Magnesium in PDB 3ajx: Crystal Structure of 3-Hexulose-6-Phosphate Synthase
Enzymatic activity of Crystal Structure of 3-Hexulose-6-Phosphate Synthase
All present enzymatic activity of Crystal Structure of 3-Hexulose-6-Phosphate Synthase:
4.1.2.43;
Protein crystallography data
The structure of Crystal Structure of 3-Hexulose-6-Phosphate Synthase, PDB code: 3ajx
was solved by
A.Kita,
I.Orita,
H.Yurimoto,
N.Kato,
Y.Sakai,
K.Miki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.04 /
1.60
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.043,
57.354,
113.623,
90.00,
90.69,
90.00
|
R / Rfree (%)
|
19.4 /
21.5
|
Other elements in 3ajx:
The structure of Crystal Structure of 3-Hexulose-6-Phosphate Synthase also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of 3-Hexulose-6-Phosphate Synthase
(pdb code 3ajx). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of 3-Hexulose-6-Phosphate Synthase, PDB code: 3ajx:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 3ajx
Go back to
Magnesium Binding Sites List in 3ajx
Magnesium binding site 1 out
of 4 in the Crystal Structure of 3-Hexulose-6-Phosphate Synthase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of 3-Hexulose-6-Phosphate Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg9100
b:34.7
occ:1.00
|
O
|
A:HOH5853
|
1.6
|
24.1
|
1.0
|
O
|
A:HOH5854
|
2.0
|
35.9
|
1.0
|
OD2
|
A:ASP1059
|
2.1
|
13.0
|
1.0
|
O
|
A:HOH5856
|
2.1
|
29.6
|
1.0
|
O
|
A:HOH5852
|
2.7
|
30.8
|
1.0
|
OE2
|
A:GLU1030
|
2.7
|
17.4
|
1.0
|
CG
|
A:ASP1059
|
3.2
|
11.5
|
1.0
|
O
|
A:HOH5851
|
3.3
|
16.2
|
1.0
|
CD
|
A:GLU1030
|
3.4
|
15.3
|
1.0
|
OE1
|
A:GLU1030
|
3.5
|
11.7
|
1.0
|
NZ
|
A:LYS1061
|
3.7
|
17.2
|
1.0
|
OE2
|
A:GLU1132
|
3.7
|
22.1
|
1.0
|
CE1
|
A:HIS1134
|
3.7
|
17.1
|
1.0
|
OD1
|
A:ASP1059
|
3.9
|
9.5
|
1.0
|
O
|
A:HOH5855
|
4.0
|
25.7
|
1.0
|
CB
|
A:ASP1059
|
4.3
|
9.7
|
1.0
|
ND1
|
A:HIS1134
|
4.3
|
15.9
|
1.0
|
NE2
|
A:HIS1134
|
4.4
|
15.6
|
1.0
|
OE1
|
A:GLU1132
|
4.5
|
20.7
|
1.0
|
CD
|
A:GLU1132
|
4.5
|
19.7
|
1.0
|
OD2
|
A:ASP1109
|
4.6
|
13.6
|
1.0
|
CG
|
A:GLU1030
|
4.7
|
10.5
|
1.0
|
O
|
A:HOH5859
|
4.8
|
34.0
|
1.0
|
CE2
|
A:PHE1057
|
4.8
|
9.0
|
1.0
|
CE
|
A:LYS1061
|
4.9
|
11.7
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 3ajx
Go back to
Magnesium Binding Sites List in 3ajx
Magnesium binding site 2 out
of 4 in the Crystal Structure of 3-Hexulose-6-Phosphate Synthase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of 3-Hexulose-6-Phosphate Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg9200
b:28.9
occ:1.00
|
O
|
B:HOH5860
|
2.0
|
26.3
|
1.0
|
OD2
|
B:ASP2059
|
2.0
|
17.7
|
1.0
|
OE2
|
B:GLU2030
|
2.0
|
15.8
|
1.0
|
O
|
B:HOH5861
|
2.2
|
31.2
|
1.0
|
O
|
B:HOH5863
|
2.4
|
26.0
|
1.0
|
O
|
B:HOH5862
|
2.4
|
29.4
|
1.0
|
CD
|
B:GLU2030
|
3.2
|
13.6
|
1.0
|
CG
|
B:ASP2059
|
3.2
|
13.1
|
1.0
|
OE1
|
B:GLU2030
|
3.7
|
12.5
|
1.0
|
O
|
B:HOH5865
|
3.7
|
28.9
|
1.0
|
NZ
|
B:LYS2061
|
3.7
|
15.5
|
1.0
|
CB
|
B:ASP2059
|
4.0
|
10.3
|
1.0
|
OD2
|
B:ASP2008
|
4.0
|
25.9
|
1.0
|
OD1
|
B:ASP2059
|
4.2
|
12.1
|
1.0
|
O
|
B:HOH5864
|
4.2
|
31.4
|
1.0
|
CG
|
B:GLU2030
|
4.4
|
12.6
|
1.0
|
CE1
|
B:HIS2134
|
4.4
|
15.9
|
1.0
|
OD1
|
B:ASP2008
|
4.5
|
29.8
|
1.0
|
CA
|
B:GLY2032
|
4.5
|
10.2
|
1.0
|
CB
|
B:ALA2006
|
4.6
|
11.1
|
1.0
|
O
|
A:HOH5866
|
4.7
|
33.0
|
1.0
|
CG
|
B:ASP2008
|
4.7
|
24.5
|
1.0
|
N
|
B:THR2033
|
4.8
|
9.7
|
1.0
|
OG1
|
B:THR2033
|
4.8
|
11.5
|
1.0
|
OE2
|
B:GLU2132
|
4.9
|
25.0
|
1.0
|
NE2
|
B:HIS2134
|
5.0
|
14.1
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 3ajx
Go back to
Magnesium Binding Sites List in 3ajx
Magnesium binding site 3 out
of 4 in the Crystal Structure of 3-Hexulose-6-Phosphate Synthase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of 3-Hexulose-6-Phosphate Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg9300
b:42.3
occ:1.00
|
OD2
|
C:ASP3059
|
2.1
|
16.0
|
1.0
|
O
|
C:HOH5871
|
2.1
|
24.0
|
1.0
|
O
|
C:HOH5874
|
2.3
|
28.5
|
1.0
|
O
|
C:HOH5872
|
2.6
|
28.7
|
1.0
|
OE2
|
C:GLU3030
|
2.6
|
18.0
|
1.0
|
O
|
C:HOH5870
|
2.8
|
29.0
|
1.0
|
CG
|
C:ASP3059
|
3.2
|
12.6
|
1.0
|
CD
|
C:GLU3030
|
3.3
|
14.2
|
1.0
|
OE1
|
C:GLU3030
|
3.4
|
11.2
|
1.0
|
OE2
|
C:GLU3132
|
3.7
|
24.8
|
1.0
|
O
|
C:HOH5869
|
3.7
|
19.4
|
1.0
|
NZ
|
C:LYS3061
|
3.7
|
16.4
|
1.0
|
CE1
|
C:HIS3134
|
3.8
|
12.9
|
1.0
|
OD1
|
C:ASP3059
|
3.9
|
12.2
|
1.0
|
O
|
C:HOH5873
|
3.9
|
26.0
|
1.0
|
CB
|
C:ASP3059
|
4.2
|
9.6
|
1.0
|
ND1
|
C:HIS3134
|
4.4
|
13.3
|
1.0
|
NE2
|
C:HIS3134
|
4.5
|
13.2
|
1.0
|
OE1
|
C:GLU3132
|
4.5
|
25.0
|
1.0
|
CD
|
C:GLU3132
|
4.5
|
21.2
|
1.0
|
OD2
|
C:ASP3109
|
4.6
|
14.1
|
1.0
|
CG
|
C:GLU3030
|
4.6
|
11.1
|
1.0
|
CE1
|
C:PHE3057
|
4.7
|
8.1
|
1.0
|
CE
|
C:LYS3061
|
5.0
|
11.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 3ajx
Go back to
Magnesium Binding Sites List in 3ajx
Magnesium binding site 4 out
of 4 in the Crystal Structure of 3-Hexulose-6-Phosphate Synthase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of 3-Hexulose-6-Phosphate Synthase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg9400
b:35.4
occ:1.00
|
O
|
D:HOH5878
|
1.9
|
29.7
|
1.0
|
OE2
|
D:GLU4030
|
2.0
|
15.5
|
1.0
|
OD2
|
D:ASP4059
|
2.0
|
18.2
|
1.0
|
O
|
D:HOH5879
|
2.3
|
30.8
|
1.0
|
O
|
D:HOH5880
|
2.4
|
33.6
|
1.0
|
O
|
D:HOH5877
|
2.5
|
25.6
|
1.0
|
CD
|
D:GLU4030
|
3.0
|
13.9
|
1.0
|
O
|
D:HOH5882
|
3.2
|
36.6
|
1.0
|
CG
|
D:ASP4059
|
3.2
|
13.3
|
1.0
|
OE1
|
D:GLU4030
|
3.4
|
12.0
|
1.0
|
NZ
|
D:LYS4061
|
3.8
|
15.3
|
1.0
|
CB
|
D:ASP4059
|
4.0
|
10.3
|
1.0
|
OD1
|
D:ASP4059
|
4.1
|
12.1
|
1.0
|
O
|
D:HOH5881
|
4.2
|
37.4
|
1.0
|
CG
|
D:GLU4030
|
4.3
|
12.6
|
1.0
|
CE1
|
D:HIS4134
|
4.4
|
17.9
|
1.0
|
O
|
C:HOH5883
|
4.5
|
32.1
|
1.0
|
OE2
|
D:GLU4132
|
4.6
|
23.2
|
1.0
|
CB
|
D:ALA4006
|
4.6
|
8.4
|
1.0
|
OD2
|
D:ASP4008
|
4.7
|
25.6
|
1.0
|
OD1
|
D:ASP4008
|
4.8
|
31.0
|
1.0
|
CA
|
D:GLY4032
|
4.8
|
9.0
|
1.0
|
NE2
|
D:HIS4134
|
4.9
|
15.7
|
1.0
|
|
Reference:
I.Orita,
A.Kita,
H.Yurimoto,
N.Kato,
Y.Sakai,
K.Miki.
Crystal Structure of 3-Hexulose-6-Phosphate Synthase, A Member of the Orotidine 5'-Monophosphate Decarboxylase Suprafamily Proteins V. 78 3488 2010.
ISSN: ISSN 0887-3585
PubMed: 20938979
DOI: 10.1002/PROT.22860
Page generated: Wed Aug 14 08:37:00 2024
|