Manganese in PDB 4eac: Crystal Structure of Mannonate Dehydratase From Escherichia Coli Strain K12
Enzymatic activity of Crystal Structure of Mannonate Dehydratase From Escherichia Coli Strain K12
All present enzymatic activity of Crystal Structure of Mannonate Dehydratase From Escherichia Coli Strain K12:
4.2.1.8;
Protein crystallography data
The structure of Crystal Structure of Mannonate Dehydratase From Escherichia Coli Strain K12, PDB code: 4eac
was solved by
X.Qiu,
Y.Zhu,
Y.Yuan,
Y.Zhang,
H.Liu,
Y.Gao,
M.Teng,
L.Niu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.42 /
2.30
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
158.961,
238.461,
54.345,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.3 /
21.9
|
Other elements in 4eac:
The structure of Crystal Structure of Mannonate Dehydratase From Escherichia Coli Strain K12 also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of Mannonate Dehydratase From Escherichia Coli Strain K12
(pdb code 4eac). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Crystal Structure of Mannonate Dehydratase From Escherichia Coli Strain K12, PDB code: 4eac:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 4eac
Go back to
Manganese Binding Sites List in 4eac
Manganese binding site 1 out
of 4 in the Crystal Structure of Mannonate Dehydratase From Escherichia Coli Strain K12
 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 Mannonate Dehydratase From Escherichia Coli Strain K12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn402
b:11.3
occ:1.00
|
ND1
|
A:HIS298
|
2.1
|
11.9
|
1.0
|
O
|
A:HOH764
|
2.2
|
16.6
|
1.0
|
NE2
|
A:HIS233
|
2.2
|
14.9
|
1.0
|
OD2
|
A:ASP351
|
2.4
|
14.7
|
1.0
|
SG
|
A:CYS271
|
2.5
|
11.4
|
1.0
|
CE1
|
A:HIS233
|
3.1
|
13.9
|
1.0
|
CE1
|
A:HIS298
|
3.1
|
12.4
|
1.0
|
CG
|
A:HIS298
|
3.1
|
13.1
|
1.0
|
CB
|
A:CYS271
|
3.3
|
13.8
|
1.0
|
CD2
|
A:HIS233
|
3.3
|
15.0
|
1.0
|
CG
|
A:ASP351
|
3.3
|
14.4
|
1.0
|
CB
|
A:HIS298
|
3.4
|
12.1
|
1.0
|
O
|
A:HOH753
|
3.6
|
23.3
|
1.0
|
OD1
|
A:ASP351
|
3.6
|
16.0
|
1.0
|
NH2
|
A:ARG300
|
4.1
|
13.4
|
1.0
|
OG
|
A:SER274
|
4.2
|
14.2
|
1.0
|
NE2
|
A:HIS298
|
4.2
|
11.7
|
1.0
|
ND1
|
A:HIS233
|
4.3
|
15.5
|
1.0
|
CD2
|
A:HIS298
|
4.3
|
13.3
|
1.0
|
NE
|
A:ARG300
|
4.4
|
12.8
|
1.0
|
CG
|
A:HIS233
|
4.4
|
15.5
|
1.0
|
CA
|
A:CYS271
|
4.5
|
13.7
|
1.0
|
CB
|
A:ASP351
|
4.6
|
13.4
|
1.0
|
CZ
|
A:ARG300
|
4.8
|
12.8
|
1.0
|
CA
|
A:HIS298
|
5.0
|
12.7
|
1.0
|
|
Manganese binding site 2 out
of 4 in 4eac
Go back to
Manganese Binding Sites List in 4eac
Manganese binding site 2 out
of 4 in the Crystal Structure of Mannonate Dehydratase From Escherichia Coli Strain K12
 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 Mannonate Dehydratase From Escherichia Coli Strain K12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn402
b:12.2
occ:1.00
|
ND1
|
B:HIS298
|
2.1
|
11.3
|
1.0
|
NE2
|
B:HIS233
|
2.2
|
15.1
|
1.0
|
O
|
B:HOH739
|
2.3
|
14.6
|
1.0
|
SG
|
B:CYS271
|
2.4
|
11.2
|
1.0
|
OD2
|
B:ASP351
|
2.4
|
16.1
|
1.0
|
CE1
|
B:HIS298
|
3.1
|
11.6
|
1.0
|
CG
|
B:HIS298
|
3.1
|
12.7
|
1.0
|
CE1
|
B:HIS233
|
3.1
|
14.6
|
1.0
|
CD2
|
B:HIS233
|
3.2
|
13.9
|
1.0
|
CG
|
B:ASP351
|
3.3
|
15.2
|
1.0
|
CB
|
B:CYS271
|
3.3
|
14.1
|
1.0
|
CB
|
B:HIS298
|
3.4
|
12.9
|
1.0
|
O
|
B:HOH735
|
3.4
|
18.6
|
1.0
|
OD1
|
B:ASP351
|
3.6
|
15.9
|
1.0
|
NH2
|
B:ARG300
|
4.1
|
14.0
|
1.0
|
OG
|
B:SER274
|
4.2
|
17.8
|
1.0
|
NE2
|
B:HIS298
|
4.2
|
12.7
|
1.0
|
CD2
|
B:HIS298
|
4.2
|
13.2
|
1.0
|
ND1
|
B:HIS233
|
4.3
|
14.3
|
1.0
|
CG
|
B:HIS233
|
4.4
|
15.1
|
1.0
|
NE
|
B:ARG300
|
4.4
|
12.7
|
1.0
|
CA
|
B:CYS271
|
4.5
|
14.4
|
1.0
|
CB
|
B:ASP351
|
4.5
|
14.0
|
1.0
|
CZ
|
B:ARG300
|
4.7
|
13.5
|
1.0
|
CA
|
B:HIS298
|
5.0
|
13.3
|
1.0
|
|
Manganese binding site 3 out
of 4 in 4eac
Go back to
Manganese Binding Sites List in 4eac
Manganese binding site 3 out
of 4 in the Crystal Structure of Mannonate Dehydratase From Escherichia Coli Strain K12
 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 Mannonate Dehydratase From Escherichia Coli Strain K12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn402
b:16.3
occ:1.00
|
O
|
C:HOH692
|
2.1
|
23.8
|
1.0
|
ND1
|
C:HIS298
|
2.1
|
16.3
|
1.0
|
SG
|
C:CYS271
|
2.3
|
15.9
|
1.0
|
NE2
|
C:HIS233
|
2.3
|
18.5
|
1.0
|
OD2
|
C:ASP351
|
2.4
|
18.4
|
1.0
|
CG
|
C:HIS298
|
3.1
|
15.9
|
1.0
|
CE1
|
C:HIS298
|
3.1
|
17.0
|
1.0
|
CD2
|
C:HIS233
|
3.2
|
18.5
|
1.0
|
CG
|
C:ASP351
|
3.3
|
18.4
|
1.0
|
CE1
|
C:HIS233
|
3.3
|
18.9
|
1.0
|
CB
|
C:CYS271
|
3.3
|
17.6
|
1.0
|
CB
|
C:HIS298
|
3.4
|
15.3
|
1.0
|
OD1
|
C:ASP351
|
3.5
|
19.0
|
1.0
|
NH2
|
C:ARG300
|
4.2
|
18.0
|
1.0
|
NE2
|
C:HIS298
|
4.2
|
16.6
|
1.0
|
CD2
|
C:HIS298
|
4.2
|
16.1
|
1.0
|
OG
|
C:SER274
|
4.2
|
20.1
|
1.0
|
NE
|
C:ARG300
|
4.3
|
17.5
|
1.0
|
ND1
|
C:HIS233
|
4.4
|
19.9
|
1.0
|
CG
|
C:HIS233
|
4.4
|
19.2
|
1.0
|
CA
|
C:CYS271
|
4.6
|
17.2
|
1.0
|
CB
|
C:ASP351
|
4.6
|
17.4
|
1.0
|
CZ
|
C:ARG300
|
4.8
|
18.2
|
1.0
|
CA
|
C:HIS298
|
4.9
|
15.2
|
1.0
|
NH2
|
C:ARG349
|
5.0
|
16.2
|
1.0
|
|
Manganese binding site 4 out
of 4 in 4eac
Go back to
Manganese Binding Sites List in 4eac
Manganese binding site 4 out
of 4 in the Crystal Structure of Mannonate Dehydratase From Escherichia Coli Strain K12
 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 Mannonate Dehydratase From Escherichia Coli Strain K12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn402
b:26.0
occ:1.00
|
O
|
D:HOH642
|
1.9
|
12.3
|
1.0
|
ND1
|
D:HIS298
|
2.1
|
25.5
|
1.0
|
NE2
|
D:HIS233
|
2.3
|
28.7
|
1.0
|
SG
|
D:CYS271
|
2.3
|
22.8
|
1.0
|
OD2
|
D:ASP351
|
2.5
|
26.3
|
1.0
|
CG
|
D:HIS298
|
3.1
|
25.3
|
1.0
|
CE1
|
D:HIS298
|
3.1
|
26.9
|
1.0
|
CE1
|
D:HIS233
|
3.2
|
28.5
|
1.0
|
CD2
|
D:HIS233
|
3.3
|
28.8
|
1.0
|
CG
|
D:ASP351
|
3.3
|
25.9
|
1.0
|
CB
|
D:CYS271
|
3.3
|
26.2
|
1.0
|
CB
|
D:HIS298
|
3.4
|
24.8
|
1.0
|
OD1
|
D:ASP351
|
3.5
|
28.2
|
1.0
|
NE2
|
D:HIS298
|
4.2
|
26.8
|
1.0
|
CD2
|
D:HIS298
|
4.2
|
25.8
|
1.0
|
NH2
|
D:ARG300
|
4.2
|
25.1
|
1.0
|
OG
|
D:SER274
|
4.2
|
27.4
|
1.0
|
ND1
|
D:HIS233
|
4.4
|
30.4
|
1.0
|
CG
|
D:HIS233
|
4.4
|
30.4
|
1.0
|
NE
|
D:ARG300
|
4.5
|
23.2
|
1.0
|
CA
|
D:CYS271
|
4.6
|
25.8
|
1.0
|
CB
|
D:ASP351
|
4.6
|
23.9
|
1.0
|
CZ
|
D:ARG300
|
4.8
|
24.2
|
1.0
|
CA
|
D:HIS298
|
4.9
|
24.6
|
1.0
|
|
Reference:
X.Qiu,
Y.Tao,
Y.Zhu,
Y.Yuan,
Y.Zhang,
H.Liu,
Y.Gao,
M.Teng,
L.Niu.
Structural Insights Into Decreased Enzymatic Activity Induced By An Insert Sequence in Mannonate Dehydratase From Gram Negative Bacterium. J.Struct.Biol. V. 180 327 2012.
ISSN: ISSN 1047-8477
PubMed: 22796868
DOI: 10.1016/J.JSB.2012.06.013
Page generated: Sat Oct 5 19:15:41 2024
|