Manganese in PDB 3a6h: W154A Mutant Creatininase
Enzymatic activity of W154A Mutant Creatininase
All present enzymatic activity of W154A Mutant Creatininase:
3.5.2.10;
Protein crystallography data
The structure of W154A Mutant Creatininase, PDB code: 3a6h
was solved by
Y.Nakajima,
K.Yamashita,
K.Ito,
T.Yoshimoto,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.800,
60.240,
146.200,
90.00,
100.30,
90.00
|
R / Rfree (%)
|
19.9 /
23.1
|
Other elements in 3a6h:
The structure of W154A Mutant Creatininase also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the W154A Mutant Creatininase
(pdb code 3a6h). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the
W154A Mutant Creatininase, PDB code: 3a6h:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
Manganese binding site 1 out
of 6 in 3a6h
Go back to
Manganese Binding Sites List in 3a6h
Manganese binding site 1 out
of 6 in the W154A Mutant Creatininase
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of W154A Mutant Creatininase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn300
b:36.3
occ:1.00
|
OD2
|
A:ASP45
|
2.2
|
18.5
|
1.0
|
O
|
A:HOH1001
|
2.2
|
19.7
|
1.0
|
ND1
|
A:HIS120
|
2.3
|
26.7
|
1.0
|
OE2
|
A:GLU34
|
2.3
|
21.3
|
1.0
|
CE1
|
A:HIS120
|
3.1
|
27.6
|
1.0
|
CL
|
A:CL302
|
3.2
|
33.3
|
1.0
|
CG
|
A:ASP45
|
3.2
|
17.4
|
1.0
|
CD
|
A:GLU34
|
3.3
|
19.6
|
1.0
|
CG
|
A:HIS120
|
3.4
|
28.1
|
1.0
|
ZN
|
A:ZN301
|
3.5
|
33.1
|
1.0
|
OE1
|
A:GLU34
|
3.5
|
18.6
|
1.0
|
OD1
|
A:ASP45
|
3.6
|
17.0
|
1.0
|
CA
|
A:HIS120
|
3.7
|
27.8
|
1.0
|
CB
|
A:HIS120
|
3.8
|
26.7
|
1.0
|
OE1
|
A:GLU122
|
4.1
|
23.9
|
1.0
|
NE2
|
A:HIS120
|
4.3
|
28.4
|
1.0
|
N
|
A:TYR121
|
4.4
|
26.3
|
1.0
|
O
|
A:GLY119
|
4.4
|
23.6
|
1.0
|
ND1
|
A:HIS178
|
4.5
|
19.7
|
1.0
|
C
|
A:HIS120
|
4.5
|
27.5
|
1.0
|
CD2
|
A:HIS120
|
4.5
|
27.3
|
1.0
|
CE1
|
A:HIS178
|
4.5
|
18.0
|
1.0
|
CB
|
A:ASP45
|
4.5
|
17.8
|
1.0
|
NE2
|
A:HIS36
|
4.6
|
13.9
|
1.0
|
CE1
|
A:HIS36
|
4.6
|
16.7
|
1.0
|
CG
|
A:GLU34
|
4.6
|
16.7
|
1.0
|
CB
|
A:GLU34
|
4.9
|
17.7
|
1.0
|
N
|
A:HIS120
|
4.9
|
25.4
|
1.0
|
CD
|
A:GLU122
|
4.9
|
24.6
|
1.0
|
|
Manganese binding site 2 out
of 6 in 3a6h
Go back to
Manganese Binding Sites List in 3a6h
Manganese binding site 2 out
of 6 in the W154A Mutant Creatininase
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of W154A Mutant Creatininase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn300
b:39.0
occ:1.00
|
OD2
|
B:ASP45
|
2.2
|
18.0
|
1.0
|
OE2
|
B:GLU34
|
2.2
|
21.3
|
1.0
|
O
|
B:HOH1002
|
2.3
|
17.8
|
1.0
|
ND1
|
B:HIS120
|
2.3
|
23.2
|
1.0
|
CE1
|
B:HIS120
|
3.1
|
22.1
|
1.0
|
CL
|
B:CL303
|
3.2
|
32.0
|
1.0
|
CD
|
B:GLU34
|
3.2
|
20.8
|
1.0
|
CG
|
B:ASP45
|
3.2
|
18.7
|
1.0
|
CG
|
B:HIS120
|
3.5
|
21.8
|
1.0
|
OE1
|
B:GLU34
|
3.5
|
18.8
|
1.0
|
ZN
|
B:ZN301
|
3.6
|
33.8
|
1.0
|
OD1
|
B:ASP45
|
3.7
|
18.6
|
1.0
|
CA
|
B:HIS120
|
3.8
|
25.9
|
1.0
|
CB
|
B:HIS120
|
3.9
|
24.6
|
1.0
|
OE1
|
B:GLU122
|
4.1
|
25.8
|
1.0
|
NE2
|
B:HIS120
|
4.3
|
23.2
|
1.0
|
O
|
B:GLY119
|
4.4
|
27.4
|
1.0
|
N
|
B:TYR121
|
4.4
|
25.1
|
1.0
|
CE1
|
B:HIS178
|
4.5
|
21.3
|
1.0
|
NE2
|
B:HIS36
|
4.5
|
16.2
|
1.0
|
ND1
|
B:HIS178
|
4.5
|
22.5
|
1.0
|
CD2
|
B:HIS120
|
4.5
|
22.6
|
1.0
|
CB
|
B:ASP45
|
4.5
|
18.0
|
1.0
|
C
|
B:HIS120
|
4.5
|
25.7
|
1.0
|
CE1
|
B:HIS36
|
4.6
|
18.0
|
1.0
|
CG
|
B:GLU34
|
4.6
|
18.5
|
1.0
|
CB
|
B:GLU34
|
4.8
|
16.7
|
1.0
|
N
|
B:HIS120
|
4.9
|
26.4
|
1.0
|
CD
|
B:GLU122
|
4.9
|
24.7
|
1.0
|
|
Manganese binding site 3 out
of 6 in 3a6h
Go back to
Manganese Binding Sites List in 3a6h
Manganese binding site 3 out
of 6 in the W154A Mutant Creatininase
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of W154A Mutant Creatininase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn300
b:44.6
occ:1.00
|
OD1
|
C:ASP45
|
2.1
|
23.2
|
1.0
|
OE2
|
C:GLU34
|
2.3
|
23.6
|
1.0
|
ND1
|
C:HIS120
|
2.3
|
25.9
|
1.0
|
O
|
C:HOH1003
|
2.3
|
20.3
|
1.0
|
CE1
|
C:HIS120
|
3.1
|
25.2
|
1.0
|
CL
|
C:CL304
|
3.1
|
29.4
|
1.0
|
CG
|
C:ASP45
|
3.2
|
23.4
|
1.0
|
CD
|
C:GLU34
|
3.3
|
20.9
|
1.0
|
CG
|
C:HIS120
|
3.5
|
26.2
|
1.0
|
ZN
|
C:ZN301
|
3.5
|
37.7
|
1.0
|
OD2
|
C:ASP45
|
3.6
|
23.2
|
1.0
|
OE1
|
C:GLU34
|
3.7
|
22.1
|
1.0
|
CA
|
C:HIS120
|
3.8
|
28.7
|
1.0
|
CB
|
C:HIS120
|
3.9
|
27.1
|
1.0
|
OE1
|
C:GLU122
|
4.2
|
25.7
|
1.0
|
O
|
C:GLY119
|
4.3
|
32.3
|
1.0
|
NE2
|
C:HIS120
|
4.3
|
24.6
|
1.0
|
ND1
|
C:HIS178
|
4.5
|
27.3
|
1.0
|
CB
|
C:ASP45
|
4.5
|
21.2
|
1.0
|
CE1
|
C:HIS36
|
4.5
|
22.3
|
1.0
|
N
|
C:TYR121
|
4.5
|
27.7
|
1.0
|
CD2
|
C:HIS120
|
4.5
|
24.9
|
1.0
|
CE1
|
C:HIS178
|
4.5
|
26.9
|
1.0
|
NE2
|
C:HIS36
|
4.6
|
21.9
|
1.0
|
C
|
C:HIS120
|
4.6
|
28.7
|
1.0
|
CG
|
C:GLU34
|
4.6
|
20.6
|
1.0
|
CB
|
C:GLU34
|
4.8
|
19.2
|
1.0
|
N
|
C:HIS120
|
4.9
|
30.4
|
1.0
|
|
Manganese binding site 4 out
of 6 in 3a6h
Go back to
Manganese Binding Sites List in 3a6h
Manganese binding site 4 out
of 6 in the W154A Mutant Creatininase
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of W154A Mutant Creatininase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn300
b:38.7
occ:1.00
|
OD2
|
D:ASP45
|
2.2
|
20.4
|
1.0
|
O
|
D:HOH1004
|
2.3
|
17.8
|
1.0
|
ND1
|
D:HIS120
|
2.3
|
25.1
|
1.0
|
OE2
|
D:GLU34
|
2.3
|
22.9
|
1.0
|
CE1
|
D:HIS120
|
3.1
|
25.5
|
1.0
|
CL
|
D:CL305
|
3.2
|
35.1
|
1.0
|
CG
|
D:ASP45
|
3.2
|
19.5
|
1.0
|
CD
|
D:GLU34
|
3.3
|
20.4
|
1.0
|
CG
|
D:HIS120
|
3.4
|
25.9
|
1.0
|
ZN
|
D:ZN301
|
3.5
|
35.2
|
1.0
|
OD1
|
D:ASP45
|
3.6
|
20.1
|
1.0
|
OE1
|
D:GLU34
|
3.6
|
21.1
|
1.0
|
CA
|
D:HIS120
|
3.8
|
27.2
|
1.0
|
CB
|
D:HIS120
|
3.8
|
26.2
|
1.0
|
OE1
|
D:GLU122
|
4.2
|
23.7
|
1.0
|
NE2
|
D:HIS120
|
4.3
|
27.1
|
1.0
|
ND1
|
D:HIS178
|
4.3
|
22.0
|
1.0
|
CE1
|
D:HIS178
|
4.4
|
23.1
|
1.0
|
O
|
D:GLY119
|
4.4
|
26.2
|
1.0
|
N
|
D:TYR121
|
4.5
|
26.4
|
1.0
|
CD2
|
D:HIS120
|
4.5
|
24.7
|
1.0
|
NE2
|
D:HIS36
|
4.5
|
15.3
|
1.0
|
CB
|
D:ASP45
|
4.5
|
19.7
|
1.0
|
C
|
D:HIS120
|
4.5
|
26.8
|
1.0
|
CE1
|
D:HIS36
|
4.6
|
17.4
|
1.0
|
CG
|
D:GLU34
|
4.6
|
18.3
|
1.0
|
CB
|
D:GLU34
|
4.8
|
17.3
|
1.0
|
N
|
D:HIS120
|
4.9
|
25.2
|
1.0
|
|
Manganese binding site 5 out
of 6 in 3a6h
Go back to
Manganese Binding Sites List in 3a6h
Manganese binding site 5 out
of 6 in the W154A Mutant Creatininase
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of W154A Mutant Creatininase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn300
b:54.9
occ:1.00
|
OD2
|
E:ASP45
|
2.3
|
28.6
|
1.0
|
ND1
|
E:HIS120
|
2.3
|
30.1
|
1.0
|
OE2
|
E:GLU34
|
2.3
|
26.4
|
1.0
|
O
|
E:HOH1005
|
2.5
|
30.4
|
1.0
|
CL
|
E:CL306
|
3.0
|
37.7
|
1.0
|
CE1
|
E:HIS120
|
3.2
|
30.2
|
1.0
|
CG
|
E:ASP45
|
3.2
|
27.9
|
1.0
|
CG
|
E:HIS120
|
3.4
|
31.8
|
1.0
|
CD
|
E:GLU34
|
3.4
|
27.2
|
1.0
|
ZN
|
E:ZN301
|
3.6
|
45.4
|
1.0
|
CA
|
E:HIS120
|
3.6
|
31.5
|
1.0
|
OD1
|
E:ASP45
|
3.6
|
30.3
|
1.0
|
CB
|
E:HIS120
|
3.7
|
31.6
|
1.0
|
OE1
|
E:GLU34
|
3.8
|
28.1
|
1.0
|
OE1
|
E:GLU122
|
4.1
|
31.3
|
1.0
|
O
|
E:GLY119
|
4.2
|
30.5
|
1.0
|
N
|
E:TYR121
|
4.3
|
33.4
|
1.0
|
NE2
|
E:HIS120
|
4.3
|
30.9
|
1.0
|
C
|
E:HIS120
|
4.4
|
32.3
|
1.0
|
CB
|
E:ASP45
|
4.4
|
27.4
|
1.0
|
CD2
|
E:HIS120
|
4.5
|
30.4
|
1.0
|
CE1
|
E:HIS178
|
4.6
|
35.1
|
1.0
|
ND1
|
E:HIS178
|
4.7
|
36.7
|
1.0
|
CE1
|
E:HIS36
|
4.7
|
29.9
|
1.0
|
CG
|
E:GLU34
|
4.7
|
27.2
|
1.0
|
N
|
E:HIS120
|
4.7
|
30.4
|
1.0
|
NE2
|
E:HIS36
|
4.7
|
29.9
|
1.0
|
CB
|
E:GLU34
|
4.9
|
26.1
|
1.0
|
C
|
E:GLY119
|
4.9
|
30.7
|
1.0
|
CD
|
E:GLU122
|
5.0
|
30.4
|
1.0
|
|
Manganese binding site 6 out
of 6 in 3a6h
Go back to
Manganese Binding Sites List in 3a6h
Manganese binding site 6 out
of 6 in the W154A Mutant Creatininase
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of W154A Mutant Creatininase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn300
b:52.1
occ:1.00
|
OD1
|
F:ASP45
|
2.2
|
29.5
|
1.0
|
OE2
|
F:GLU34
|
2.4
|
28.7
|
1.0
|
ND1
|
F:HIS120
|
2.4
|
31.6
|
1.0
|
O
|
F:HOH1006
|
2.4
|
24.1
|
1.0
|
CL
|
F:CL307
|
2.9
|
47.7
|
1.0
|
CE1
|
F:HIS120
|
3.2
|
31.0
|
1.0
|
CG
|
F:ASP45
|
3.2
|
28.7
|
1.0
|
CD
|
F:GLU34
|
3.5
|
26.1
|
1.0
|
CG
|
F:HIS120
|
3.5
|
32.6
|
1.0
|
ZN
|
F:ZN301
|
3.6
|
45.7
|
1.0
|
OD2
|
F:ASP45
|
3.7
|
29.1
|
1.0
|
CA
|
F:HIS120
|
3.7
|
33.5
|
1.0
|
CB
|
F:HIS120
|
3.9
|
32.8
|
1.0
|
OE1
|
F:GLU34
|
3.9
|
28.8
|
1.0
|
OE1
|
F:GLU122
|
4.1
|
30.0
|
1.0
|
O
|
F:GLY119
|
4.2
|
32.4
|
1.0
|
N
|
F:TYR121
|
4.3
|
33.7
|
1.0
|
NE2
|
F:HIS120
|
4.4
|
32.0
|
1.0
|
C
|
F:HIS120
|
4.4
|
33.6
|
1.0
|
CB
|
F:ASP45
|
4.5
|
27.1
|
1.0
|
CD2
|
F:HIS120
|
4.5
|
31.9
|
1.0
|
CE1
|
F:HIS36
|
4.6
|
27.1
|
1.0
|
ND1
|
F:HIS178
|
4.7
|
35.1
|
1.0
|
CE1
|
F:HIS178
|
4.7
|
32.5
|
1.0
|
CG
|
F:GLU34
|
4.8
|
26.3
|
1.0
|
NE2
|
F:HIS36
|
4.8
|
27.9
|
1.0
|
N
|
F:HIS120
|
4.8
|
31.7
|
1.0
|
CB
|
F:GLU34
|
4.9
|
25.7
|
1.0
|
C
|
F:GLY119
|
4.9
|
32.3
|
1.0
|
CD
|
F:GLU122
|
5.0
|
29.9
|
1.0
|
|
Reference:
K.Yamashita,
Y.Nakajima,
H.Matsushita,
Y.Nishiya,
R.Yamazawa,
Y.F.Wu,
F.Matsubara,
H.Oyama,
K.Ito,
T.Yoshimoto.
Substitution of GLU122 By Glutamine Revealed the Function of the Second Water Molecule As A Proton Donor in the Binuclear Metal Enzyme Creatininase J.Mol.Biol. V. 396 1081 2010.
ISSN: ISSN 0022-2836
PubMed: 20043918
DOI: 10.1016/J.JMB.2009.12.045
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