Manganese in PDB 3uva: Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn
Enzymatic activity of Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn
All present enzymatic activity of Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn:
5.3.1.14;
Protein crystallography data
The structure of Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn, PDB code: 3uva
was solved by
T.T.N.Doan,
P.Prabhu,
M.Jeya,
J.K.Kim,
L.W.Kang,
J.K.Lee,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.87 /
2.69
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.374,
164.779,
92.816,
90.00,
117.01,
90.00
|
R / Rfree (%)
|
18.5 /
26.6
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn
(pdb code 3uva). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the
Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn, PDB code: 3uva:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 3uva
Go back to
Manganese Binding Sites List in 3uva
Manganese binding site 1 out
of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn
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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn419
b:69.1
occ:1.00
|
OE2
|
A:GLU225
|
2.3
|
26.6
|
1.0
|
OD2
|
A:ASP325
|
2.9
|
41.8
|
1.0
|
OD2
|
A:ASP258
|
3.1
|
29.5
|
1.0
|
CD
|
A:GLU225
|
3.1
|
26.5
|
1.0
|
OE1
|
A:GLU225
|
3.2
|
25.8
|
1.0
|
ND1
|
A:HIS285
|
3.3
|
36.0
|
1.0
|
CG
|
A:ASP325
|
3.4
|
37.4
|
1.0
|
O
|
A:HOH519
|
3.5
|
34.1
|
1.0
|
MN
|
A:MN420
|
3.7
|
81.7
|
1.0
|
CG
|
A:ASP258
|
3.9
|
26.5
|
1.0
|
OD1
|
A:ASP325
|
3.9
|
40.2
|
1.0
|
CB
|
A:ASP258
|
4.0
|
25.2
|
1.0
|
CE1
|
A:HIS261
|
4.0
|
29.6
|
1.0
|
NE2
|
A:HIS261
|
4.1
|
30.6
|
1.0
|
CB
|
A:ASP325
|
4.1
|
34.5
|
1.0
|
CB
|
A:HIS285
|
4.1
|
30.7
|
1.0
|
CG
|
A:HIS285
|
4.1
|
33.3
|
1.0
|
CE1
|
A:HIS285
|
4.3
|
38.2
|
1.0
|
CG
|
A:GLU225
|
4.5
|
26.7
|
1.0
|
O
|
A:HOH513
|
4.6
|
15.7
|
1.0
|
CD2
|
A:LEU256
|
4.8
|
27.0
|
1.0
|
ND1
|
A:HIS261
|
4.9
|
28.0
|
1.0
|
|
Manganese binding site 2 out
of 8 in 3uva
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Manganese Binding Sites List in 3uva
Manganese binding site 2 out
of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn
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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn420
b:81.7
occ:1.00
|
NE2
|
A:HIS261
|
2.5
|
30.6
|
1.0
|
OD2
|
A:ASP293
|
2.6
|
40.6
|
1.0
|
OD1
|
A:ASP293
|
3.0
|
34.2
|
1.0
|
CG
|
A:ASP293
|
3.2
|
34.9
|
1.0
|
O
|
A:HOH513
|
3.2
|
15.7
|
1.0
|
CE1
|
A:HIS261
|
3.4
|
29.6
|
1.0
|
OD1
|
A:ASP295
|
3.5
|
35.6
|
1.0
|
CD2
|
A:HIS261
|
3.6
|
28.0
|
1.0
|
NZ
|
A:LYS227
|
3.6
|
33.9
|
1.0
|
MN
|
A:MN419
|
3.7
|
69.1
|
1.0
|
OD2
|
A:ASP258
|
3.9
|
29.5
|
1.0
|
OD1
|
A:ASP325
|
4.0
|
40.2
|
1.0
|
OD2
|
A:ASP295
|
4.2
|
35.2
|
1.0
|
CG
|
A:ASP295
|
4.2
|
33.6
|
1.0
|
CG
|
A:ASP258
|
4.4
|
26.5
|
1.0
|
ND1
|
A:HIS261
|
4.6
|
28.0
|
1.0
|
CG
|
A:ASP325
|
4.6
|
37.4
|
1.0
|
CG
|
A:HIS261
|
4.7
|
27.4
|
1.0
|
CB
|
A:ASP293
|
4.7
|
32.6
|
1.0
|
OD1
|
A:ASP258
|
4.7
|
29.4
|
1.0
|
OE2
|
A:GLU225
|
4.8
|
26.6
|
1.0
|
OD2
|
A:ASP325
|
4.9
|
41.8
|
1.0
|
|
Manganese binding site 3 out
of 8 in 3uva
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Manganese Binding Sites List in 3uva
Manganese binding site 3 out
of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn
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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn419
b:82.2
occ:1.00
|
OE2
|
B:GLU225
|
2.6
|
27.6
|
1.0
|
OD2
|
B:ASP258
|
2.7
|
28.4
|
1.0
|
OD2
|
B:ASP325
|
3.2
|
36.1
|
1.0
|
ND1
|
B:HIS285
|
3.2
|
32.3
|
1.0
|
CG
|
B:ASP325
|
3.3
|
34.3
|
1.0
|
O
|
B:HOH488
|
3.4
|
29.0
|
1.0
|
O
|
B:HOH465
|
3.5
|
26.2
|
1.0
|
CD
|
B:GLU225
|
3.6
|
27.3
|
1.0
|
CG
|
B:ASP258
|
3.6
|
26.7
|
1.0
|
OD1
|
B:ASP325
|
3.7
|
36.9
|
1.0
|
CB
|
B:ASP325
|
3.8
|
32.3
|
1.0
|
O
|
B:HOH479
|
3.8
|
29.7
|
1.0
|
CB
|
B:ASP258
|
3.8
|
26.1
|
1.0
|
OE1
|
B:GLU225
|
3.9
|
28.3
|
1.0
|
NE2
|
B:HIS261
|
4.0
|
34.9
|
1.0
|
MN
|
B:MN420
|
4.0
|
75.0
|
1.0
|
CE1
|
B:HIS261
|
4.1
|
34.6
|
1.0
|
CG
|
B:HIS285
|
4.1
|
31.0
|
1.0
|
CE1
|
B:HIS285
|
4.2
|
32.9
|
1.0
|
CB
|
B:HIS285
|
4.2
|
29.1
|
1.0
|
OD1
|
B:ASP258
|
4.8
|
28.0
|
1.0
|
CG
|
B:GLU225
|
4.9
|
27.9
|
1.0
|
CD2
|
B:HIS261
|
5.0
|
32.1
|
1.0
|
|
Manganese binding site 4 out
of 8 in 3uva
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Manganese Binding Sites List in 3uva
Manganese binding site 4 out
of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn
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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn420
b:75.0
occ:1.00
|
O
|
B:HOH488
|
2.4
|
29.0
|
1.0
|
NE2
|
B:HIS261
|
3.1
|
34.9
|
1.0
|
OD1
|
B:ASP293
|
3.2
|
39.6
|
1.0
|
OD2
|
B:ASP295
|
3.5
|
44.8
|
1.0
|
OD1
|
B:ASP295
|
3.6
|
43.1
|
1.0
|
CG
|
B:ASP293
|
3.8
|
36.5
|
1.0
|
OD2
|
B:ASP293
|
3.9
|
42.6
|
1.0
|
CE1
|
B:HIS261
|
4.0
|
34.6
|
1.0
|
CG
|
B:ASP295
|
4.0
|
40.3
|
1.0
|
OD1
|
B:ASP325
|
4.0
|
36.9
|
1.0
|
MN
|
B:MN419
|
4.0
|
82.2
|
1.0
|
CD2
|
B:HIS261
|
4.0
|
32.1
|
1.0
|
NZ
|
B:LYS227
|
4.3
|
30.0
|
1.0
|
OD2
|
B:ASP258
|
4.3
|
28.4
|
1.0
|
O
|
B:HOH465
|
4.5
|
26.2
|
1.0
|
CG
|
B:ASP325
|
4.7
|
34.3
|
1.0
|
OD2
|
B:ASP325
|
4.7
|
36.1
|
1.0
|
CE
|
B:LYS227
|
4.9
|
27.9
|
1.0
|
CB
|
B:ASP293
|
5.0
|
34.0
|
1.0
|
|
Manganese binding site 5 out
of 8 in 3uva
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Manganese Binding Sites List in 3uva
Manganese binding site 5 out
of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn
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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn419
b:81.8
occ:1.00
|
OD2
|
C:ASP258
|
2.6
|
31.6
|
1.0
|
OE2
|
C:GLU225
|
2.6
|
31.1
|
1.0
|
OD2
|
C:ASP325
|
2.9
|
37.0
|
1.0
|
ND1
|
C:HIS285
|
3.2
|
35.4
|
1.0
|
OE1
|
C:GLU225
|
3.2
|
24.8
|
1.0
|
CD
|
C:GLU225
|
3.3
|
26.4
|
1.0
|
CG
|
C:ASP258
|
3.7
|
26.6
|
1.0
|
CG
|
C:ASP325
|
3.8
|
36.5
|
1.0
|
O
|
C:HOH509
|
3.9
|
38.4
|
1.0
|
NE2
|
C:HIS261
|
4.0
|
24.5
|
1.0
|
CE1
|
C:HIS285
|
4.0
|
36.8
|
1.0
|
CE1
|
C:HIS261
|
4.1
|
25.0
|
1.0
|
CG
|
C:HIS285
|
4.1
|
33.7
|
1.0
|
MN
|
C:MN420
|
4.2
|
67.8
|
1.0
|
CB
|
C:HIS285
|
4.3
|
30.9
|
1.0
|
CB
|
C:ASP325
|
4.3
|
34.3
|
1.0
|
CB
|
C:ASP258
|
4.3
|
24.3
|
1.0
|
CG
|
C:GLU225
|
4.7
|
24.9
|
1.0
|
OD1
|
C:ASP325
|
4.7
|
40.3
|
1.0
|
OD1
|
C:ASP258
|
4.7
|
24.9
|
1.0
|
CD2
|
C:HIS261
|
5.0
|
24.4
|
1.0
|
|
Manganese binding site 6 out
of 8 in 3uva
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Manganese Binding Sites List in 3uva
Manganese binding site 6 out
of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn
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 L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn420
b:67.8
occ:1.00
|
OD2
|
C:ASP293
|
2.7
|
37.3
|
1.0
|
OD1
|
C:ASP293
|
2.7
|
34.1
|
1.0
|
NE2
|
C:HIS261
|
2.9
|
24.5
|
1.0
|
OD1
|
C:ASP295
|
3.0
|
38.2
|
1.0
|
CG
|
C:ASP293
|
3.1
|
33.3
|
1.0
|
O
|
C:HOH509
|
3.1
|
38.4
|
1.0
|
CD2
|
C:HIS261
|
3.5
|
24.4
|
1.0
|
OD2
|
C:ASP295
|
3.5
|
37.4
|
1.0
|
OD2
|
C:ASP258
|
3.5
|
31.6
|
1.0
|
CG
|
C:ASP295
|
3.6
|
35.9
|
1.0
|
OD1
|
C:ASP258
|
3.8
|
24.9
|
1.0
|
CG
|
C:ASP258
|
3.9
|
26.6
|
1.0
|
CE1
|
C:HIS261
|
4.1
|
25.0
|
1.0
|
OD1
|
C:ASP325
|
4.1
|
40.3
|
1.0
|
MN
|
C:MN419
|
4.2
|
81.8
|
1.0
|
OD2
|
C:ASP325
|
4.3
|
37.0
|
1.0
|
CG
|
C:ASP325
|
4.3
|
36.5
|
1.0
|
OG
|
C:SER287
|
4.5
|
26.8
|
1.0
|
CB
|
C:ASP293
|
4.6
|
31.7
|
1.0
|
CG
|
C:HIS261
|
4.8
|
24.9
|
1.0
|
NZ
|
C:LYS227
|
4.8
|
25.9
|
1.0
|
O
|
C:ASP293
|
5.0
|
32.0
|
1.0
|
|
Manganese binding site 7 out
of 8 in 3uva
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Manganese Binding Sites List in 3uva
Manganese binding site 7 out
of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn419
b:71.4
occ:1.00
|
OE2
|
D:GLU225
|
2.4
|
38.5
|
1.0
|
OD2
|
D:ASP258
|
2.6
|
25.1
|
1.0
|
CD
|
D:GLU225
|
3.1
|
35.3
|
1.0
|
OE1
|
D:GLU225
|
3.2
|
36.4
|
1.0
|
ND1
|
D:HIS285
|
3.2
|
27.2
|
1.0
|
CG
|
D:ASP258
|
3.5
|
24.9
|
1.0
|
OD2
|
D:ASP325
|
3.6
|
33.1
|
1.0
|
CG
|
D:ASP325
|
3.7
|
34.9
|
1.0
|
CB
|
D:ASP258
|
3.7
|
25.8
|
1.0
|
CE1
|
D:HIS261
|
3.7
|
28.3
|
1.0
|
NE2
|
D:HIS261
|
4.0
|
28.2
|
1.0
|
CB
|
D:HIS285
|
4.0
|
25.9
|
1.0
|
MN
|
D:MN420
|
4.0
|
75.3
|
1.0
|
CG
|
D:HIS285
|
4.0
|
26.6
|
1.0
|
OD1
|
D:ASP325
|
4.1
|
39.2
|
1.0
|
CB
|
D:ASP325
|
4.1
|
33.0
|
1.0
|
O
|
D:HOH484
|
4.2
|
18.1
|
1.0
|
CE1
|
D:HIS285
|
4.3
|
30.5
|
1.0
|
CG
|
D:GLU225
|
4.5
|
32.7
|
1.0
|
ND1
|
D:HIS261
|
4.6
|
27.0
|
1.0
|
OD1
|
D:ASP258
|
4.6
|
26.9
|
1.0
|
CD1
|
D:LEU256
|
4.7
|
32.6
|
1.0
|
CD2
|
D:HIS261
|
4.9
|
26.0
|
1.0
|
CA
|
D:ASP258
|
5.0
|
26.5
|
1.0
|
|
Manganese binding site 8 out
of 8 in 3uva
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Manganese Binding Sites List in 3uva
Manganese binding site 8 out
of 8 in the Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn
Mono view
Stereo pair view
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A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Crystal Structure of L-Rhamnose Isomerase Mutant W38F From Bacillus Halodurans in Complex with Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn420
b:75.3
occ:1.00
|
OD2
|
D:ASP293
|
2.3
|
35.1
|
1.0
|
NE2
|
D:HIS261
|
2.7
|
28.2
|
1.0
|
CE1
|
D:HIS261
|
3.3
|
28.3
|
1.0
|
CG
|
D:ASP293
|
3.4
|
32.7
|
1.0
|
NZ
|
D:LYS227
|
3.7
|
25.8
|
1.0
|
O
|
D:HOH486
|
3.8
|
30.6
|
1.0
|
CD2
|
D:HIS261
|
3.9
|
26.0
|
1.0
|
OD1
|
D:ASP293
|
3.9
|
37.2
|
1.0
|
MN
|
D:MN419
|
4.0
|
71.4
|
1.0
|
OD1
|
D:ASP325
|
4.1
|
39.2
|
1.0
|
OD2
|
D:ASP258
|
4.2
|
25.1
|
1.0
|
OD2
|
D:ASP295
|
4.3
|
37.0
|
1.0
|
OD1
|
D:ASP295
|
4.3
|
36.6
|
1.0
|
ND1
|
D:HIS261
|
4.6
|
27.0
|
1.0
|
CG
|
D:ASP295
|
4.7
|
32.4
|
1.0
|
CB
|
D:ASP293
|
4.7
|
30.2
|
1.0
|
CG
|
D:ASP325
|
4.8
|
34.9
|
1.0
|
CE
|
D:LYS227
|
4.9
|
26.1
|
1.0
|
CG
|
D:HIS261
|
4.9
|
26.1
|
1.0
|
OE2
|
D:GLU225
|
4.9
|
38.5
|
1.0
|
CD
|
D:LYS227
|
4.9
|
26.9
|
1.0
|
CG
|
D:ASP258
|
5.0
|
24.9
|
1.0
|
|
Reference:
P.Prabhu,
T.N.Doan,
M.Tiwari,
R.Singh,
S.C.Kim,
M.K.Hong,
Y.C.Kang,
L.W.Kang,
J.K.Lee.
Structure-Based Studies on the Metal Binding of Two-Metal-Dependent Sugar Isomerases. Febs J. V. 281 3446 2014.
ISSN: ISSN 1742-464X
PubMed: 24925069
DOI: 10.1111/FEBS.12872
Page generated: Sat Oct 5 18:14:24 2024
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