Manganese in PDB 6omr: Crystal Structure of PTMU3 Complexed with Ptn Substrate
Protein crystallography data
The structure of Crystal Structure of PTMU3 Complexed with Ptn Substrate, PDB code: 6omr
was solved by
Y.C.Liu,
L.B.Dong,
B.Shen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.83 /
2.45
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
113.620,
122.420,
140.063,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.2 /
25.1
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of PTMU3 Complexed with Ptn Substrate
(pdb code 6omr). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the
Crystal Structure of PTMU3 Complexed with Ptn Substrate, PDB code: 6omr:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
Manganese binding site 1 out
of 5 in 6omr
Go back to
Manganese Binding Sites List in 6omr
Manganese binding site 1 out
of 5 in the Crystal Structure of PTMU3 Complexed with Ptn Substrate
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Crystal Structure of PTMU3 Complexed with Ptn Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn404
b:26.6
occ:1.00
|
OD1
|
A:ASP308
|
1.9
|
21.7
|
1.0
|
NE2
|
A:HIS189
|
2.1
|
21.3
|
1.0
|
OD1
|
A:ASP10
|
2.2
|
22.3
|
1.0
|
OE1
|
A:GLU241
|
2.3
|
24.2
|
1.0
|
OD2
|
A:ASP10
|
2.4
|
27.5
|
1.0
|
NE2
|
A:HIS12
|
2.4
|
23.8
|
1.0
|
CG
|
A:ASP10
|
2.6
|
26.2
|
1.0
|
CE1
|
A:HIS189
|
3.1
|
22.3
|
1.0
|
CG
|
A:ASP308
|
3.1
|
23.8
|
1.0
|
CD2
|
A:HIS189
|
3.2
|
21.7
|
1.0
|
CD
|
A:GLU241
|
3.3
|
22.9
|
1.0
|
CD2
|
A:HIS12
|
3.3
|
23.4
|
1.0
|
CE1
|
A:HIS12
|
3.4
|
24.8
|
1.0
|
MN
|
A:MN405
|
3.6
|
27.4
|
1.0
|
CB
|
A:GLU241
|
3.8
|
22.0
|
1.0
|
CG
|
A:GLU241
|
3.8
|
22.5
|
1.0
|
OD2
|
A:ASP308
|
3.9
|
21.4
|
1.0
|
CB
|
A:ASP10
|
4.1
|
27.4
|
1.0
|
CB
|
A:ASP308
|
4.2
|
25.1
|
1.0
|
ND1
|
A:HIS189
|
4.2
|
21.1
|
1.0
|
OE2
|
A:GLU241
|
4.3
|
21.9
|
1.0
|
CG
|
A:HIS189
|
4.3
|
21.8
|
1.0
|
ND1
|
A:HIS311
|
4.4
|
23.3
|
1.0
|
CG
|
A:HIS12
|
4.5
|
24.0
|
1.0
|
ND1
|
A:HIS12
|
4.5
|
23.6
|
1.0
|
CE1
|
A:HIS311
|
4.5
|
22.6
|
1.0
|
CA
|
A:ASP308
|
4.6
|
24.3
|
1.0
|
O
|
A:HOH607
|
4.6
|
33.6
|
1.0
|
N
|
A:SER11
|
4.9
|
21.7
|
1.0
|
C
|
A:ASP10
|
4.9
|
23.0
|
1.0
|
CD2
|
A:PHE88
|
4.9
|
20.1
|
1.0
|
CA
|
A:ASP10
|
4.9
|
25.3
|
1.0
|
|
Manganese binding site 2 out
of 5 in 6omr
Go back to
Manganese Binding Sites List in 6omr
Manganese binding site 2 out
of 5 in the Crystal Structure of PTMU3 Complexed with Ptn Substrate
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Crystal Structure of PTMU3 Complexed with Ptn Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn405
b:27.4
occ:1.00
|
OE2
|
A:GLU313
|
2.0
|
24.3
|
1.0
|
ND1
|
A:HIS311
|
2.3
|
23.3
|
1.0
|
OE2
|
A:GLU241
|
2.3
|
21.9
|
1.0
|
OD2
|
A:ASP308
|
2.3
|
21.4
|
1.0
|
OE1
|
A:GLU241
|
2.3
|
24.2
|
1.0
|
CD
|
A:GLU241
|
2.6
|
22.9
|
1.0
|
O
|
A:HOH607
|
2.7
|
33.6
|
1.0
|
CG
|
A:ASP308
|
3.0
|
23.8
|
1.0
|
OD1
|
A:ASP308
|
3.0
|
21.7
|
1.0
|
CD
|
A:GLU313
|
3.1
|
26.7
|
1.0
|
CE1
|
A:HIS311
|
3.2
|
22.6
|
1.0
|
CG
|
A:HIS311
|
3.3
|
23.2
|
1.0
|
CB
|
A:HIS311
|
3.6
|
26.7
|
1.0
|
CG
|
A:GLU313
|
3.6
|
27.9
|
1.0
|
MN
|
A:MN404
|
3.6
|
26.6
|
1.0
|
CG
|
A:GLU241
|
4.1
|
22.5
|
1.0
|
OE1
|
A:GLU313
|
4.2
|
26.1
|
1.0
|
NE2
|
A:HIS12
|
4.3
|
23.8
|
1.0
|
NE2
|
A:HIS311
|
4.3
|
23.1
|
1.0
|
CD2
|
A:HIS311
|
4.4
|
24.0
|
1.0
|
CB
|
A:ASP308
|
4.5
|
25.1
|
1.0
|
CE1
|
A:HIS189
|
4.5
|
22.3
|
1.0
|
NE2
|
A:HIS189
|
4.6
|
21.3
|
1.0
|
CD2
|
A:HIS12
|
4.8
|
23.4
|
1.0
|
|
Manganese binding site 3 out
of 5 in 6omr
Go back to
Manganese Binding Sites List in 6omr
Manganese binding site 3 out
of 5 in the Crystal Structure of PTMU3 Complexed with Ptn Substrate
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Crystal Structure of PTMU3 Complexed with Ptn Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn406
b:47.6
occ:1.00
|
OD1
|
A:ASP38
|
2.5
|
57.4
|
1.0
|
CG
|
A:ASP38
|
3.3
|
47.4
|
1.0
|
OD2
|
A:ASP38
|
3.8
|
43.8
|
1.0
|
CB
|
A:ASP38
|
4.4
|
46.9
|
1.0
|
|
Manganese binding site 4 out
of 5 in 6omr
Go back to
Manganese Binding Sites List in 6omr
Manganese binding site 4 out
of 5 in the Crystal Structure of PTMU3 Complexed with Ptn Substrate
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Crystal Structure of PTMU3 Complexed with Ptn Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn403
b:26.8
occ:1.00
|
OD1
|
B:ASP308
|
2.0
|
21.7
|
1.0
|
OE1
|
B:GLU241
|
2.1
|
20.4
|
1.0
|
OD1
|
B:ASP10
|
2.1
|
26.0
|
1.0
|
NE2
|
B:HIS189
|
2.2
|
20.7
|
1.0
|
NE2
|
B:HIS12
|
2.4
|
38.0
|
1.0
|
OD2
|
B:ASP10
|
2.5
|
27.6
|
1.0
|
CG
|
B:ASP10
|
2.6
|
28.5
|
1.0
|
CD
|
B:GLU241
|
3.1
|
25.8
|
1.0
|
CG
|
B:ASP308
|
3.2
|
26.3
|
1.0
|
CE1
|
B:HIS189
|
3.2
|
21.6
|
1.0
|
CD2
|
B:HIS189
|
3.2
|
20.4
|
1.0
|
CD2
|
B:HIS12
|
3.3
|
39.0
|
1.0
|
CE1
|
B:HIS12
|
3.3
|
38.5
|
1.0
|
CG
|
B:GLU241
|
3.4
|
23.3
|
1.0
|
CB
|
B:GLU241
|
3.9
|
24.6
|
1.0
|
OD2
|
B:ASP308
|
3.9
|
27.7
|
1.0
|
CB
|
B:ASP10
|
4.1
|
28.8
|
1.0
|
CB
|
B:ASP308
|
4.1
|
29.2
|
1.0
|
MN
|
B:MN404
|
4.2
|
35.7
|
1.0
|
OE2
|
B:GLU241
|
4.3
|
24.9
|
1.0
|
ND1
|
B:HIS189
|
4.3
|
21.3
|
1.0
|
CG
|
B:HIS189
|
4.3
|
20.7
|
1.0
|
CG
|
B:HIS12
|
4.4
|
39.6
|
1.0
|
ND1
|
B:HIS12
|
4.4
|
39.0
|
1.0
|
O
|
B:HOH598
|
4.4
|
30.9
|
1.0
|
CA
|
B:ASP308
|
4.5
|
31.7
|
1.0
|
N
|
B:SER11
|
4.7
|
29.4
|
1.0
|
ND1
|
B:HIS311
|
4.7
|
49.4
|
1.0
|
CE1
|
B:HIS311
|
4.8
|
53.2
|
1.0
|
C
|
B:ASP10
|
4.8
|
27.9
|
1.0
|
CA
|
B:ASP10
|
4.9
|
28.2
|
1.0
|
CD2
|
B:PHE88
|
4.9
|
31.7
|
1.0
|
CA
|
B:SER11
|
5.0
|
29.6
|
1.0
|
|
Manganese binding site 5 out
of 5 in 6omr
Go back to
Manganese Binding Sites List in 6omr
Manganese binding site 5 out
of 5 in the Crystal Structure of PTMU3 Complexed with Ptn Substrate
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Crystal Structure of PTMU3 Complexed with Ptn Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn404
b:35.7
occ:1.00
|
OE1
|
B:GLU313
|
2.2
|
34.0
|
1.0
|
OD2
|
B:ASP308
|
2.2
|
27.7
|
1.0
|
OE2
|
B:GLU241
|
2.3
|
24.9
|
1.0
|
OE1
|
B:GLU241
|
2.3
|
20.4
|
1.0
|
ND1
|
B:HIS311
|
2.4
|
49.4
|
1.0
|
CD
|
B:GLU241
|
2.6
|
25.8
|
1.0
|
O
|
B:HOH598
|
2.7
|
30.9
|
1.0
|
CG
|
B:ASP308
|
3.1
|
26.3
|
1.0
|
CG
|
B:HIS311
|
3.3
|
51.0
|
1.0
|
OD1
|
B:ASP308
|
3.4
|
21.7
|
1.0
|
CD
|
B:GLU313
|
3.4
|
43.4
|
1.0
|
CE1
|
B:HIS311
|
3.4
|
53.2
|
1.0
|
CB
|
B:HIS311
|
3.4
|
48.2
|
1.0
|
C22
|
B:MYM402
|
3.6
|
70.5
|
1.0
|
CG
|
B:GLU241
|
4.0
|
23.3
|
1.0
|
CG
|
B:GLU313
|
4.2
|
46.5
|
1.0
|
MN
|
B:MN403
|
4.2
|
26.8
|
1.0
|
C23
|
B:MYM402
|
4.3
|
71.3
|
1.0
|
OE2
|
B:GLU313
|
4.4
|
43.4
|
1.0
|
C21
|
B:MYM402
|
4.4
|
70.5
|
1.0
|
CB
|
B:GLU313
|
4.4
|
45.3
|
1.0
|
C24
|
B:MYM402
|
4.5
|
70.3
|
1.0
|
CD2
|
B:HIS311
|
4.5
|
53.5
|
1.0
|
CB
|
B:ASP308
|
4.5
|
29.2
|
1.0
|
NE2
|
B:HIS311
|
4.5
|
55.6
|
1.0
|
C08
|
B:MYM402
|
4.5
|
70.9
|
1.0
|
NE2
|
B:HIS12
|
4.6
|
38.0
|
1.0
|
C07
|
B:MYM402
|
4.7
|
73.8
|
1.0
|
CE1
|
B:HIS189
|
4.9
|
21.6
|
1.0
|
CD2
|
B:HIS12
|
4.9
|
39.0
|
1.0
|
CA
|
B:HIS311
|
5.0
|
45.8
|
1.0
|
|
Reference:
L.B.Dong,
Y.C.Liu,
A.J.Cepeda,
E.Kalkreuter,
M.R.Deng,
J.D.Rudolf,
C.Chang,
A.Joachimiak,
G.N.Phillips Jr.,
B.Shen.
Characterization and Crystal Structure of A Nonheme Diiron Monooxygenase Involved in Platensimycin and Platencin Biosynthesis. J.Am.Chem.Soc. V. 141 12406 2019.
ISSN: ESSN 1520-5126
PubMed: 31291107
DOI: 10.1021/JACS.9B06183
Page generated: Sun Oct 6 05:43:51 2024
|