Manganese in PDB 7p9q: Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
Protein crystallography data
The structure of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn., PDB code: 7p9q
was solved by
D.Gahloth,
D.Leys,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.42 /
2.53
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.2,
195.45,
105.21,
90,
116.35,
90
|
R / Rfree (%)
|
18.4 /
22.1
|
Other elements in 7p9q:
The structure of Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
(pdb code 7p9q). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the
Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn., PDB code: 7p9q:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
Manganese binding site 1 out
of 6 in 7p9q
Go back to
Manganese Binding Sites List in 7p9q
Manganese binding site 1 out
of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
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 Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn502
b:93.7
occ:1.00
|
O2P
|
A:4LU503
|
2.2
|
86.0
|
1.0
|
ND1
|
A:HIS173
|
2.3
|
90.0
|
1.0
|
OD1
|
A:ASN150
|
2.3
|
71.8
|
1.0
|
OE1
|
A:GLU217
|
2.3
|
84.4
|
1.0
|
O
|
A:HOH652
|
2.4
|
75.6
|
1.0
|
O
|
A:HOH603
|
2.5
|
105.0
|
1.0
|
CE1
|
A:HIS173
|
3.0
|
83.5
|
1.0
|
CD
|
A:GLU217
|
3.2
|
74.0
|
1.0
|
P
|
A:4LU503
|
3.3
|
88.7
|
1.0
|
CG
|
A:HIS173
|
3.5
|
88.5
|
1.0
|
CG
|
A:ASN150
|
3.5
|
75.7
|
1.0
|
O3P
|
A:4LU503
|
3.5
|
71.2
|
1.0
|
OE2
|
A:GLU217
|
3.6
|
79.5
|
1.0
|
O
|
A:ALA211
|
3.7
|
73.5
|
1.0
|
NA
|
A:NA501
|
3.8
|
51.8
|
1.0
|
CB
|
A:HIS173
|
3.9
|
87.2
|
1.0
|
O
|
A:HOH671
|
4.0
|
48.2
|
1.0
|
ND2
|
A:ASN150
|
4.2
|
69.8
|
1.0
|
O
|
A:PRO212
|
4.2
|
84.1
|
1.0
|
NE2
|
A:HIS173
|
4.3
|
81.6
|
1.0
|
O1P
|
A:4LU503
|
4.3
|
83.4
|
1.0
|
O5'
|
A:4LU503
|
4.4
|
93.2
|
1.0
|
CG
|
A:GLU217
|
4.4
|
72.4
|
1.0
|
CD2
|
A:HIS173
|
4.5
|
81.3
|
1.0
|
CB
|
A:ASN150
|
4.6
|
73.7
|
1.0
|
CB
|
A:ALA211
|
4.6
|
84.0
|
1.0
|
O
|
A:VAL215
|
4.7
|
80.1
|
1.0
|
O
|
A:THR151
|
4.7
|
71.1
|
1.0
|
C
|
A:ALA211
|
4.8
|
82.4
|
1.0
|
C
|
A:PRO212
|
4.9
|
83.4
|
1.0
|
|
Manganese binding site 2 out
of 6 in 7p9q
Go back to
Manganese Binding Sites List in 7p9q
Manganese binding site 2 out
of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
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 Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn502
b:92.5
occ:1.00
|
OD1
|
B:ASN150
|
2.3
|
67.5
|
1.0
|
OE1
|
B:GLU217
|
2.3
|
90.5
|
1.0
|
ND1
|
B:HIS173
|
2.4
|
101.3
|
1.0
|
O2P
|
B:4LU503
|
2.4
|
87.5
|
1.0
|
O
|
B:HOH633
|
2.5
|
90.8
|
1.0
|
CE1
|
B:HIS173
|
3.0
|
100.2
|
1.0
|
CD
|
B:GLU217
|
3.1
|
84.9
|
1.0
|
OE2
|
B:GLU217
|
3.4
|
102.9
|
1.0
|
CG
|
B:ASN150
|
3.5
|
71.7
|
1.0
|
P
|
B:4LU503
|
3.5
|
89.8
|
1.0
|
O
|
B:ALA211
|
3.5
|
78.6
|
1.0
|
CG
|
B:HIS173
|
3.6
|
93.1
|
1.0
|
O3P
|
B:4LU503
|
3.6
|
69.6
|
1.0
|
O
|
B:HOH653
|
3.8
|
62.5
|
1.0
|
NA
|
B:NA501
|
3.9
|
52.6
|
1.0
|
O
|
B:PRO212
|
4.0
|
97.9
|
1.0
|
CB
|
B:HIS173
|
4.1
|
92.0
|
1.0
|
ND2
|
B:ASN150
|
4.2
|
70.8
|
1.0
|
NE2
|
B:HIS173
|
4.3
|
92.0
|
1.0
|
CG
|
B:GLU217
|
4.4
|
81.7
|
1.0
|
O1P
|
B:4LU503
|
4.4
|
89.6
|
1.0
|
O
|
B:VAL215
|
4.5
|
87.9
|
1.0
|
CB
|
B:ALA211
|
4.5
|
80.6
|
1.0
|
CD2
|
B:HIS173
|
4.6
|
90.2
|
1.0
|
CB
|
B:ASN150
|
4.6
|
71.2
|
1.0
|
C
|
B:ALA211
|
4.6
|
84.8
|
1.0
|
O5'
|
B:4LU503
|
4.7
|
100.1
|
1.0
|
C
|
B:PRO212
|
4.7
|
92.6
|
1.0
|
O
|
B:THR151
|
4.8
|
71.8
|
1.0
|
CA
|
B:ASN150
|
5.0
|
71.0
|
1.0
|
|
Manganese binding site 3 out
of 6 in 7p9q
Go back to
Manganese Binding Sites List in 7p9q
Manganese binding site 3 out
of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
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 Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn502
b:136.8
occ:1.00
|
OD1
|
C:ASN150
|
2.2
|
114.6
|
1.0
|
OE1
|
C:GLU217
|
2.2
|
134.1
|
1.0
|
ND1
|
C:HIS173
|
2.4
|
135.2
|
1.0
|
O2P
|
C:4LU503
|
2.4
|
109.3
|
1.0
|
O
|
C:HOH638
|
2.7
|
80.2
|
1.0
|
CD
|
C:GLU217
|
3.0
|
120.7
|
1.0
|
CE1
|
C:HIS173
|
3.1
|
141.9
|
1.0
|
OE2
|
C:GLU217
|
3.3
|
117.8
|
1.0
|
CG
|
C:ASN150
|
3.4
|
117.1
|
1.0
|
CG
|
C:HIS173
|
3.5
|
132.2
|
1.0
|
P
|
C:4LU503
|
3.5
|
124.5
|
1.0
|
O3P
|
C:4LU503
|
3.7
|
119.5
|
1.0
|
O
|
C:ALA211
|
3.7
|
133.2
|
1.0
|
O
|
C:HOH619
|
3.9
|
76.1
|
1.0
|
CB
|
C:HIS173
|
4.0
|
127.4
|
1.0
|
NA
|
C:NA501
|
4.1
|
82.0
|
1.0
|
ND2
|
C:ASN150
|
4.1
|
119.0
|
1.0
|
O
|
C:PRO212
|
4.2
|
136.9
|
1.0
|
CG
|
C:GLU217
|
4.3
|
113.0
|
1.0
|
NE2
|
C:HIS173
|
4.3
|
147.5
|
1.0
|
CB
|
C:ASN150
|
4.4
|
115.4
|
1.0
|
O
|
C:VAL215
|
4.5
|
112.9
|
1.0
|
O1P
|
C:4LU503
|
4.5
|
96.2
|
1.0
|
CD2
|
C:HIS173
|
4.6
|
143.1
|
1.0
|
CB
|
C:ALA211
|
4.7
|
128.9
|
1.0
|
O5'
|
C:4LU503
|
4.7
|
118.1
|
1.0
|
O
|
C:THR151
|
4.7
|
104.6
|
1.0
|
C
|
C:ALA211
|
4.8
|
132.6
|
1.0
|
CA
|
C:ASN150
|
4.9
|
105.5
|
1.0
|
C
|
C:PRO212
|
4.9
|
129.8
|
1.0
|
N
|
C:THR151
|
5.0
|
104.6
|
1.0
|
|
Manganese binding site 4 out
of 6 in 7p9q
Go back to
Manganese Binding Sites List in 7p9q
Manganese binding site 4 out
of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
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 Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn502
b:137.2
occ:1.00
|
OE1
|
D:GLU217
|
2.2
|
129.7
|
1.0
|
OD1
|
D:ASN150
|
2.5
|
109.7
|
1.0
|
ND1
|
D:HIS173
|
2.5
|
119.5
|
1.0
|
O2P
|
D:4LU503
|
2.6
|
115.2
|
1.0
|
O
|
D:HOH646
|
2.7
|
131.3
|
1.0
|
CD
|
D:GLU217
|
2.9
|
121.8
|
1.0
|
CE1
|
D:HIS173
|
3.1
|
120.0
|
1.0
|
OE2
|
D:GLU217
|
3.3
|
132.0
|
1.0
|
O
|
D:ALA211
|
3.4
|
126.0
|
1.0
|
O3P
|
D:4LU503
|
3.4
|
121.7
|
1.0
|
P
|
D:4LU503
|
3.6
|
121.7
|
1.0
|
CG
|
D:ASN150
|
3.7
|
111.3
|
1.0
|
CG
|
D:HIS173
|
3.8
|
109.8
|
1.0
|
O
|
D:PRO212
|
3.9
|
135.1
|
1.0
|
O
|
D:HOH614
|
4.0
|
80.2
|
1.0
|
NA
|
D:NA501
|
4.1
|
78.7
|
1.0
|
CG
|
D:GLU217
|
4.2
|
115.0
|
1.0
|
O
|
D:VAL215
|
4.3
|
113.2
|
1.0
|
CB
|
D:ALA211
|
4.3
|
131.5
|
1.0
|
CB
|
D:HIS173
|
4.3
|
110.4
|
1.0
|
NE2
|
D:HIS173
|
4.4
|
114.8
|
1.0
|
C
|
D:ALA211
|
4.4
|
126.9
|
1.0
|
ND2
|
D:ASN150
|
4.5
|
109.9
|
1.0
|
O5'
|
D:4LU503
|
4.6
|
116.1
|
1.0
|
C
|
D:PRO212
|
4.7
|
127.2
|
1.0
|
CD2
|
D:HIS173
|
4.7
|
111.8
|
1.0
|
CB
|
D:ASN150
|
4.7
|
113.2
|
1.0
|
O1P
|
D:4LU503
|
4.8
|
99.1
|
1.0
|
CB
|
D:GLU217
|
4.8
|
108.9
|
1.0
|
O
|
D:THR151
|
4.9
|
96.1
|
1.0
|
|
Manganese binding site 5 out
of 6 in 7p9q
Go back to
Manganese Binding Sites List in 7p9q
Manganese binding site 5 out
of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
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 Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn502
b:135.3
occ:1.00
|
OE1
|
E:GLU217
|
2.0
|
129.8
|
1.0
|
O2P
|
E:4LU503
|
2.2
|
129.6
|
1.0
|
OD1
|
E:ASN150
|
2.4
|
126.3
|
1.0
|
ND1
|
E:HIS173
|
2.7
|
121.9
|
1.0
|
CD
|
E:GLU217
|
2.8
|
124.9
|
1.0
|
OE2
|
E:GLU217
|
3.2
|
131.0
|
1.0
|
CE1
|
E:HIS173
|
3.4
|
126.1
|
1.0
|
P
|
E:4LU503
|
3.5
|
125.5
|
1.0
|
CG
|
E:ASN150
|
3.6
|
127.5
|
1.0
|
O
|
E:ALA211
|
3.6
|
129.5
|
1.0
|
O3P
|
E:4LU503
|
3.7
|
138.1
|
1.0
|
NA
|
E:NA501
|
3.8
|
84.8
|
1.0
|
CG
|
E:HIS173
|
3.9
|
123.6
|
1.0
|
CG
|
E:GLU217
|
4.1
|
118.5
|
1.0
|
O
|
E:PRO212
|
4.2
|
131.0
|
1.0
|
O
|
E:HOH624
|
4.2
|
92.8
|
1.0
|
ND2
|
E:ASN150
|
4.2
|
124.8
|
1.0
|
CB
|
E:HIS173
|
4.3
|
128.8
|
1.0
|
CB
|
E:ALA211
|
4.4
|
134.3
|
1.0
|
O5'
|
E:4LU503
|
4.4
|
119.8
|
1.0
|
O
|
E:THR151
|
4.5
|
128.2
|
1.0
|
O
|
E:VAL215
|
4.5
|
130.3
|
1.0
|
O1P
|
E:4LU503
|
4.6
|
102.7
|
1.0
|
C
|
E:ALA211
|
4.6
|
135.7
|
1.0
|
NE2
|
E:HIS173
|
4.6
|
124.0
|
1.0
|
CB
|
E:ASN150
|
4.6
|
125.3
|
1.0
|
CB
|
E:GLU217
|
4.8
|
116.5
|
1.0
|
CD2
|
E:HIS173
|
4.9
|
123.2
|
1.0
|
N
|
E:THR151
|
5.0
|
125.0
|
1.0
|
C
|
E:PRO212
|
5.0
|
143.9
|
1.0
|
CA
|
E:ASN150
|
5.0
|
124.1
|
1.0
|
O
|
E:THR206
|
5.0
|
109.8
|
1.0
|
|
Manganese binding site 6 out
of 6 in 7p9q
Go back to
Manganese Binding Sites List in 7p9q
Manganese binding site 6 out
of 6 in the Crystal Structure of Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn.
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 Indole 3-Carboxylic Acid Decarboxylase From Arthrobacter Nicotianae FI1612 in Complex with Co-Factor Prfmn. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn502
b:140.8
occ:1.00
|
OE1
|
F:GLU217
|
2.0
|
163.0
|
1.0
|
O2P
|
F:4LU503
|
2.4
|
128.6
|
1.0
|
OD1
|
F:ASN150
|
2.6
|
169.4
|
1.0
|
ND1
|
F:HIS173
|
2.7
|
135.1
|
1.0
|
CD
|
F:GLU217
|
2.8
|
161.6
|
1.0
|
OE2
|
F:GLU217
|
3.2
|
173.8
|
1.0
|
CE1
|
F:HIS173
|
3.3
|
137.3
|
1.0
|
O
|
F:ALA211
|
3.4
|
130.3
|
1.0
|
P
|
F:4LU503
|
3.5
|
140.2
|
1.0
|
O3P
|
F:4LU503
|
3.6
|
147.4
|
1.0
|
NA
|
F:NA501
|
3.6
|
103.7
|
1.0
|
CG
|
F:ASN150
|
3.8
|
158.3
|
1.0
|
CG
|
F:HIS173
|
3.9
|
134.2
|
1.0
|
O
|
F:PRO212
|
4.0
|
152.0
|
1.0
|
CG
|
F:GLU217
|
4.1
|
149.0
|
1.0
|
CB
|
F:ALA211
|
4.2
|
138.9
|
1.0
|
C
|
F:ALA211
|
4.4
|
140.9
|
1.0
|
O
|
F:VAL215
|
4.4
|
135.9
|
1.0
|
CB
|
F:HIS173
|
4.4
|
136.9
|
1.0
|
ND2
|
F:ASN150
|
4.5
|
151.3
|
1.0
|
O1P
|
F:4LU503
|
4.6
|
127.0
|
1.0
|
NE2
|
F:HIS173
|
4.6
|
132.0
|
1.0
|
O5'
|
F:4LU503
|
4.6
|
131.0
|
1.0
|
CB
|
F:GLU217
|
4.7
|
140.2
|
1.0
|
O
|
F:THR151
|
4.7
|
132.7
|
1.0
|
C
|
F:PRO212
|
4.8
|
156.3
|
1.0
|
CB
|
F:ASN150
|
4.8
|
156.5
|
1.0
|
CD2
|
F:HIS173
|
4.9
|
131.2
|
1.0
|
CA
|
F:ALA211
|
5.0
|
140.0
|
1.0
|
|
Reference:
D.Gahloth,
K.Fisher,
K.A.P.Payne,
M.Cliff,
C.Levy,
D.Leys.
Structural and Biochemical Characterization of the Prenylated Flavin Mononucleotide-Dependent Indole-3-Carboxylic Acid Decarboxylase. J.Biol.Chem. V. 298 01771 2022.
ISSN: ESSN 1083-351X
PubMed: 35218772
DOI: 10.1016/J.JBC.2022.101771
Page generated: Sun Oct 6 10:23:51 2024
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