Manganese in PDB 6omq: Crystal Structure of PTMU3 Complexed with Ptm Substrate
Protein crystallography data
The structure of Crystal Structure of PTMU3 Complexed with Ptm Substrate, PDB code: 6omq
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)
|
29.73 /
1.86
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
112.564,
122.864,
139.936,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.1 /
23.5
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of PTMU3 Complexed with Ptm Substrate
(pdb code 6omq). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the
Crystal Structure of PTMU3 Complexed with Ptm Substrate, PDB code: 6omq:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
Manganese binding site 1 out
of 7 in 6omq
Go back to
Manganese Binding Sites List in 6omq
Manganese binding site 1 out
of 7 in the Crystal Structure of PTMU3 Complexed with Ptm 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 Ptm Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn406
b:10.2
occ:1.00
|
OD1
|
A:ASP308
|
1.9
|
11.4
|
1.0
|
NE2
|
A:HIS12
|
2.2
|
10.5
|
1.0
|
OE1
|
A:GLU241
|
2.2
|
13.0
|
1.0
|
NE2
|
A:HIS189
|
2.3
|
13.5
|
1.0
|
OD1
|
A:ASP10
|
2.3
|
10.8
|
1.0
|
OD2
|
A:ASP10
|
2.3
|
10.4
|
1.0
|
CG
|
A:ASP10
|
2.6
|
10.5
|
1.0
|
CG
|
A:ASP308
|
3.1
|
10.7
|
1.0
|
CD2
|
A:HIS12
|
3.2
|
11.2
|
1.0
|
CE1
|
A:HIS12
|
3.2
|
10.7
|
1.0
|
CE1
|
A:HIS189
|
3.2
|
12.5
|
1.0
|
CD2
|
A:HIS189
|
3.3
|
12.2
|
1.0
|
CD
|
A:GLU241
|
3.3
|
13.1
|
1.0
|
MN
|
A:MN407
|
3.8
|
11.5
|
1.0
|
CG
|
A:GLU241
|
3.8
|
12.3
|
1.0
|
OD2
|
A:ASP308
|
3.8
|
11.9
|
1.0
|
CB
|
A:GLU241
|
3.9
|
12.3
|
1.0
|
CB
|
A:ASP308
|
4.1
|
9.7
|
1.0
|
CB
|
A:ASP10
|
4.1
|
9.9
|
1.0
|
ND1
|
A:HIS12
|
4.3
|
12.2
|
1.0
|
CG
|
A:HIS12
|
4.3
|
10.5
|
1.0
|
ND1
|
A:HIS189
|
4.4
|
11.7
|
1.0
|
OE2
|
A:GLU241
|
4.4
|
12.6
|
1.0
|
ND1
|
A:HIS311
|
4.4
|
9.7
|
1.0
|
CG
|
A:HIS189
|
4.5
|
12.9
|
1.0
|
CA
|
A:ASP308
|
4.5
|
9.2
|
1.0
|
O
|
A:HOH757
|
4.6
|
12.9
|
1.0
|
CE1
|
A:HIS311
|
4.6
|
11.1
|
1.0
|
N
|
A:SER11
|
4.7
|
8.9
|
1.0
|
C
|
A:ASP10
|
4.9
|
8.4
|
1.0
|
CD2
|
A:PHE88
|
4.9
|
10.9
|
1.0
|
CA
|
A:ASP10
|
4.9
|
9.7
|
1.0
|
|
Manganese binding site 2 out
of 7 in 6omq
Go back to
Manganese Binding Sites List in 6omq
Manganese binding site 2 out
of 7 in the Crystal Structure of PTMU3 Complexed with Ptm 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 Ptm Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn407
b:11.5
occ:1.00
|
OE2
|
A:GLU313
|
2.1
|
11.8
|
1.0
|
OD2
|
A:ASP308
|
2.2
|
11.9
|
1.0
|
OE1
|
A:GLU241
|
2.2
|
13.0
|
1.0
|
ND1
|
A:HIS311
|
2.2
|
9.7
|
1.0
|
O
|
A:HOH757
|
2.3
|
12.9
|
1.0
|
OE2
|
A:GLU241
|
2.4
|
12.6
|
1.0
|
CD
|
A:GLU241
|
2.6
|
13.1
|
1.0
|
CG
|
A:ASP308
|
3.0
|
10.7
|
1.0
|
OD1
|
A:ASP308
|
3.1
|
11.4
|
1.0
|
CE1
|
A:HIS311
|
3.2
|
11.1
|
1.0
|
CD
|
A:GLU313
|
3.2
|
10.6
|
1.0
|
CG
|
A:HIS311
|
3.2
|
10.9
|
1.0
|
CB
|
A:HIS311
|
3.5
|
10.7
|
1.0
|
CG
|
A:GLU313
|
3.6
|
11.4
|
1.0
|
MN
|
A:MN406
|
3.8
|
10.2
|
1.0
|
CG
|
A:GLU241
|
4.1
|
12.3
|
1.0
|
O
|
A:HOH753
|
4.1
|
39.0
|
1.0
|
OE1
|
A:GLU313
|
4.2
|
10.7
|
1.0
|
NE2
|
A:HIS12
|
4.2
|
10.5
|
1.0
|
NE2
|
A:HIS311
|
4.3
|
10.4
|
1.0
|
CD2
|
A:HIS311
|
4.4
|
10.6
|
1.0
|
CB
|
A:ASP308
|
4.4
|
9.7
|
1.0
|
O
|
A:HOH801
|
4.6
|
35.3
|
1.0
|
CD2
|
A:HIS12
|
4.6
|
11.2
|
1.0
|
CE1
|
A:HIS189
|
4.7
|
12.5
|
1.0
|
O
|
A:HOH553
|
4.8
|
31.1
|
1.0
|
NE2
|
A:HIS189
|
4.9
|
13.5
|
1.0
|
O
|
A:HOH815
|
5.0
|
38.9
|
1.0
|
CA
|
A:HIS311
|
5.0
|
11.9
|
1.0
|
|
Manganese binding site 3 out
of 7 in 6omq
Go back to
Manganese Binding Sites List in 6omq
Manganese binding site 3 out
of 7 in the Crystal Structure of PTMU3 Complexed with Ptm 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 Ptm Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn408
b:42.8
occ:1.00
|
O
|
A:LEU312
|
2.3
|
12.7
|
1.0
|
OE1
|
B:GLN260
|
2.4
|
19.3
|
1.0
|
O
|
A:GLY314
|
2.5
|
12.3
|
1.0
|
O
|
B:HOH783
|
2.5
|
16.4
|
1.0
|
O
|
A:HOH746
|
2.5
|
12.9
|
1.0
|
O
|
A:HOH645
|
2.5
|
13.4
|
1.0
|
O
|
B:HOH587
|
3.2
|
26.0
|
1.0
|
C
|
A:LEU312
|
3.4
|
14.1
|
1.0
|
CD
|
B:GLN260
|
3.4
|
17.7
|
1.0
|
C
|
A:GLY314
|
3.6
|
12.7
|
1.0
|
O
|
A:PHE316
|
4.0
|
15.4
|
1.0
|
N
|
A:GLY314
|
4.1
|
12.8
|
1.0
|
CG
|
B:GLN260
|
4.1
|
16.2
|
1.0
|
CA
|
A:LEU312
|
4.2
|
15.5
|
1.0
|
O
|
A:HIS311
|
4.3
|
12.4
|
1.0
|
O
|
A:HOH858
|
4.3
|
38.6
|
1.0
|
O
|
A:HOH673
|
4.3
|
15.8
|
1.0
|
CB
|
B:GLN260
|
4.4
|
15.0
|
1.0
|
O
|
A:HOH755
|
4.4
|
32.5
|
1.0
|
N
|
A:GLU313
|
4.4
|
12.9
|
1.0
|
C
|
A:GLU313
|
4.4
|
13.4
|
1.0
|
NE2
|
B:GLN260
|
4.4
|
17.4
|
1.0
|
CA
|
A:GLY314
|
4.4
|
12.0
|
1.0
|
N
|
A:THR315
|
4.5
|
12.2
|
1.0
|
O
|
B:HOH536
|
4.5
|
20.3
|
1.0
|
O
|
B:HOH756
|
4.6
|
45.7
|
1.0
|
CA
|
A:GLU313
|
4.6
|
13.2
|
1.0
|
C
|
A:THR315
|
4.7
|
13.7
|
1.0
|
CA
|
A:THR315
|
4.7
|
13.0
|
1.0
|
CE1
|
A:HIS287
|
4.8
|
12.6
|
1.0
|
O
|
A:THR315
|
4.9
|
13.1
|
1.0
|
N
|
A:PHE316
|
4.9
|
15.8
|
1.0
|
O
|
A:HOH758
|
4.9
|
34.8
|
1.0
|
O
|
A:HOH644
|
4.9
|
13.1
|
1.0
|
O
|
A:GLU313
|
5.0
|
12.8
|
1.0
|
O
|
A:HOH864
|
5.0
|
46.2
|
1.0
|
|
Manganese binding site 4 out
of 7 in 6omq
Go back to
Manganese Binding Sites List in 6omq
Manganese binding site 4 out
of 7 in the Crystal Structure of PTMU3 Complexed with Ptm 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 Ptm Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn406
b:11.7
occ:1.00
|
OD1
|
B:ASP10
|
1.9
|
12.3
|
1.0
|
OD1
|
B:ASP308
|
2.0
|
10.9
|
1.0
|
OE1
|
B:GLU241
|
2.0
|
16.0
|
1.0
|
NE2
|
B:HIS189
|
2.2
|
11.2
|
1.0
|
NE2
|
B:HIS12
|
2.2
|
10.8
|
1.0
|
OD2
|
B:ASP10
|
2.6
|
13.8
|
1.0
|
CG
|
B:ASP10
|
2.6
|
13.9
|
1.0
|
CG
|
B:ASP308
|
3.1
|
10.4
|
1.0
|
CE1
|
B:HIS189
|
3.1
|
12.7
|
1.0
|
CD2
|
B:HIS12
|
3.2
|
13.2
|
1.0
|
CD
|
B:GLU241
|
3.2
|
13.3
|
1.0
|
CE1
|
B:HIS12
|
3.3
|
14.3
|
1.0
|
CD2
|
B:HIS189
|
3.3
|
11.4
|
1.0
|
OD2
|
B:ASP308
|
3.6
|
11.2
|
1.0
|
MN
|
B:MN407
|
3.8
|
16.4
|
1.0
|
CG
|
B:GLU241
|
3.8
|
13.6
|
1.0
|
CB
|
B:GLU241
|
3.9
|
13.0
|
1.0
|
CB
|
B:ASP10
|
4.1
|
13.4
|
1.0
|
CB
|
B:ASP308
|
4.1
|
12.1
|
1.0
|
O
|
B:HOH760
|
4.2
|
19.4
|
1.0
|
OE2
|
B:GLU241
|
4.3
|
15.0
|
1.0
|
ND1
|
B:HIS189
|
4.3
|
11.5
|
1.0
|
CG
|
B:HIS12
|
4.3
|
12.9
|
1.0
|
ND1
|
B:HIS12
|
4.4
|
12.4
|
1.0
|
CG
|
B:HIS189
|
4.4
|
11.5
|
1.0
|
CA
|
B:ASP308
|
4.5
|
12.8
|
1.0
|
ND1
|
B:HIS311
|
4.6
|
22.2
|
1.0
|
CE1
|
B:HIS311
|
4.8
|
24.8
|
1.0
|
N
|
B:SER11
|
4.8
|
12.4
|
1.0
|
C
|
B:ASP10
|
4.9
|
13.3
|
1.0
|
CA
|
B:ASP10
|
5.0
|
14.2
|
1.0
|
|
Manganese binding site 5 out
of 7 in 6omq
Go back to
Manganese Binding Sites List in 6omq
Manganese binding site 5 out
of 7 in the Crystal Structure of PTMU3 Complexed with Ptm 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 Ptm Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn407
b:16.4
occ:1.00
|
OE1
|
B:GLU313
|
1.7
|
13.2
|
1.0
|
OD2
|
B:ASP308
|
2.2
|
11.2
|
1.0
|
OE2
|
B:GLU241
|
2.2
|
15.0
|
1.0
|
OE1
|
B:GLU241
|
2.3
|
16.0
|
1.0
|
ND1
|
B:HIS311
|
2.4
|
22.2
|
1.0
|
O
|
B:HOH760
|
2.5
|
19.4
|
1.0
|
CD
|
B:GLU241
|
2.5
|
13.3
|
1.0
|
CD
|
B:GLU313
|
3.0
|
15.8
|
1.0
|
CG
|
B:ASP308
|
3.0
|
10.4
|
1.0
|
OD1
|
B:ASP308
|
3.3
|
10.9
|
1.0
|
CG
|
B:HIS311
|
3.3
|
21.4
|
1.0
|
CE1
|
B:HIS311
|
3.4
|
24.8
|
1.0
|
CB
|
B:HIS311
|
3.5
|
20.0
|
1.0
|
CG
|
B:GLU313
|
3.7
|
18.9
|
1.0
|
MN
|
B:MN406
|
3.8
|
11.7
|
1.0
|
OE2
|
B:GLU313
|
4.0
|
19.3
|
1.0
|
CG
|
B:GLU241
|
4.0
|
13.6
|
1.0
|
C41
|
B:MZD405
|
4.2
|
28.3
|
1.0
|
NE2
|
B:HIS12
|
4.3
|
10.8
|
1.0
|
CB
|
B:GLU313
|
4.3
|
19.6
|
1.0
|
CB
|
B:ASP308
|
4.4
|
12.1
|
1.0
|
CD2
|
B:HIS311
|
4.5
|
21.5
|
1.0
|
NE2
|
B:HIS311
|
4.5
|
20.0
|
1.0
|
C43
|
B:MZD405
|
4.6
|
29.3
|
1.0
|
C42
|
B:MZD405
|
4.7
|
28.6
|
1.0
|
CE1
|
B:HIS189
|
4.7
|
12.7
|
1.0
|
CD2
|
B:HIS12
|
4.7
|
13.2
|
1.0
|
C16
|
B:MZD405
|
4.9
|
27.3
|
1.0
|
NE2
|
B:HIS189
|
4.9
|
11.2
|
1.0
|
|
Manganese binding site 6 out
of 7 in 6omq
Go back to
Manganese Binding Sites List in 6omq
Manganese binding site 6 out
of 7 in the Crystal Structure of PTMU3 Complexed with Ptm Substrate
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Crystal Structure of PTMU3 Complexed with Ptm Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn408
b:28.5
occ:1.00
|
O
|
B:HOH514
|
2.4
|
33.6
|
1.0
|
O
|
B:HOH594
|
2.4
|
29.3
|
1.0
|
O
|
B:HOH752
|
4.2
|
29.4
|
1.0
|
OD2
|
B:ASP17
|
4.2
|
24.7
|
1.0
|
OE2
|
B:GLU21
|
4.4
|
28.6
|
1.0
|
OE1
|
B:GLU21
|
4.5
|
29.7
|
1.0
|
O
|
B:HOH881
|
4.8
|
38.6
|
1.0
|
CD
|
B:GLU21
|
4.9
|
32.0
|
1.0
|
|
Manganese binding site 7 out
of 7 in 6omq
Go back to
Manganese Binding Sites List in 6omq
Manganese binding site 7 out
of 7 in the Crystal Structure of PTMU3 Complexed with Ptm Substrate
Mono view
Stereo pair view
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A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Crystal Structure of PTMU3 Complexed with Ptm Substrate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn409
b:64.0
occ:1.00
|
O
|
B:HOH782
|
2.4
|
21.8
|
1.0
|
O
|
B:LEU312
|
2.4
|
21.5
|
1.0
|
O
|
B:HOH517
|
2.5
|
23.2
|
1.0
|
OE1
|
A:GLN260
|
2.5
|
21.1
|
1.0
|
O
|
B:GLY314
|
2.7
|
17.2
|
1.0
|
O
|
A:HOH791
|
2.9
|
32.9
|
1.0
|
C
|
B:LEU312
|
3.4
|
24.0
|
1.0
|
CD
|
A:GLN260
|
3.4
|
21.2
|
1.0
|
O
|
A:HOH594
|
3.5
|
41.9
|
1.0
|
C
|
B:GLY314
|
3.8
|
16.4
|
1.0
|
CA
|
B:LEU312
|
4.0
|
24.1
|
1.0
|
O
|
B:PHE316
|
4.0
|
27.0
|
1.0
|
O
|
B:HOH630
|
4.1
|
21.5
|
1.0
|
CG
|
A:GLN260
|
4.1
|
21.4
|
1.0
|
N
|
B:GLY314
|
4.2
|
19.8
|
1.0
|
NE2
|
A:GLN260
|
4.3
|
18.5
|
1.0
|
O
|
A:HOH536
|
4.4
|
29.3
|
1.0
|
CB
|
A:GLN260
|
4.4
|
22.5
|
1.0
|
O
|
B:HOH887
|
4.4
|
45.1
|
1.0
|
O
|
B:HIS311
|
4.5
|
19.3
|
1.0
|
N
|
B:GLU313
|
4.5
|
21.2
|
1.0
|
C
|
B:GLU313
|
4.5
|
20.9
|
1.0
|
CA
|
B:GLY314
|
4.6
|
20.0
|
1.0
|
O
|
B:HOH795
|
4.6
|
49.4
|
1.0
|
N
|
B:THR315
|
4.7
|
18.5
|
1.0
|
CE1
|
B:HIS287
|
4.7
|
17.2
|
1.0
|
CA
|
B:THR315
|
4.8
|
18.9
|
1.0
|
C
|
B:THR315
|
4.8
|
21.8
|
1.0
|
CB
|
B:LEU312
|
4.9
|
26.6
|
1.0
|
NE2
|
B:HIS287
|
4.9
|
16.6
|
1.0
|
CA
|
B:GLU313
|
4.9
|
22.0
|
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 05:43:04 2024
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