Magnesium in PDB 2wva: Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis
Enzymatic activity of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis
All present enzymatic activity of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis:
4.1.1.1;
Protein crystallography data
The structure of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis, PDB code: 2wva
was solved by
X.Y.Pei,
K.Erixon,
B.F.Luisi,
F.J.Leeper,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
34.65 /
2.20
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.619,
111.585,
167.432,
89.82,
90.11,
78.94
|
|
R / Rfree (%)
|
19.4 /
21.3
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis
(pdb code 2wva). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis, PDB code: 2wva:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 2wva
Go back to
Magnesium Binding Sites List in 2wva
Magnesium binding site 1 out
of 8 in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:50.9
occ:1.00
|
O21
|
A:TPU600
|
2.2
|
50.5
|
1.0
|
|
OD1
|
A:ASN467
|
2.2
|
58.1
|
1.0
|
|
OD1
|
A:ASP440
|
2.3
|
51.0
|
1.0
|
|
O12
|
A:TPU600
|
2.3
|
48.9
|
1.0
|
|
O
|
A:GLY469
|
2.3
|
55.5
|
1.0
|
|
O
|
A:HOH2332
|
2.4
|
52.9
|
1.0
|
|
CG
|
A:ASN467
|
3.1
|
58.6
|
1.0
|
|
P2
|
A:TPU600
|
3.1
|
49.8
|
1.0
|
|
O11
|
A:TPU600
|
3.1
|
48.6
|
1.0
|
|
P1
|
A:TPU600
|
3.2
|
48.4
|
1.0
|
|
ND2
|
A:ASN467
|
3.3
|
58.5
|
1.0
|
|
CG
|
A:ASP440
|
3.4
|
51.3
|
1.0
|
|
C
|
A:GLY469
|
3.5
|
56.3
|
1.0
|
|
O23
|
A:TPU600
|
3.9
|
49.8
|
1.0
|
|
N
|
A:ASP440
|
3.9
|
49.5
|
1.0
|
|
O5G
|
A:TPU600
|
4.0
|
48.2
|
1.0
|
|
OD2
|
A:ASP440
|
4.0
|
52.1
|
1.0
|
|
O
|
A:ILE465
|
4.1
|
54.4
|
1.0
|
|
N
|
A:GLY441
|
4.1
|
49.1
|
1.0
|
|
N
|
A:THR471
|
4.2
|
56.5
|
1.0
|
|
N
|
A:GLY469
|
4.2
|
57.8
|
1.0
|
|
O13
|
A:TPU600
|
4.4
|
47.6
|
1.0
|
|
CA
|
A:GLY469
|
4.4
|
57.2
|
1.0
|
|
O22
|
A:TPU600
|
4.4
|
49.9
|
1.0
|
|
N
|
A:TYR470
|
4.5
|
56.3
|
1.0
|
|
CA
|
A:GLY439
|
4.5
|
48.4
|
1.0
|
|
CB
|
A:ASN467
|
4.5
|
59.5
|
1.0
|
|
CA
|
A:TYR470
|
4.5
|
55.5
|
1.0
|
|
N
|
A:ASN467
|
4.5
|
57.8
|
1.0
|
|
C
|
A:GLY439
|
4.6
|
48.8
|
1.0
|
|
CB
|
A:ASP440
|
4.6
|
50.8
|
1.0
|
|
CA
|
A:ASP440
|
4.7
|
49.9
|
1.0
|
|
OG1
|
A:THR471
|
4.7
|
58.7
|
1.0
|
|
O
|
A:HOH2335
|
4.8
|
53.2
|
1.0
|
|
C
|
A:ASN467
|
4.9
|
59.5
|
1.0
|
|
CA
|
A:ASN467
|
4.9
|
59.2
|
1.0
|
|
CB
|
A:THR471
|
4.9
|
58.0
|
1.0
|
|
C
|
A:TYR470
|
4.9
|
56.3
|
1.0
|
|
C
|
A:ASP440
|
5.0
|
49.6
|
1.0
|
|
N
|
A:TYR468
|
5.0
|
59.1
|
1.0
|
|
CA
|
A:GLY441
|
5.0
|
48.6
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 2wva
Go back to
Magnesium Binding Sites List in 2wva
Magnesium binding site 2 out
of 8 in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:57.0
occ:1.00
|
OD1
|
B:ASN467
|
2.1
|
63.5
|
1.0
|
|
O12
|
B:TPU600
|
2.1
|
53.7
|
1.0
|
|
O21
|
B:TPU600
|
2.3
|
54.6
|
1.0
|
|
OD1
|
B:ASP440
|
2.3
|
52.4
|
1.0
|
|
O
|
B:HOH2293
|
2.4
|
53.0
|
1.0
|
|
O
|
B:GLY469
|
2.4
|
63.7
|
1.0
|
|
CG
|
B:ASN467
|
2.9
|
64.0
|
1.0
|
|
P2
|
B:TPU600
|
3.0
|
54.5
|
1.0
|
|
ND2
|
B:ASN467
|
3.1
|
63.9
|
1.0
|
|
O23
|
B:TPU600
|
3.1
|
55.0
|
1.0
|
|
P1
|
B:TPU600
|
3.4
|
53.2
|
1.0
|
|
CG
|
B:ASP440
|
3.5
|
52.7
|
1.0
|
|
O11
|
B:TPU600
|
3.6
|
53.7
|
1.0
|
|
C
|
B:GLY469
|
3.6
|
63.6
|
1.0
|
|
N
|
B:ASP440
|
4.0
|
52.3
|
1.0
|
|
OD2
|
B:ASP440
|
4.1
|
53.2
|
1.0
|
|
O
|
B:ILE465
|
4.1
|
61.1
|
1.0
|
|
N
|
B:THR471
|
4.2
|
65.4
|
1.0
|
|
N
|
B:GLY469
|
4.3
|
64.4
|
1.0
|
|
N
|
B:GLY441
|
4.3
|
50.9
|
1.0
|
|
CB
|
B:ASN467
|
4.3
|
64.9
|
1.0
|
|
O13
|
B:TPU600
|
4.3
|
53.0
|
1.0
|
|
N
|
B:ASN467
|
4.4
|
63.7
|
1.0
|
|
O5G
|
B:TPU600
|
4.5
|
52.5
|
1.0
|
|
CA
|
B:GLY439
|
4.5
|
52.5
|
1.0
|
|
CA
|
B:GLY469
|
4.5
|
63.8
|
1.0
|
|
OG1
|
B:THR471
|
4.5
|
68.2
|
1.0
|
|
O22
|
B:TPU600
|
4.5
|
54.8
|
1.0
|
|
N
|
B:TYR470
|
4.6
|
63.2
|
1.0
|
|
C
|
B:GLY439
|
4.6
|
52.1
|
1.0
|
|
CA
|
B:TYR470
|
4.6
|
63.0
|
1.0
|
|
CB
|
B:ASP440
|
4.7
|
52.5
|
1.0
|
|
O
|
B:HOH2252
|
4.7
|
48.1
|
1.0
|
|
CB
|
B:THR471
|
4.8
|
67.6
|
1.0
|
|
CA
|
B:ASP440
|
4.8
|
51.9
|
1.0
|
|
CA
|
B:ASN467
|
4.8
|
64.9
|
1.0
|
|
C
|
B:ASN467
|
4.8
|
65.1
|
1.0
|
|
N
|
B:TYR468
|
4.9
|
65.2
|
1.0
|
|
C
|
B:TYR470
|
4.9
|
64.3
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 2wva
Go back to
Magnesium Binding Sites List in 2wva
Magnesium binding site 3 out
of 8 in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg601
b:60.7
occ:1.00
|
OD1
|
E:ASN467
|
2.2
|
58.8
|
1.0
|
|
O
|
E:HOH2246
|
2.2
|
37.1
|
1.0
|
|
O12
|
E:TPU600
|
2.2
|
48.0
|
1.0
|
|
OD1
|
E:ASP440
|
2.4
|
50.1
|
1.0
|
|
O21
|
E:TPU600
|
2.4
|
48.9
|
1.0
|
|
O
|
E:GLY469
|
2.6
|
61.6
|
1.0
|
|
CG
|
E:ASN467
|
2.9
|
59.4
|
1.0
|
|
ND2
|
E:ASN467
|
3.1
|
59.0
|
1.0
|
|
P2
|
E:TPU600
|
3.1
|
48.4
|
1.0
|
|
O23
|
E:TPU600
|
3.3
|
48.4
|
1.0
|
|
P1
|
E:TPU600
|
3.3
|
47.2
|
1.0
|
|
CG
|
E:ASP440
|
3.6
|
50.4
|
1.0
|
|
O11
|
E:TPU600
|
3.6
|
47.4
|
1.0
|
|
C
|
E:GLY469
|
3.8
|
61.9
|
1.0
|
|
N
|
E:ASP440
|
3.9
|
48.3
|
1.0
|
|
O
|
E:ILE465
|
3.9
|
56.9
|
1.0
|
|
O13
|
E:TPU600
|
4.0
|
47.0
|
1.0
|
|
OD2
|
E:ASP440
|
4.2
|
51.3
|
1.0
|
|
CA
|
E:GLY439
|
4.3
|
47.5
|
1.0
|
|
N
|
E:THR471
|
4.3
|
63.1
|
1.0
|
|
CB
|
E:ASN467
|
4.3
|
60.6
|
1.0
|
|
N
|
E:GLY441
|
4.4
|
47.9
|
1.0
|
|
N
|
E:ASN467
|
4.4
|
59.8
|
1.0
|
|
N
|
E:GLY469
|
4.5
|
62.1
|
1.0
|
|
C
|
E:GLY439
|
4.5
|
47.7
|
1.0
|
|
OG1
|
E:THR471
|
4.6
|
65.5
|
1.0
|
|
O
|
E:HOH2249
|
4.6
|
53.7
|
1.0
|
|
CB
|
E:ASP440
|
4.7
|
50.0
|
1.0
|
|
O22
|
E:TPU600
|
4.7
|
48.5
|
1.0
|
|
O5G
|
E:TPU600
|
4.7
|
46.7
|
1.0
|
|
CA
|
E:ASP440
|
4.7
|
48.9
|
1.0
|
|
CA
|
E:GLY469
|
4.7
|
62.2
|
1.0
|
|
N
|
E:TYR470
|
4.8
|
62.0
|
1.0
|
|
CA
|
E:ASN467
|
4.8
|
60.9
|
1.0
|
|
CA
|
E:TYR470
|
4.8
|
61.6
|
1.0
|
|
CB
|
E:THR471
|
4.8
|
64.7
|
1.0
|
|
C
|
E:ASN467
|
4.9
|
61.4
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 2wva
Go back to
Magnesium Binding Sites List in 2wva
Magnesium binding site 4 out
of 8 in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg569
b:52.7
occ:1.00
|
O12
|
F:TPU600
|
2.1
|
52.9
|
1.0
|
|
OD1
|
F:ASN467
|
2.2
|
64.2
|
1.0
|
|
O
|
F:GLY469
|
2.3
|
64.3
|
1.0
|
|
O21
|
F:TPU600
|
2.4
|
54.3
|
1.0
|
|
OD1
|
F:ASP440
|
2.5
|
53.0
|
1.0
|
|
O
|
F:HOH2332
|
2.5
|
52.8
|
1.0
|
|
CG
|
F:ASN467
|
3.0
|
64.9
|
1.0
|
|
ND2
|
F:ASN467
|
3.1
|
64.9
|
1.0
|
|
P2
|
F:TPU600
|
3.1
|
53.5
|
1.0
|
|
O23
|
F:TPU600
|
3.1
|
53.7
|
1.0
|
|
P1
|
F:TPU600
|
3.3
|
52.2
|
1.0
|
|
C
|
F:GLY469
|
3.5
|
64.4
|
1.0
|
|
O11
|
F:TPU600
|
3.6
|
52.6
|
1.0
|
|
CG
|
F:ASP440
|
3.7
|
53.3
|
1.0
|
|
N
|
F:THR471
|
4.0
|
66.8
|
1.0
|
|
N
|
F:ASP440
|
4.2
|
52.4
|
1.0
|
|
OD2
|
F:ASP440
|
4.2
|
53.9
|
1.0
|
|
O
|
F:ILE465
|
4.3
|
59.8
|
1.0
|
|
O13
|
F:TPU600
|
4.3
|
51.6
|
1.0
|
|
N
|
F:GLY469
|
4.3
|
65.0
|
1.0
|
|
N
|
F:GLY441
|
4.4
|
51.4
|
1.0
|
|
N
|
F:TYR470
|
4.4
|
64.5
|
1.0
|
|
CB
|
F:ASN467
|
4.4
|
66.0
|
1.0
|
|
OG1
|
F:THR471
|
4.4
|
69.9
|
1.0
|
|
O5G
|
F:TPU600
|
4.4
|
51.9
|
1.0
|
|
CA
|
F:TYR470
|
4.4
|
64.6
|
1.0
|
|
CA
|
F:GLY469
|
4.5
|
64.7
|
1.0
|
|
N
|
F:ASN467
|
4.6
|
64.1
|
1.0
|
|
CA
|
F:GLY439
|
4.6
|
52.2
|
1.0
|
|
CB
|
F:THR471
|
4.6
|
69.1
|
1.0
|
|
O22
|
F:TPU600
|
4.6
|
53.9
|
1.0
|
|
O
|
F:HOH2290
|
4.7
|
29.4
|
1.0
|
|
C
|
F:TYR470
|
4.7
|
65.9
|
1.0
|
|
C
|
F:GLY439
|
4.8
|
51.9
|
1.0
|
|
CB
|
F:ASP440
|
4.8
|
52.7
|
1.0
|
|
C
|
F:ASN467
|
4.9
|
66.1
|
1.0
|
|
CA
|
F:ASN467
|
4.9
|
65.8
|
1.0
|
|
CA
|
F:THR471
|
4.9
|
68.4
|
1.0
|
|
CA
|
F:ASP440
|
4.9
|
51.9
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 2wva
Go back to
Magnesium Binding Sites List in 2wva
Magnesium binding site 5 out
of 8 in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Mg601
b:51.6
occ:1.00
|
OD1
|
V:ASN467
|
2.5
|
55.0
|
1.0
|
|
O12
|
V:TPU600
|
2.6
|
42.3
|
1.0
|
|
O21
|
V:TPU600
|
2.6
|
43.3
|
1.0
|
|
OD1
|
V:ASP440
|
2.7
|
46.3
|
1.0
|
|
O23
|
V:TPU600
|
2.8
|
42.9
|
1.0
|
|
O
|
V:ILE465
|
3.0
|
53.4
|
1.0
|
|
CG
|
V:ASN467
|
3.0
|
55.3
|
1.0
|
|
ND2
|
V:ASN467
|
3.1
|
54.8
|
1.0
|
|
P2
|
V:TPU600
|
3.1
|
42.6
|
1.0
|
|
N
|
V:ASP440
|
3.4
|
45.9
|
1.0
|
|
CA
|
V:GLY439
|
3.5
|
45.3
|
1.0
|
|
P1
|
V:TPU600
|
3.6
|
41.5
|
1.0
|
|
O11
|
V:TPU600
|
3.7
|
41.6
|
1.0
|
|
CG
|
V:ASP440
|
3.8
|
46.9
|
1.0
|
|
O
|
V:GLY469
|
3.8
|
56.6
|
1.0
|
|
C
|
V:GLY439
|
3.9
|
45.5
|
1.0
|
|
C
|
V:ILE465
|
4.1
|
53.8
|
1.0
|
|
O13
|
V:TPU600
|
4.1
|
41.3
|
1.0
|
|
N
|
V:ASN467
|
4.2
|
56.3
|
1.0
|
|
CB
|
V:ILE465
|
4.3
|
52.6
|
1.0
|
|
CB
|
V:ASN467
|
4.3
|
56.4
|
1.0
|
|
CG2
|
V:ILE465
|
4.4
|
53.1
|
1.0
|
|
CA
|
V:ASP440
|
4.5
|
46.2
|
1.0
|
|
OD2
|
V:ASP440
|
4.6
|
47.8
|
1.0
|
|
O
|
V:HOH2344
|
4.6
|
53.2
|
1.0
|
|
CB
|
V:ASP440
|
4.6
|
47.0
|
1.0
|
|
O22
|
V:TPU600
|
4.6
|
42.4
|
1.0
|
|
N
|
V:GLY441
|
4.7
|
44.8
|
1.0
|
|
O
|
V:HOH2266
|
4.8
|
40.4
|
1.0
|
|
CA
|
V:ASN467
|
4.8
|
56.9
|
1.0
|
|
CA
|
V:ILE465
|
4.8
|
53.1
|
1.0
|
|
N
|
V:GLY439
|
4.8
|
45.7
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 2wva
Go back to
Magnesium Binding Sites List in 2wva
Magnesium binding site 6 out
of 8 in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Mg601
b:54.1
occ:1.00
|
OD1
|
X:ASN467
|
2.1
|
52.4
|
1.0
|
|
O
|
X:GLY469
|
2.1
|
51.2
|
1.0
|
|
O21
|
X:TPU600
|
2.2
|
45.0
|
1.0
|
|
OD1
|
X:ASP440
|
2.3
|
40.8
|
1.0
|
|
O12
|
X:TPU600
|
2.3
|
43.2
|
1.0
|
|
O
|
X:HOH2301
|
2.3
|
27.8
|
1.0
|
|
CG
|
X:ASN467
|
3.0
|
53.1
|
1.0
|
|
ND2
|
X:ASN467
|
3.2
|
52.9
|
1.0
|
|
P2
|
X:TPU600
|
3.3
|
44.3
|
1.0
|
|
C
|
X:GLY469
|
3.4
|
51.6
|
1.0
|
|
CG
|
X:ASP440
|
3.4
|
41.1
|
1.0
|
|
P1
|
X:TPU600
|
3.4
|
42.6
|
1.0
|
|
O11
|
X:TPU600
|
3.6
|
42.9
|
1.0
|
|
O23
|
X:TPU600
|
3.8
|
44.6
|
1.0
|
|
OD2
|
X:ASP440
|
3.9
|
42.0
|
1.0
|
|
N
|
X:GLY469
|
4.0
|
52.6
|
1.0
|
|
N
|
X:ASP440
|
4.1
|
40.1
|
1.0
|
|
N
|
X:THR471
|
4.1
|
52.4
|
1.0
|
|
O5G
|
X:TPU600
|
4.1
|
42.5
|
1.0
|
|
O
|
X:ILE465
|
4.2
|
49.5
|
1.0
|
|
N
|
X:GLY441
|
4.2
|
39.2
|
1.0
|
|
CA
|
X:GLY469
|
4.2
|
52.2
|
1.0
|
|
N
|
X:TYR470
|
4.3
|
51.5
|
1.0
|
|
CB
|
X:ASN467
|
4.4
|
54.2
|
1.0
|
|
N
|
X:ASN467
|
4.4
|
52.8
|
1.0
|
|
CA
|
X:TYR470
|
4.5
|
50.9
|
1.0
|
|
OG1
|
X:THR471
|
4.6
|
55.1
|
1.0
|
|
O13
|
X:TPU600
|
4.6
|
42.0
|
1.0
|
|
CB
|
X:ASP440
|
4.6
|
40.9
|
1.0
|
|
O22
|
X:TPU600
|
4.6
|
44.7
|
1.0
|
|
C
|
X:ASN467
|
4.7
|
54.2
|
1.0
|
|
CA
|
X:GLY439
|
4.7
|
40.2
|
1.0
|
|
O
|
X:HOH2334
|
4.7
|
48.9
|
1.0
|
|
CA
|
X:ASN467
|
4.7
|
54.0
|
1.0
|
|
C
|
X:GLY439
|
4.7
|
39.8
|
1.0
|
|
N
|
X:TYR468
|
4.8
|
53.6
|
1.0
|
|
CA
|
X:ASP440
|
4.8
|
40.1
|
1.0
|
|
CB
|
X:THR471
|
4.8
|
54.2
|
1.0
|
|
C
|
X:TYR470
|
4.8
|
52.0
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 2wva
Go back to
Magnesium Binding Sites List in 2wva
Magnesium binding site 7 out
of 8 in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Mg601
b:63.4
occ:1.00
|
O12
|
Y:TPU600
|
2.1
|
56.8
|
1.0
|
|
O
|
Y:GLY469
|
2.1
|
65.4
|
1.0
|
|
OD1
|
Y:ASN467
|
2.1
|
63.0
|
1.0
|
|
OD1
|
Y:ASP440
|
2.1
|
55.6
|
1.0
|
|
O
|
Y:HOH2274
|
2.3
|
44.5
|
1.0
|
|
O21
|
Y:TPU600
|
2.4
|
58.2
|
1.0
|
|
CG
|
Y:ASN467
|
3.1
|
63.9
|
1.0
|
|
CG
|
Y:ASP440
|
3.3
|
55.8
|
1.0
|
|
C
|
Y:GLY469
|
3.3
|
65.3
|
1.0
|
|
P2
|
Y:TPU600
|
3.3
|
57.8
|
1.0
|
|
ND2
|
Y:ASN467
|
3.4
|
63.8
|
1.0
|
|
P1
|
Y:TPU600
|
3.5
|
56.1
|
1.0
|
|
O23
|
Y:TPU600
|
3.7
|
58.3
|
1.0
|
|
OD2
|
Y:ASP440
|
3.8
|
56.5
|
1.0
|
|
O11
|
Y:TPU600
|
3.8
|
56.7
|
1.0
|
|
N
|
Y:GLY469
|
3.9
|
65.4
|
1.0
|
|
N
|
Y:ASP440
|
4.0
|
54.6
|
1.0
|
|
N
|
Y:GLY441
|
4.1
|
53.7
|
1.0
|
|
CA
|
Y:GLY469
|
4.1
|
65.3
|
1.0
|
|
N
|
Y:THR471
|
4.2
|
67.6
|
1.0
|
|
O
|
Y:ILE465
|
4.2
|
60.8
|
1.0
|
|
N
|
Y:TYR470
|
4.3
|
65.2
|
1.0
|
|
N
|
Y:ASN467
|
4.4
|
63.9
|
1.0
|
|
O13
|
Y:TPU600
|
4.4
|
55.6
|
1.0
|
|
CB
|
Y:ASN467
|
4.4
|
65.2
|
1.0
|
|
CA
|
Y:TYR470
|
4.4
|
65.2
|
1.0
|
|
O5G
|
Y:TPU600
|
4.5
|
55.4
|
1.0
|
|
CB
|
Y:ASP440
|
4.5
|
55.3
|
1.0
|
|
O
|
Y:HOH2300
|
4.5
|
53.2
|
1.0
|
|
OG1
|
Y:THR471
|
4.6
|
70.4
|
1.0
|
|
C
|
Y:ASN467
|
4.7
|
65.6
|
1.0
|
|
CA
|
Y:ASP440
|
4.7
|
54.5
|
1.0
|
|
CA
|
Y:GLY439
|
4.7
|
54.1
|
1.0
|
|
N
|
Y:TYR468
|
4.7
|
65.7
|
1.0
|
|
C
|
Y:GLY439
|
4.7
|
54.0
|
1.0
|
|
CA
|
Y:ASN467
|
4.8
|
65.2
|
1.0
|
|
O22
|
Y:TPU600
|
4.8
|
58.1
|
1.0
|
|
C
|
Y:TYR470
|
4.9
|
66.5
|
1.0
|
|
C
|
Y:ASP440
|
4.9
|
53.8
|
1.0
|
|
CB
|
Y:THR471
|
4.9
|
69.8
|
1.0
|
|
CA
|
Y:GLY441
|
4.9
|
53.0
|
1.0
|
|
C
|
Y:TYR468
|
4.9
|
66.0
|
1.0
|
|
O
|
Y:ASN467
|
5.0
|
65.9
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 2wva
Go back to
Magnesium Binding Sites List in 2wva
Magnesium binding site 8 out
of 8 in the Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Z:Mg569
b:55.7
occ:1.00
|
O12
|
Z:TPU600
|
2.2
|
57.5
|
1.0
|
|
OD1
|
Z:ASN467
|
2.2
|
64.6
|
1.0
|
|
OD1
|
Z:ASP440
|
2.3
|
56.0
|
1.0
|
|
O
|
Z:GLY469
|
2.3
|
66.2
|
1.0
|
|
O
|
Z:HOH2334
|
2.4
|
53.2
|
1.0
|
|
O21
|
Z:TPU600
|
2.4
|
59.2
|
1.0
|
|
CG
|
Z:ASN467
|
3.1
|
65.6
|
1.0
|
|
P2
|
Z:TPU600
|
3.2
|
58.7
|
1.0
|
|
ND2
|
Z:ASN467
|
3.3
|
65.4
|
1.0
|
|
P1
|
Z:TPU600
|
3.4
|
56.8
|
1.0
|
|
CG
|
Z:ASP440
|
3.4
|
56.0
|
1.0
|
|
O23
|
Z:TPU600
|
3.5
|
58.9
|
1.0
|
|
C
|
Z:GLY469
|
3.5
|
66.4
|
1.0
|
|
O11
|
Z:TPU600
|
3.7
|
57.5
|
1.0
|
|
N
|
Z:ASP440
|
3.9
|
54.6
|
1.0
|
|
OD2
|
Z:ASP440
|
4.0
|
56.7
|
1.0
|
|
O
|
Z:ILE465
|
4.1
|
59.3
|
1.0
|
|
N
|
Z:GLY441
|
4.2
|
53.4
|
1.0
|
|
N
|
Z:THR471
|
4.2
|
69.0
|
1.0
|
|
N
|
Z:GLY469
|
4.2
|
66.8
|
1.0
|
|
O13
|
Z:TPU600
|
4.3
|
56.1
|
1.0
|
|
CA
|
Z:GLY469
|
4.4
|
66.6
|
1.0
|
|
CB
|
Z:ASN467
|
4.5
|
67.0
|
1.0
|
|
N
|
Z:TYR470
|
4.5
|
66.5
|
1.0
|
|
CA
|
Z:GLY439
|
4.5
|
54.2
|
1.0
|
|
N
|
Z:ASN467
|
4.5
|
64.7
|
1.0
|
|
CA
|
Z:TYR470
|
4.5
|
66.4
|
1.0
|
|
O5G
|
Z:TPU600
|
4.6
|
56.2
|
1.0
|
|
C
|
Z:GLY439
|
4.6
|
53.9
|
1.0
|
|
CB
|
Z:ASP440
|
4.6
|
55.2
|
1.0
|
|
OG1
|
Z:THR471
|
4.6
|
72.2
|
1.0
|
|
CA
|
Z:ASP440
|
4.7
|
54.2
|
1.0
|
|
O22
|
Z:TPU600
|
4.7
|
58.8
|
1.0
|
|
C
|
Z:ASN467
|
4.8
|
67.3
|
1.0
|
|
CA
|
Z:ASN467
|
4.8
|
66.8
|
1.0
|
|
CB
|
Z:THR471
|
4.9
|
71.4
|
1.0
|
|
C
|
Z:TYR470
|
4.9
|
67.9
|
1.0
|
|
C
|
Z:ASP440
|
5.0
|
53.5
|
1.0
|
|
N
|
Z:TYR468
|
5.0
|
67.2
|
1.0
|
|
Reference:
X.Y.Pei,
K.Erixon,
B.F.Luisi,
F.J.Leeper.
Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase From Zymomonas Mobilis Biochemistry V. 49 1727 2010.
ISSN: ISSN 0006-2960
PubMed: 20099870
DOI: 10.1021/BI901864J
Page generated: Wed Aug 14 06:14:23 2024
|
