C:GLN184
|
5.0
|
36.0
|
1.0
|
|
Manganese binding site 4 out
of 5 in 5t2k
Go back to
Manganese Binding Sites List in 5t2k
Manganese binding site 4 out
of 5 in the Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn301
b:25.3
occ:1.00
|
MN
|
D:76R301
|
0.0
|
25.3
|
1.0
|
NB
|
D:76R301
|
2.1
|
27.6
|
1.0
|
NA
|
D:76R301
|
2.1
|
32.5
|
1.0
|
ND
|
D:76R301
|
2.1
|
31.5
|
1.0
|
NC
|
D:76R301
|
2.1
|
23.3
|
1.0
|
NE2
|
D:HIS171
|
2.3
|
24.9
|
1.0
|
C4D
|
D:76R301
|
3.1
|
34.0
|
1.0
|
C1A
|
D:76R301
|
3.1
|
37.3
|
1.0
|
C4B
|
D:76R301
|
3.1
|
23.6
|
1.0
|
C4A
|
D:76R301
|
3.1
|
28.5
|
1.0
|
C1D
|
D:76R301
|
3.1
|
28.8
|
1.0
|
C1C
|
D:76R301
|
3.1
|
20.7
|
1.0
|
C4C
|
D:76R301
|
3.1
|
23.4
|
1.0
|
C1B
|
D:76R301
|
3.1
|
21.2
|
1.0
|
CD2
|
D:HIS171
|
3.2
|
21.2
|
1.0
|
HD2
|
D:HIS171
|
3.3
|
25.4
|
1.0
|
CE1
|
D:HIS171
|
3.4
|
21.9
|
1.0
|
CHA
|
D:76R301
|
3.4
|
35.6
|
1.0
|
CHC
|
D:76R301
|
3.5
|
19.6
|
1.0
|
CHD
|
D:76R301
|
3.5
|
26.6
|
1.0
|
CHB
|
D:76R301
|
3.5
|
24.9
|
1.0
|
HE1
|
D:HIS171
|
3.6
|
26.2
|
1.0
|
HG13
|
D:ILE186
|
3.7
|
25.3
|
1.0
|
HG3
|
D:GLN184
|
3.8
|
37.5
|
1.0
|
HD11
|
D:ILE186
|
3.9
|
30.7
|
1.0
|
HE1
|
D:MET216
|
4.0
|
33.6
|
1.0
|
C3B
|
D:76R301
|
4.3
|
24.1
|
1.0
|
HE1
|
D:MET168
|
4.3
|
28.8
|
1.0
|
C2B
|
D:76R301
|
4.3
|
22.2
|
1.0
|
C3D
|
D:76R301
|
4.4
|
33.9
|
1.0
|
C2A
|
D:76R301
|
4.4
|
35.6
|
1.0
|
C3A
|
D:76R301
|
4.4
|
31.5
|
1.0
|
C2D
|
D:76R301
|
4.4
|
38.9
|
1.0
|
CG
|
D:HIS171
|
4.4
|
21.5
|
1.0
|
C3C
|
D:76R301
|
4.4
|
22.4
|
1.0
|
C2C
|
D:76R301
|
4.4
|
20.9
|
1.0
|
CG1
|
D:ILE186
|
4.4
|
21.1
|
1.0
|
ND1
|
D:HIS171
|
4.5
|
22.6
|
1.0
|
HHA
|
D:76R301
|
4.5
|
42.8
|
1.0
|
HHC
|
D:76R301
|
4.5
|
23.5
|
1.0
|
CD1
|
D:ILE186
|
4.5
|
25.6
|
1.0
|
HHB
|
D:76R301
|
4.6
|
29.9
|
1.0
|
HHD
|
D:76R301
|
4.6
|
32.0
|
1.0
|
HG12
|
D:ILE186
|
4.6
|
25.3
|
1.0
|
HD12
|
D:ILE186
|
4.7
|
30.7
|
1.0
|
CG
|
D:GLN184
|
4.8
|
31.2
|
1.0
|
HE21
|
D:GLN184
|
4.8
|
47.0
|
1.0
|
CE
|
D:MET216
|
4.9
|
28.0
|
1.0
|
HE3
|
D:MET168
|
5.0
|
28.8
|
1.0
|
HBB1
|
D:76R301
|
5.0
|
44.5
|
1.0
|
|
Manganese binding site 5 out
of 5 in 5t2k
Go back to
Manganese Binding Sites List in 5t2k
Manganese binding site 5 out
of 5 in the Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn301
b:21.9
occ:1.00
|
MN
|
E:76R301
|
0.0
|
21.9
|
1.0
|
NC
|
E:76R301
|
2.1
|
24.1
|
1.0
|
NB
|
E:76R301
|
2.1
|
21.8
|
1.0
|
NA
|
E:76R301
|
2.1
|
22.0
|
1.0
|
ND
|
E:76R301
|
2.1
|
24.6
|
1.0
|
NE2
|
E:HIS171
|
2.3
|
22.4
|
1.0
|
C1C
|
E:76R301
|
3.1
|
19.5
|
1.0
|
C4B
|
E:76R301
|
3.1
|
20.7
|
1.0
|
C1A
|
E:76R301
|
3.1
|
26.1
|
1.0
|
C4C
|
E:76R301
|
3.1
|
24.0
|
1.0
|
C4D
|
E:76R301
|
3.1
|
28.0
|
1.0
|
C4A
|
E:76R301
|
3.1
|
23.1
|
1.0
|
C1D
|
E:76R301
|
3.1
|
25.0
|
1.0
|
C1B
|
E:76R301
|
3.1
|
22.5
|
1.0
|
CD2
|
E:HIS171
|
3.2
|
19.8
|
1.0
|
CE1
|
E:HIS171
|
3.3
|
20.7
|
1.0
|
HD2
|
E:HIS171
|
3.3
|
23.8
|
1.0
|
CHC
|
E:76R301
|
3.5
|
21.9
|
1.0
|
CHA
|
E:76R301
|
3.5
|
24.4
|
1.0
|
CHD
|
E:76R301
|
3.5
|
23.6
|
1.0
|
HE1
|
E:HIS171
|
3.5
|
24.8
|
1.0
|
CHB
|
E:76R301
|
3.5
|
22.0
|
1.0
|
HG13
|
E:ILE186
|
3.8
|
28.3
|
1.0
|
HG3
|
E:GLN184
|
3.8
|
32.6
|
1.0
|
HE1
|
E:MET216
|
4.0
|
25.8
|
1.0
|
HD11
|
E:ILE186
|
4.0
|
27.6
|
1.0
|
C3B
|
E:76R301
|
4.3
|
21.4
|
1.0
|
C2B
|
E:76R301
|
4.4
|
15.7
|
1.0
|
C3C
|
E:76R301
|
4.4
|
22.4
|
1.0
|
C2C
|
E:76R301
|
4.4
|
20.7
|
1.0
|
C2A
|
E:76R301
|
4.4
|
25.9
|
1.0
|
CG
|
E:HIS171
|
4.4
|
18.4
|
1.0
|
ND1
|
E:HIS171
|
4.4
|
19.8
|
1.0
|
C3D
|
E:76R301
|
4.4
|
36.1
|
1.0
|
C2D
|
E:76R301
|
4.4
|
36.1
|
1.0
|
C3A
|
E:76R301
|
4.4
|
23.0
|
1.0
|
CG1
|
E:ILE186
|
4.5
|
23.6
|
1.0
|
HHC
|
E:76R301
|
4.5
|
26.3
|
1.0
|
HE1
|
E:MET168
|
4.5
|
26.6
|
1.0
|
HHA
|
E:76R301
|
4.5
|
29.3
|
1.0
|
HHD
|
E:76R301
|
4.6
|
28.3
|
1.0
|
HHB
|
E:76R301
|
4.6
|
26.4
|
1.0
|
HG12
|
E:ILE186
|
4.6
|
28.3
|
1.0
|
CD1
|
E:ILE186
|
4.7
|
23.0
|
1.0
|
O
|
E:HOH599
|
4.7
|
48.5
|
1.0
|
CG
|
E:GLN184
|
4.8
|
27.2
|
1.0
|
CE
|
E:MET216
|
4.8
|
21.5
|
1.0
|
HD12
|
E:ILE186
|
4.8
|
27.6
|
1.0
|
HE21
|
E:GLN184
|
5.0
|
41.6
|
1.0
|
HE2
|
E:MET216
|
5.0
|
25.8
|
1.0
|
|
Reference:
A.I.Celis,
G.H.Gauss,
B.R.Streit,
K.Shisler,
G.C.Moraski,
K.R.Rodgers,
G.S.Lukat-Rodgers,
J.W.Peters,
J.L.Dubois.
Structure-Based Mechanism For Oxidative Decarboxylation Reactions Mediated By Amino Acids and Heme Propionates in Coproheme Decarboxylase (Hemq). J. Am. Chem. Soc. 2017.
ISSN: ESSN 1520-5126
PubMed: 27936663
DOI: 10.1021/JACS.6B11324
Page generated: Sun Oct 6 02:54:49 2024
|