Magnesium in PDB 6eer: Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea
Protein crystallography data
The structure of Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea, PDB code: 6eer
was solved by
E.T.Yukl,
D.Avalos,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.30 /
1.82
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
110.242,
93.464,
187.903,
90.00,
95.02,
90.00
|
R / Rfree (%)
|
17.6 /
21.3
|
Other elements in 6eer:
The structure of Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea
(pdb code 6eer). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea, PDB code: 6eer:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6eer
Go back to
Magnesium Binding Sites List in 6eer
Magnesium binding site 1 out
of 4 in the Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg901
b:15.5
occ:1.00
|
O
|
A:ILE365
|
2.2
|
14.3
|
1.0
|
O
|
A:ALA699
|
2.3
|
16.0
|
1.0
|
O
|
A:ALA362
|
2.3
|
11.9
|
1.0
|
OD1
|
A:ASN700
|
2.4
|
17.0
|
1.0
|
O
|
A:HOH1131
|
2.5
|
22.3
|
1.0
|
OD1
|
A:ASP360
|
2.8
|
17.4
|
1.0
|
C
|
A:ALA699
|
3.2
|
15.8
|
1.0
|
C
|
A:ALA362
|
3.2
|
15.5
|
1.0
|
C
|
A:ILE365
|
3.4
|
13.6
|
1.0
|
OD2
|
A:ASP360
|
3.5
|
21.7
|
1.0
|
CG
|
A:ASN700
|
3.5
|
19.4
|
1.0
|
CG
|
A:ASP360
|
3.5
|
19.4
|
1.0
|
CA
|
A:ASN700
|
3.8
|
17.0
|
1.0
|
N
|
A:ASN700
|
3.9
|
13.2
|
1.0
|
CA
|
A:ALA362
|
4.1
|
11.8
|
1.0
|
N
|
A:PRO363
|
4.1
|
11.9
|
1.0
|
N
|
A:ILE365
|
4.1
|
14.0
|
1.0
|
CB
|
A:ALA362
|
4.1
|
13.9
|
1.0
|
CA
|
A:ILE365
|
4.1
|
14.6
|
1.0
|
CA
|
A:PRO363
|
4.1
|
16.0
|
1.0
|
O
|
A:HOH1515
|
4.2
|
26.8
|
1.0
|
CB
|
A:ALA699
|
4.2
|
12.3
|
1.0
|
CA
|
A:ALA699
|
4.2
|
11.6
|
1.0
|
CB
|
A:ILE365
|
4.2
|
14.1
|
1.0
|
CB
|
A:ASN700
|
4.2
|
13.3
|
1.0
|
N
|
A:ALA362
|
4.3
|
13.2
|
1.0
|
C
|
A:PRO363
|
4.3
|
16.5
|
1.0
|
N
|
A:GLU366
|
4.4
|
13.2
|
1.0
|
ND2
|
A:ASN700
|
4.5
|
19.1
|
1.0
|
O
|
A:PRO363
|
4.5
|
13.1
|
1.0
|
CD
|
A:PRO367
|
4.7
|
12.0
|
1.0
|
CA
|
A:GLU366
|
4.8
|
13.2
|
1.0
|
N
|
A:GLN364
|
4.9
|
11.9
|
1.0
|
CB
|
A:ASP360
|
4.9
|
17.4
|
1.0
|
O
|
A:ALA576
|
5.0
|
23.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6eer
Go back to
Magnesium Binding Sites List in 6eer
Magnesium binding site 2 out
of 4 in the Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg901
b:24.9
occ:1.00
|
O
|
B:ILE365
|
2.3
|
19.2
|
1.0
|
O
|
B:ALA362
|
2.4
|
18.0
|
1.0
|
O
|
B:HOH1039
|
2.4
|
18.7
|
1.0
|
O
|
B:ALA699
|
2.5
|
20.0
|
1.0
|
OD1
|
B:ASN700
|
2.5
|
21.0
|
1.0
|
OD1
|
B:ASP360
|
2.7
|
20.1
|
1.0
|
OD2
|
B:ASP360
|
3.3
|
25.5
|
1.0
|
C
|
B:ALA362
|
3.3
|
20.2
|
1.0
|
C
|
B:ALA699
|
3.3
|
18.5
|
1.0
|
CG
|
B:ASP360
|
3.4
|
20.6
|
1.0
|
C
|
B:ILE365
|
3.4
|
19.3
|
1.0
|
CG
|
B:ASN700
|
3.5
|
25.9
|
1.0
|
CA
|
B:ASN700
|
3.8
|
17.3
|
1.0
|
N
|
B:ASN700
|
3.9
|
20.6
|
1.0
|
N
|
B:PRO363
|
4.1
|
19.6
|
1.0
|
CA
|
B:ALA362
|
4.1
|
18.6
|
1.0
|
N
|
B:ILE365
|
4.1
|
16.9
|
1.0
|
CA
|
B:PRO363
|
4.1
|
17.8
|
1.0
|
CB
|
B:ALA362
|
4.1
|
16.6
|
1.0
|
CA
|
B:ILE365
|
4.1
|
16.5
|
1.0
|
O
|
B:HOH1361
|
4.1
|
29.6
|
1.0
|
CB
|
B:ALA699
|
4.2
|
15.2
|
1.0
|
CB
|
B:ILE365
|
4.3
|
15.9
|
1.0
|
CA
|
B:ALA699
|
4.3
|
16.7
|
1.0
|
N
|
B:ALA362
|
4.3
|
17.4
|
1.0
|
CB
|
B:ASN700
|
4.3
|
18.1
|
1.0
|
C
|
B:PRO363
|
4.3
|
20.9
|
1.0
|
ND2
|
B:ASN700
|
4.5
|
24.9
|
1.0
|
N
|
B:GLU366
|
4.5
|
20.9
|
1.0
|
O
|
B:PRO363
|
4.5
|
27.1
|
1.0
|
CA
|
B:GLU366
|
4.8
|
19.9
|
1.0
|
CD
|
B:PRO367
|
4.9
|
20.2
|
1.0
|
N
|
B:GLN364
|
4.9
|
17.8
|
1.0
|
CB
|
B:ASP360
|
4.9
|
20.3
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6eer
Go back to
Magnesium Binding Sites List in 6eer
Magnesium binding site 3 out
of 4 in the Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg901
b:18.5
occ:1.00
|
O
|
C:ALA699
|
2.3
|
15.2
|
1.0
|
O
|
C:ILE365
|
2.3
|
11.8
|
1.0
|
O
|
C:ALA362
|
2.3
|
12.6
|
1.0
|
OD1
|
C:ASN700
|
2.4
|
16.9
|
1.0
|
O
|
C:HOH1103
|
2.5
|
19.6
|
1.0
|
OD1
|
C:ASP360
|
2.8
|
16.6
|
1.0
|
C
|
C:ALA699
|
3.2
|
17.4
|
1.0
|
C
|
C:ALA362
|
3.3
|
16.9
|
1.0
|
OD2
|
C:ASP360
|
3.4
|
21.1
|
1.0
|
C
|
C:ILE365
|
3.4
|
11.8
|
1.0
|
CG
|
C:ASP360
|
3.5
|
19.1
|
1.0
|
CG
|
C:ASN700
|
3.5
|
18.5
|
1.0
|
CA
|
C:ASN700
|
3.8
|
16.3
|
1.0
|
N
|
C:ASN700
|
3.9
|
11.9
|
1.0
|
CB
|
C:ALA699
|
4.1
|
13.0
|
1.0
|
CA
|
C:ALA362
|
4.1
|
13.8
|
1.0
|
N
|
C:ILE365
|
4.1
|
14.7
|
1.0
|
N
|
C:PRO363
|
4.1
|
13.8
|
1.0
|
CA
|
C:PRO363
|
4.1
|
15.8
|
1.0
|
CB
|
C:ALA362
|
4.1
|
13.4
|
1.0
|
CA
|
C:ILE365
|
4.2
|
15.9
|
1.0
|
CA
|
C:ALA699
|
4.2
|
14.0
|
1.0
|
O
|
C:HOH1380
|
4.2
|
26.0
|
1.0
|
CB
|
C:ASN700
|
4.2
|
13.9
|
1.0
|
N
|
C:ALA362
|
4.3
|
13.6
|
1.0
|
C
|
C:PRO363
|
4.3
|
17.0
|
1.0
|
CB
|
C:ILE365
|
4.3
|
11.6
|
1.0
|
ND2
|
C:ASN700
|
4.4
|
17.1
|
1.0
|
N
|
C:GLU366
|
4.5
|
12.0
|
1.0
|
O
|
C:PRO363
|
4.5
|
14.0
|
1.0
|
CA
|
C:GLU366
|
4.7
|
12.5
|
1.0
|
CD
|
C:PRO367
|
4.8
|
11.8
|
1.0
|
N
|
C:GLN364
|
4.9
|
16.1
|
1.0
|
CB
|
C:ASP360
|
4.9
|
16.5
|
1.0
|
O
|
C:ALA576
|
5.0
|
21.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6eer
Go back to
Magnesium Binding Sites List in 6eer
Magnesium binding site 4 out
of 4 in the Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Glycine-Bound Goxa From Pseudoalteromonas Luteoviolacea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg901
b:23.6
occ:1.00
|
O
|
D:ALA699
|
2.2
|
19.6
|
1.0
|
O
|
D:ILE365
|
2.3
|
19.6
|
1.0
|
O
|
D:ALA362
|
2.3
|
20.2
|
1.0
|
OD1
|
D:ASN700
|
2.4
|
17.7
|
1.0
|
O
|
D:HOH1262
|
2.5
|
23.7
|
1.0
|
OD1
|
D:ASP360
|
2.8
|
20.9
|
1.0
|
C
|
D:ALA699
|
3.1
|
17.8
|
1.0
|
C
|
D:ALA362
|
3.2
|
24.4
|
1.0
|
C
|
D:ILE365
|
3.5
|
16.5
|
1.0
|
CG
|
D:ASN700
|
3.5
|
21.4
|
1.0
|
CG
|
D:ASP360
|
3.6
|
24.0
|
1.0
|
OD2
|
D:ASP360
|
3.6
|
24.9
|
1.0
|
CA
|
D:ASN700
|
3.8
|
23.9
|
1.0
|
N
|
D:ASN700
|
3.8
|
18.4
|
1.0
|
CA
|
D:ALA362
|
4.0
|
16.0
|
1.0
|
N
|
D:PRO363
|
4.0
|
21.3
|
1.0
|
CB
|
D:ALA362
|
4.1
|
17.4
|
1.0
|
CA
|
D:PRO363
|
4.1
|
26.7
|
1.0
|
CB
|
D:ALA699
|
4.1
|
15.1
|
1.0
|
CA
|
D:ALA699
|
4.1
|
14.8
|
1.0
|
N
|
D:ILE365
|
4.1
|
16.8
|
1.0
|
CA
|
D:ILE365
|
4.2
|
16.4
|
1.0
|
N
|
D:ALA362
|
4.2
|
17.6
|
1.0
|
CB
|
D:ILE365
|
4.2
|
15.9
|
1.0
|
CB
|
D:ASN700
|
4.2
|
20.6
|
1.0
|
O
|
D:HOH1320
|
4.3
|
32.8
|
1.0
|
C
|
D:PRO363
|
4.4
|
26.7
|
1.0
|
ND2
|
D:ASN700
|
4.5
|
22.4
|
1.0
|
N
|
D:GLU366
|
4.5
|
16.7
|
1.0
|
O
|
D:PRO363
|
4.6
|
29.9
|
1.0
|
CA
|
D:GLU366
|
4.8
|
16.8
|
1.0
|
CD
|
D:PRO367
|
4.8
|
18.1
|
1.0
|
N
|
D:GLN364
|
4.9
|
17.6
|
1.0
|
CG2
|
D:ILE365
|
5.0
|
17.9
|
1.0
|
|
Reference:
D.Avalos,
S.Sabuncu,
K.J.Mamounis,
V.L.Davidson,
P.Moenne-Loccoz,
E.T.Yukl.
Structural and Spectroscopic Characterization of A Product Schiff Base Intermediate in the Reaction of the Quinoprotein Glycine Oxidase, Goxa. Biochemistry V. 58 706 2019.
ISSN: ISSN 1520-4995
PubMed: 30605596
DOI: 10.1021/ACS.BIOCHEM.8B01145
Page generated: Mon Sep 30 23:55:41 2024
|