Magnesium in PDB 6xn8: Crystal Structure of 2-Hydroxyacyl Coa Lyase (Hacl) From Rhodospirillales Bacterium URHD0017
Protein crystallography data
The structure of Crystal Structure of 2-Hydroxyacyl Coa Lyase (Hacl) From Rhodospirillales Bacterium URHD0017, PDB code: 6xn8
was solved by
M.D.Miller,
W.Xu,
J.L.Olmos Jr.,
A.Chou,
J.M.Clomburg,
R.Gonzalez,
G.N.Philips Jr.,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.47 /
1.95
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
103.94,
64.431,
182.693,
90,
90.88,
90
|
R / Rfree (%)
|
18.6 /
21.2
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of 2-Hydroxyacyl Coa Lyase (Hacl) From Rhodospirillales Bacterium URHD0017
(pdb code 6xn8). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the
Crystal Structure of 2-Hydroxyacyl Coa Lyase (Hacl) From Rhodospirillales Bacterium URHD0017, PDB code: 6xn8:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 6xn8
Go back to
Magnesium Binding Sites List in 6xn8
Magnesium binding site 1 out
of 2 in the Crystal Structure of 2-Hydroxyacyl Coa Lyase (Hacl) From Rhodospirillales Bacterium URHD0017
![](/pictures/MG/pdb/xn/6xn8-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/xn/6xn8-MG-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of 2-Hydroxyacyl Coa Lyase (Hacl) From Rhodospirillales Bacterium URHD0017 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:7.3
occ:1.00
|
O22
|
A:TZD602
|
2.0
|
8.3
|
1.0
|
OD1
|
A:ASP441
|
2.0
|
6.7
|
1.0
|
O13
|
A:TZD602
|
2.1
|
8.2
|
1.0
|
OD1
|
A:ASN468
|
2.1
|
8.9
|
1.0
|
O
|
A:HOH758
|
2.1
|
7.4
|
1.0
|
O
|
A:GLY470
|
2.3
|
9.5
|
1.0
|
CG
|
A:ASN468
|
3.0
|
10.5
|
1.0
|
H
|
A:ASP441
|
3.1
|
9.5
|
1.0
|
HD21
|
A:ASN468
|
3.1
|
15.5
|
1.0
|
P1
|
A:TZD602
|
3.2
|
8.7
|
1.0
|
CG
|
A:ASP441
|
3.2
|
6.7
|
1.0
|
P2
|
A:TZD602
|
3.2
|
8.0
|
1.0
|
H
|
A:GLY470
|
3.2
|
12.0
|
1.0
|
H
|
A:ASN468
|
3.4
|
10.5
|
1.0
|
O11
|
A:TZD602
|
3.4
|
8.1
|
1.0
|
H
|
A:SER442
|
3.4
|
8.9
|
1.0
|
ND2
|
A:ASN468
|
3.5
|
12.8
|
1.0
|
C
|
A:GLY470
|
3.5
|
10.5
|
1.0
|
H
|
A:GLY472
|
3.5
|
14.1
|
1.0
|
OD2
|
A:ASP441
|
3.7
|
7.6
|
1.0
|
N
|
A:ASP441
|
3.8
|
7.8
|
1.0
|
O5G
|
A:TZD602
|
3.8
|
9.4
|
1.0
|
O23
|
A:TZD602
|
3.8
|
12.9
|
1.0
|
N
|
A:GLY470
|
4.0
|
9.9
|
1.0
|
HA3
|
A:GLY440
|
4.1
|
8.9
|
1.0
|
N
|
A:GLY472
|
4.1
|
11.7
|
1.0
|
N
|
A:SER442
|
4.2
|
7.3
|
1.0
|
N
|
A:ASN468
|
4.2
|
8.7
|
1.0
|
O
|
A:GLY472
|
4.2
|
12.2
|
1.0
|
HA
|
A:ILE471
|
4.2
|
11.6
|
1.0
|
HD22
|
A:ASN468
|
4.3
|
15.5
|
1.0
|
CB
|
A:ASN468
|
4.4
|
11.9
|
1.0
|
O
|
A:LEU466
|
4.4
|
10.3
|
1.0
|
CB
|
A:ASP441
|
4.4
|
7.7
|
1.0
|
CA
|
A:GLY470
|
4.4
|
9.3
|
1.0
|
HB2
|
A:SER442
|
4.4
|
9.5
|
1.0
|
O21
|
A:TZD602
|
4.5
|
11.2
|
1.0
|
HB3
|
A:SER442
|
4.5
|
9.5
|
1.0
|
H
|
A:GLY469
|
4.5
|
13.6
|
1.0
|
O12
|
A:TZD602
|
4.5
|
7.8
|
1.0
|
HA2
|
A:GLY440
|
4.5
|
8.9
|
1.0
|
N
|
A:ILE471
|
4.5
|
9.0
|
1.0
|
CA
|
A:ASP441
|
4.5
|
6.1
|
1.0
|
HH
|
A:TYR367
|
4.5
|
15.8
|
1.0
|
HA2
|
A:GLY472
|
4.6
|
14.0
|
1.0
|
CA
|
A:GLY440
|
4.6
|
7.3
|
1.0
|
HA
|
A:ASN467
|
4.6
|
11.2
|
1.0
|
CA
|
A:ASN468
|
4.6
|
11.6
|
1.0
|
C
|
A:GLY472
|
4.6
|
12.7
|
1.0
|
C
|
A:GLY440
|
4.6
|
7.5
|
1.0
|
N
|
A:GLY469
|
4.7
|
11.2
|
1.0
|
HB3
|
A:ASP441
|
4.7
|
9.3
|
1.0
|
CA
|
A:GLY472
|
4.7
|
11.6
|
1.0
|
C
|
A:ASN468
|
4.7
|
11.6
|
1.0
|
CA
|
A:ILE471
|
4.7
|
9.6
|
1.0
|
HB3
|
A:ASN468
|
4.8
|
14.4
|
1.0
|
CB
|
A:SER442
|
4.9
|
7.9
|
1.0
|
C
|
A:ASP441
|
4.9
|
6.6
|
1.0
|
C
|
A:ILE471
|
4.9
|
10.5
|
1.0
|
HA2
|
A:GLY470
|
4.9
|
11.2
|
1.0
|
HG1
|
A:THR391
|
5.0
|
12.7
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 6xn8
Go back to
Magnesium Binding Sites List in 6xn8
Magnesium binding site 2 out
of 2 in the Crystal Structure of 2-Hydroxyacyl Coa Lyase (Hacl) From Rhodospirillales Bacterium URHD0017
![](/pictures/MG/pdb/xn/6xn8-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/xn/6xn8-MG-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of 2-Hydroxyacyl Coa Lyase (Hacl) From Rhodospirillales Bacterium URHD0017 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:11.0
occ:1.00
|
O21
|
B:TZD602
|
1.9
|
11.2
|
1.0
|
O13
|
B:TZD602
|
2.0
|
9.8
|
1.0
|
OD1
|
B:ASN468
|
2.1
|
12.0
|
1.0
|
OD1
|
B:ASP441
|
2.2
|
15.0
|
1.0
|
O
|
B:GLY470
|
2.3
|
10.2
|
1.0
|
O
|
B:HOH722
|
2.4
|
10.8
|
1.0
|
HD21
|
B:ASN468
|
3.0
|
19.1
|
1.0
|
P1
|
B:TZD602
|
3.0
|
10.2
|
1.0
|
CG
|
B:ASN468
|
3.0
|
13.7
|
1.0
|
P2
|
B:TZD602
|
3.1
|
13.8
|
1.0
|
H
|
B:ASP441
|
3.2
|
14.7
|
1.0
|
O11
|
B:TZD602
|
3.2
|
13.5
|
1.0
|
H
|
B:GLY470
|
3.3
|
12.9
|
1.0
|
CG
|
B:ASP441
|
3.3
|
11.8
|
1.0
|
ND2
|
B:ASN468
|
3.4
|
15.8
|
1.0
|
H
|
B:GLY472
|
3.4
|
16.9
|
1.0
|
H
|
B:SER442
|
3.5
|
11.8
|
1.0
|
H
|
B:ASN468
|
3.5
|
14.6
|
1.0
|
C
|
B:GLY470
|
3.5
|
10.8
|
1.0
|
O5G
|
B:TZD602
|
3.7
|
9.7
|
1.0
|
O23
|
B:TZD602
|
3.7
|
15.3
|
1.0
|
OD2
|
B:ASP441
|
3.9
|
11.0
|
1.0
|
N
|
B:ASP441
|
3.9
|
12.1
|
1.0
|
N
|
B:GLY470
|
4.1
|
10.7
|
1.0
|
N
|
B:GLY472
|
4.1
|
14.0
|
1.0
|
HA3
|
B:GLY440
|
4.1
|
12.2
|
1.0
|
HA
|
B:ILE471
|
4.1
|
11.4
|
1.0
|
O
|
B:GLY472
|
4.1
|
10.9
|
1.0
|
HD22
|
B:ASN468
|
4.2
|
19.1
|
1.0
|
N
|
B:SER442
|
4.3
|
9.8
|
1.0
|
O22
|
B:TZD602
|
4.3
|
14.1
|
1.0
|
N
|
B:ASN468
|
4.3
|
12.1
|
1.0
|
CA
|
B:GLY470
|
4.4
|
13.6
|
1.0
|
CB
|
B:ASN468
|
4.4
|
13.5
|
1.0
|
O12
|
B:TZD602
|
4.4
|
10.1
|
1.0
|
O
|
B:LEU466
|
4.4
|
13.4
|
1.0
|
HB3
|
B:SER442
|
4.4
|
12.8
|
1.0
|
HB2
|
B:SER442
|
4.5
|
12.8
|
1.0
|
N
|
B:ILE471
|
4.5
|
7.6
|
1.0
|
HA2
|
B:GLY472
|
4.5
|
14.7
|
1.0
|
CB
|
B:ASP441
|
4.5
|
10.2
|
1.0
|
HA2
|
B:GLY440
|
4.6
|
12.2
|
1.0
|
C
|
B:GLY472
|
4.6
|
14.9
|
1.0
|
H
|
B:GLY469
|
4.6
|
14.7
|
1.0
|
HH
|
B:TYR367
|
4.6
|
21.3
|
1.0
|
CA
|
B:GLY472
|
4.6
|
12.2
|
1.0
|
CA
|
B:GLY440
|
4.7
|
10.1
|
1.0
|
CA
|
B:ILE471
|
4.7
|
9.4
|
1.0
|
CA
|
B:ASP441
|
4.7
|
10.7
|
1.0
|
CA
|
B:ASN468
|
4.7
|
15.4
|
1.0
|
C
|
B:GLY440
|
4.7
|
10.5
|
1.0
|
HA
|
B:ASN467
|
4.8
|
16.4
|
1.0
|
N
|
B:GLY469
|
4.8
|
12.2
|
1.0
|
HB3
|
B:ASN468
|
4.8
|
16.3
|
1.0
|
HG1
|
B:THR391
|
4.8
|
16.9
|
1.0
|
C
|
B:ASN468
|
4.8
|
12.7
|
1.0
|
CB
|
B:SER442
|
4.8
|
10.6
|
1.0
|
C
|
B:ILE471
|
4.9
|
12.0
|
1.0
|
HB3
|
B:ASP441
|
4.9
|
12.3
|
1.0
|
HA2
|
B:GLY470
|
4.9
|
16.4
|
1.0
|
C
|
B:ASP441
|
5.0
|
11.2
|
1.0
|
|
Reference:
A.Chou,
M.D.Miller,
J.L.Olmos Jr.,
W.Xu,
J.M.Clomburg,
R.Gonzalez,
G.N.Philips Jr..
Crystal Structure of 2-Hydroxyacyl Coa Lyase (Hacl) From Rhodospirillales Bacterium URHD0017 To Be Published.
Page generated: Sun Jul 11 15:02:54 2021
|