Magnesium in PDB 6z9j: Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant
Enzymatic activity of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant
All present enzymatic activity of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant:
4.1.2.4;
Protein crystallography data
The structure of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant, PDB code: 6z9j
was solved by
J.Paakkonen,
N.Hakulinen,
J.Rouvinen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
31.30 /
1.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.504,
52.811,
80.675,
90.00,
111.23,
90.00
|
R / Rfree (%)
|
15.9 /
18.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant
(pdb code 6z9j). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the
Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant, PDB code: 6z9j:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 6z9j
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Magnesium Binding Sites List in 6z9j
Magnesium binding site 1 out
of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg301
b:27.6
occ:1.00
|
O
|
B:HOH534
|
1.9
|
35.3
|
1.0
|
O
|
A:HOH518
|
2.0
|
32.6
|
1.0
|
O
|
B:HOH538
|
2.0
|
36.5
|
1.0
|
O
|
B:HOH514
|
2.1
|
32.0
|
1.0
|
O
|
A:HOH573
|
2.1
|
30.9
|
1.0
|
NE2
|
A:HIS78
|
2.1
|
26.7
|
1.0
|
CD2
|
A:HIS78
|
3.0
|
33.4
|
1.0
|
CE1
|
A:HIS78
|
3.2
|
36.1
|
1.0
|
OE2
|
B:GLU27
|
3.9
|
55.4
|
1.0
|
O
|
B:HOH545
|
4.1
|
23.9
|
1.0
|
CG
|
A:HIS78
|
4.2
|
31.0
|
1.0
|
O
|
B:HOH410
|
4.2
|
37.2
|
1.0
|
OE1
|
B:GLU27
|
4.2
|
24.7
|
1.0
|
ND1
|
A:HIS78
|
4.2
|
28.7
|
1.0
|
OD2
|
B:ASP26
|
4.3
|
29.4
|
1.0
|
O
|
A:HOH681
|
4.3
|
39.1
|
1.0
|
CD
|
B:GLU27
|
4.5
|
42.9
|
1.0
|
O
|
B:HOH432
|
4.9
|
41.0
|
1.0
|
CD
|
A:PRO77
|
4.9
|
19.4
|
1.0
|
CG
|
B:ASP26
|
5.0
|
27.6
|
1.0
|
|
Magnesium binding site 2 out
of 9 in 6z9j
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Magnesium Binding Sites List in 6z9j
Magnesium binding site 2 out
of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:32.0
occ:1.00
|
O
|
A:HOH668
|
2.0
|
41.8
|
1.0
|
O
|
A:HOH605
|
2.0
|
23.8
|
1.0
|
O
|
A:HOH469
|
2.3
|
37.4
|
1.0
|
O
|
A:HOH599
|
4.0
|
34.5
|
1.0
|
O
|
A:HOH430
|
4.1
|
24.5
|
1.0
|
NZ
|
A:LYS126
|
4.1
|
24.8
|
1.0
|
O
|
A:HOH484
|
4.3
|
25.8
|
1.0
|
O
|
A:HOH450
|
4.4
|
18.4
|
1.0
|
CA
|
A:GLY162
|
4.9
|
19.2
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 6z9j
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Magnesium Binding Sites List in 6z9j
Magnesium binding site 3 out
of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg303
b:62.8
occ:1.00
|
O
|
A:HOH515
|
2.0
|
45.5
|
1.0
|
O
|
A:HOH686
|
2.5
|
63.2
|
1.0
|
O
|
A:HOH615
|
2.7
|
39.3
|
1.0
|
O
|
A:LYS37
|
3.9
|
24.9
|
1.0
|
N
|
A:PRO39
|
4.1
|
23.3
|
1.0
|
CA
|
A:PRO39
|
4.1
|
26.3
|
1.0
|
C
|
A:THR38
|
4.3
|
18.7
|
1.0
|
O
|
A:THR38
|
4.3
|
23.9
|
1.0
|
O
|
A:HOH538
|
4.4
|
41.5
|
1.0
|
CB
|
A:PRO39
|
4.5
|
34.6
|
1.0
|
O
|
A:HOH496
|
4.5
|
41.2
|
1.0
|
CD
|
A:PRO39
|
4.5
|
26.4
|
1.0
|
C
|
A:LYS37
|
4.8
|
22.0
|
1.0
|
CA
|
A:THR38
|
5.0
|
19.9
|
1.0
|
|
Magnesium binding site 4 out
of 9 in 6z9j
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Magnesium Binding Sites List in 6z9j
Magnesium binding site 4 out
of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg304
b:43.5
occ:1.00
|
O
|
A:HOH543
|
2.1
|
40.7
|
1.0
|
O
|
B:HOH604
|
2.2
|
37.1
|
1.0
|
O
|
B:HOH660
|
2.3
|
34.9
|
1.0
|
O
|
B:HOH410
|
2.3
|
37.2
|
1.0
|
O
|
A:HOH452
|
2.4
|
45.4
|
1.0
|
O
|
B:HOH421
|
2.5
|
40.2
|
1.0
|
O
|
A:PHE76
|
3.5
|
18.8
|
1.0
|
OD1
|
B:ASP26
|
3.7
|
24.1
|
1.0
|
O
|
A:HOH429
|
3.8
|
20.7
|
1.0
|
OD2
|
B:ASP26
|
3.9
|
29.4
|
1.0
|
O
|
A:HOH508
|
4.1
|
19.0
|
1.0
|
CG
|
B:ASP26
|
4.2
|
27.6
|
1.0
|
O
|
B:HOH574
|
4.4
|
27.2
|
1.0
|
O
|
A:HOH593
|
4.4
|
42.5
|
1.0
|
O
|
A:HOH573
|
4.5
|
30.9
|
1.0
|
O
|
A:HOH602
|
4.5
|
22.8
|
1.0
|
OE2
|
A:GLU89
|
4.6
|
25.1
|
1.0
|
O
|
B:HOH545
|
4.6
|
23.9
|
1.0
|
O
|
A:HOH440
|
4.6
|
44.8
|
1.0
|
C
|
A:PHE76
|
4.7
|
18.6
|
1.0
|
O
|
B:HOH432
|
4.8
|
41.0
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 6z9j
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Magnesium Binding Sites List in 6z9j
Magnesium binding site 5 out
of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg305
b:35.2
occ:1.00
|
O
|
A:HOH483
|
2.0
|
38.3
|
1.0
|
O
|
A:HOH425
|
2.1
|
47.2
|
1.0
|
O
|
A:HOH509
|
2.2
|
28.4
|
1.0
|
O
|
A:HOH461
|
2.2
|
28.3
|
1.0
|
O
|
A:HOH608
|
3.9
|
43.5
|
1.0
|
OE2
|
A:GLU148
|
4.0
|
33.7
|
1.0
|
OE1
|
A:GLU148
|
4.2
|
34.0
|
1.0
|
OE1
|
A:GLU187
|
4.2
|
26.7
|
1.0
|
OE2
|
A:GLU187
|
4.3
|
24.9
|
1.0
|
O
|
A:HOH576
|
4.3
|
30.6
|
1.0
|
CD
|
A:GLU148
|
4.5
|
37.8
|
1.0
|
CD
|
A:GLU187
|
4.7
|
31.3
|
1.0
|
O
|
A:HOH423
|
4.9
|
35.1
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 6z9j
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Magnesium Binding Sites List in 6z9j
Magnesium binding site 6 out
of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg306
b:58.5
occ:1.00
|
O
|
B:HOH415
|
2.2
|
39.2
|
1.0
|
O
|
A:HOH445
|
2.2
|
46.8
|
1.0
|
O
|
B:HOH616
|
2.3
|
44.5
|
1.0
|
O
|
B:HOH425
|
2.5
|
48.4
|
1.0
|
O
|
A:HOH578
|
3.3
|
41.9
|
1.0
|
O
|
A:ASP22
|
3.3
|
34.8
|
1.0
|
O
|
A:HOH409
|
3.5
|
34.7
|
1.0
|
CA
|
A:ASP22
|
3.8
|
24.3
|
1.0
|
O
|
B:HOH592
|
3.9
|
40.4
|
1.0
|
O
|
B:ASP22
|
3.9
|
31.0
|
1.0
|
C
|
A:ASP22
|
4.0
|
31.4
|
1.0
|
O
|
B:ASP24
|
4.1
|
20.1
|
1.0
|
CB
|
A:ASP22
|
4.1
|
39.6
|
1.0
|
NH2
|
B:ARG51
|
4.2
|
23.5
|
1.0
|
OD1
|
A:ASP22
|
4.2
|
55.0
|
1.0
|
O
|
B:HOH574
|
4.3
|
27.2
|
1.0
|
O
|
A:HOH652
|
4.4
|
49.1
|
1.0
|
CG
|
A:ASP22
|
4.6
|
63.7
|
1.0
|
NH2
|
A:ARG51
|
4.7
|
26.0
|
1.0
|
|
Magnesium binding site 7 out
of 9 in 6z9j
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Magnesium Binding Sites List in 6z9j
Magnesium binding site 7 out
of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg301
b:26.4
occ:1.00
|
OD1
|
B:ASP81
|
2.0
|
21.3
|
1.0
|
O
|
B:HOH441
|
2.0
|
28.2
|
1.0
|
O
|
B:HOH576
|
2.1
|
21.8
|
1.0
|
O
|
B:HOH573
|
2.1
|
30.1
|
1.0
|
CG
|
B:ASP81
|
3.0
|
26.2
|
1.0
|
OD2
|
B:ASP81
|
3.3
|
27.3
|
1.0
|
O
|
B:HOH602
|
3.7
|
47.5
|
1.0
|
O
|
A:HOH405
|
4.1
|
31.4
|
1.0
|
O
|
B:HOH664
|
4.3
|
26.3
|
1.0
|
CB
|
B:ASP81
|
4.4
|
13.8
|
1.0
|
O
|
B:HOH584
|
4.4
|
21.8
|
1.0
|
C
|
B:ASP81
|
4.5
|
18.0
|
1.0
|
N
|
B:ASP81
|
4.6
|
17.3
|
1.0
|
NZ
|
A:LYS58
|
4.6
|
48.4
|
1.0
|
N
|
B:ASP82
|
4.7
|
17.6
|
1.0
|
CA
|
B:ASP81
|
4.7
|
17.6
|
1.0
|
O
|
B:ASP81
|
4.7
|
18.9
|
1.0
|
O
|
A:HOH564
|
5.0
|
43.1
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 6z9j
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Magnesium Binding Sites List in 6z9j
Magnesium binding site 8 out
of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg302
b:31.9
occ:1.00
|
O
|
B:HOH566
|
1.9
|
35.5
|
1.0
|
NE2
|
B:HIS78
|
2.1
|
21.4
|
0.4
|
O
|
A:HOH535
|
2.1
|
32.9
|
1.0
|
O
|
A:HOH453
|
2.2
|
28.8
|
1.0
|
O
|
B:HOH581
|
2.2
|
34.2
|
1.0
|
O
|
A:HOH476
|
2.3
|
33.8
|
1.0
|
CE1
|
B:HIS78
|
3.0
|
35.3
|
0.4
|
CD2
|
B:HIS78
|
3.1
|
30.3
|
0.4
|
O
|
A:HOH533
|
3.9
|
25.5
|
1.0
|
OE2
|
A:GLU27
|
4.0
|
48.9
|
1.0
|
ND1
|
B:HIS78
|
4.1
|
17.4
|
0.4
|
CG
|
B:HIS78
|
4.2
|
19.5
|
0.4
|
O
|
B:HOH676
|
4.2
|
40.9
|
1.0
|
OE1
|
A:GLU27
|
4.2
|
27.1
|
1.0
|
O
|
A:HOH404
|
4.3
|
39.8
|
1.0
|
OD2
|
A:ASP26
|
4.5
|
30.3
|
1.0
|
CD
|
A:GLU27
|
4.6
|
36.6
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 6z9j
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Magnesium Binding Sites List in 6z9j
Magnesium binding site 9 out
of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg303
b:52.6
occ:1.00
|
O
|
A:HOH404
|
2.2
|
39.8
|
1.0
|
O
|
B:HOH495
|
2.2
|
48.7
|
1.0
|
O
|
B:HOH411
|
2.3
|
39.5
|
1.0
|
O
|
A:HOH589
|
2.3
|
50.7
|
1.0
|
O
|
A:HOH412
|
2.3
|
44.3
|
1.0
|
O
|
A:HOH660
|
2.5
|
39.5
|
1.0
|
O
|
B:PHE76
|
3.4
|
18.4
|
1.0
|
OD2
|
A:ASP26
|
3.8
|
30.3
|
1.0
|
OD1
|
A:ASP26
|
3.8
|
26.3
|
1.0
|
O
|
B:HOH439
|
3.9
|
23.0
|
1.0
|
O
|
B:HOH485
|
4.0
|
20.8
|
1.0
|
CG
|
A:ASP26
|
4.2
|
41.3
|
1.0
|
NE2
|
B:HIS78
|
4.3
|
30.5
|
0.6
|
O
|
B:HOH581
|
4.4
|
34.2
|
1.0
|
CD2
|
B:HIS78
|
4.5
|
29.1
|
0.6
|
O
|
B:HOH586
|
4.5
|
40.4
|
1.0
|
C
|
B:PHE76
|
4.6
|
17.6
|
1.0
|
OE2
|
B:GLU89
|
4.7
|
24.7
|
1.0
|
O
|
A:HOH549
|
4.7
|
34.0
|
1.0
|
O
|
A:HOH533
|
4.8
|
25.5
|
1.0
|
|
Reference:
S.Voutilainen,
M.Heinonen,
M.Andberg,
E.Jokinen,
H.Maaheimo,
J.Paakkonen,
N.Hakulinen,
J.Rouvinen,
H.Lahdesmaki,
S.Kaski,
J.Rousu,
M.Penttila,
A.Koivula.
Substrate Specificity of 2-Deoxy-D-Ribose 5-Phosphate Aldolase (Dera) Assessed By Different Protein Engineering and Machine Learning Methods. Appl.Microbiol.Biotechnol. V. 104 10515 2020.
ISSN: ESSN 1432-0614
PubMed: 33147349
DOI: 10.1007/S00253-020-10960-X
Page generated: Wed Oct 2 02:13:04 2024
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