Magnesium in PDB 6vmf: Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine
Protein crystallography data
The structure of Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine, PDB code: 6vmf
was solved by
E.T.Yukl,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.42 /
2.24
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
107.857,
92.985,
187.048,
90.00,
95.06,
90.00
|
R / Rfree (%)
|
20.2 /
25
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine
(pdb code 6vmf). 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 the Y766F Mutant of Goxa Soaked with Glycine, PDB code: 6vmf:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6vmf
Go back to
Magnesium Binding Sites List in 6vmf
Magnesium binding site 1 out
of 4 in the Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine
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 the Y766F Mutant of Goxa Soaked with Glycine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg901
b:38.9
occ:1.00
|
O
|
A:ALA699
|
2.2
|
30.5
|
1.0
|
O
|
A:ILE365
|
2.3
|
24.4
|
1.0
|
O
|
A:ALA362
|
2.3
|
21.0
|
1.0
|
O
|
A:HOH1033
|
2.5
|
36.7
|
1.0
|
OD1
|
A:ASN700
|
2.7
|
32.8
|
1.0
|
OD1
|
A:ASP360
|
2.9
|
36.8
|
1.0
|
C
|
A:ALA699
|
3.1
|
21.5
|
1.0
|
C
|
A:ALA362
|
3.3
|
17.9
|
1.0
|
C
|
A:ILE365
|
3.4
|
21.5
|
1.0
|
OD2
|
A:ASP360
|
3.6
|
38.0
|
1.0
|
CG
|
A:ASP360
|
3.6
|
31.2
|
1.0
|
CG
|
A:ASN700
|
3.7
|
26.1
|
1.0
|
N
|
A:ASN700
|
3.8
|
30.4
|
1.0
|
CA
|
A:ASN700
|
3.8
|
21.6
|
1.0
|
CB
|
A:ALA362
|
4.1
|
16.3
|
1.0
|
CA
|
A:ALA362
|
4.1
|
19.6
|
1.0
|
N
|
A:ILE365
|
4.1
|
22.1
|
1.0
|
N
|
A:PRO363
|
4.2
|
17.1
|
1.0
|
CA
|
A:ALA699
|
4.2
|
22.0
|
1.0
|
CB
|
A:ALA699
|
4.2
|
34.2
|
1.0
|
CA
|
A:ILE365
|
4.2
|
15.9
|
1.0
|
CA
|
A:PRO363
|
4.2
|
25.3
|
1.0
|
CB
|
A:ASN700
|
4.3
|
32.0
|
1.0
|
CB
|
A:ILE365
|
4.3
|
17.2
|
1.0
|
C
|
A:PRO363
|
4.4
|
27.4
|
1.0
|
N
|
A:ALA362
|
4.4
|
33.0
|
1.0
|
N
|
A:GLU366
|
4.5
|
27.0
|
1.0
|
O
|
A:PRO363
|
4.5
|
34.2
|
1.0
|
CD
|
A:PRO367
|
4.6
|
23.3
|
1.0
|
ND2
|
A:ASN700
|
4.7
|
31.0
|
1.0
|
CA
|
A:GLU366
|
4.7
|
21.3
|
1.0
|
N
|
A:GLN364
|
4.9
|
25.9
|
1.0
|
O
|
A:ALA576
|
5.0
|
45.1
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6vmf
Go back to
Magnesium Binding Sites List in 6vmf
Magnesium binding site 2 out
of 4 in the Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine
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 the Y766F Mutant of Goxa Soaked with Glycine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg901
b:49.4
occ:1.00
|
O
|
B:ALA699
|
2.3
|
38.4
|
1.0
|
OD1
|
B:ASN700
|
2.4
|
56.2
|
1.0
|
O
|
B:ILE365
|
2.5
|
36.7
|
1.0
|
O
|
B:ALA362
|
2.5
|
57.0
|
1.0
|
O
|
B:HOH1006
|
2.6
|
38.6
|
1.0
|
OD1
|
B:ASP360
|
2.6
|
43.3
|
1.0
|
C
|
B:ALA699
|
3.0
|
39.4
|
1.0
|
C
|
B:ALA362
|
3.3
|
45.9
|
1.0
|
CG
|
B:ASN700
|
3.5
|
53.5
|
1.0
|
CG
|
B:ASP360
|
3.5
|
51.9
|
1.0
|
CA
|
B:ASN700
|
3.5
|
51.9
|
1.0
|
N
|
B:ASN700
|
3.6
|
45.6
|
1.0
|
OD2
|
B:ASP360
|
3.6
|
51.7
|
1.0
|
C
|
B:ILE365
|
3.6
|
43.4
|
1.0
|
CA
|
B:ALA699
|
4.0
|
37.1
|
1.0
|
CB
|
B:ALA699
|
4.1
|
43.5
|
1.0
|
CA
|
B:ALA362
|
4.1
|
42.0
|
1.0
|
CB
|
B:ALA362
|
4.1
|
47.0
|
1.0
|
CB
|
B:ASN700
|
4.1
|
54.4
|
1.0
|
N
|
B:ALA362
|
4.2
|
37.2
|
1.0
|
N
|
B:PRO363
|
4.2
|
38.5
|
1.0
|
N
|
B:ILE365
|
4.3
|
41.3
|
1.0
|
CA
|
B:PRO363
|
4.3
|
48.1
|
1.0
|
CA
|
B:ILE365
|
4.3
|
35.9
|
1.0
|
CB
|
B:ILE365
|
4.4
|
32.1
|
1.0
|
C
|
B:PRO363
|
4.5
|
41.0
|
1.0
|
ND2
|
B:ASN700
|
4.5
|
49.5
|
1.0
|
O
|
B:PRO363
|
4.7
|
44.8
|
1.0
|
N
|
B:GLU366
|
4.7
|
50.1
|
1.0
|
C
|
B:ASN700
|
4.8
|
44.9
|
1.0
|
CD
|
B:PRO367
|
4.9
|
37.4
|
1.0
|
CA
|
B:GLU366
|
4.9
|
52.1
|
1.0
|
CB
|
B:ASP360
|
4.9
|
51.0
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6vmf
Go back to
Magnesium Binding Sites List in 6vmf
Magnesium binding site 3 out
of 4 in the Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine
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 the Y766F Mutant of Goxa Soaked with Glycine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg901
b:40.9
occ:1.00
|
O
|
C:ILE365
|
2.1
|
25.6
|
1.0
|
O
|
C:ALA699
|
2.3
|
34.0
|
1.0
|
O
|
C:ALA362
|
2.3
|
34.1
|
1.0
|
O
|
C:HOH1078
|
2.6
|
37.3
|
1.0
|
OD1
|
C:ASN700
|
2.8
|
39.8
|
1.0
|
OD1
|
C:ASP360
|
2.9
|
41.5
|
1.0
|
C
|
C:ILE365
|
3.2
|
23.8
|
1.0
|
C
|
C:ALA362
|
3.2
|
33.8
|
1.0
|
C
|
C:ALA699
|
3.3
|
35.6
|
1.0
|
OD2
|
C:ASP360
|
3.6
|
54.0
|
1.0
|
CG
|
C:ASP360
|
3.7
|
35.9
|
1.0
|
N
|
C:ILE365
|
3.8
|
33.9
|
1.0
|
CA
|
C:ILE365
|
3.8
|
22.5
|
1.0
|
CG
|
C:ASN700
|
3.9
|
33.0
|
1.0
|
CB
|
C:ILE365
|
3.9
|
26.1
|
1.0
|
CB
|
C:ALA362
|
4.0
|
29.5
|
1.0
|
N
|
C:ASN700
|
4.0
|
37.4
|
1.0
|
CA
|
C:ASN700
|
4.0
|
35.9
|
1.0
|
CA
|
C:ALA362
|
4.1
|
31.9
|
1.0
|
N
|
C:PRO363
|
4.1
|
32.0
|
1.0
|
CA
|
C:PRO363
|
4.1
|
36.3
|
1.0
|
C
|
C:PRO363
|
4.2
|
38.3
|
1.0
|
CB
|
C:ALA699
|
4.2
|
44.7
|
1.0
|
CA
|
C:ALA699
|
4.3
|
36.0
|
1.0
|
N
|
C:GLU366
|
4.3
|
27.4
|
1.0
|
N
|
C:ALA362
|
4.4
|
44.9
|
1.0
|
O
|
C:PRO363
|
4.4
|
31.0
|
1.0
|
CB
|
C:ASN700
|
4.6
|
38.2
|
1.0
|
CA
|
C:GLU366
|
4.6
|
24.9
|
1.0
|
N
|
C:GLN364
|
4.7
|
30.8
|
1.0
|
CG2
|
C:ILE365
|
4.7
|
30.6
|
1.0
|
CD
|
C:PRO367
|
4.7
|
27.0
|
1.0
|
ND2
|
C:ASN700
|
4.9
|
34.9
|
1.0
|
C
|
C:GLN364
|
4.9
|
41.3
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6vmf
Go back to
Magnesium Binding Sites List in 6vmf
Magnesium binding site 4 out
of 4 in the Crystal Structure of the Y766F Mutant of Goxa Soaked with Glycine
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 the Y766F Mutant of Goxa Soaked with Glycine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg901
b:45.0
occ:1.00
|
O
|
D:ILE365
|
2.2
|
26.3
|
1.0
|
O
|
D:HOH1166
|
2.3
|
40.5
|
1.0
|
O
|
D:ALA362
|
2.4
|
43.5
|
1.0
|
O
|
D:ALA699
|
2.4
|
37.5
|
1.0
|
OD1
|
D:ASN700
|
2.5
|
43.3
|
1.0
|
OD1
|
D:ASP360
|
2.8
|
34.7
|
1.0
|
C
|
D:ALA362
|
3.2
|
37.1
|
1.0
|
C
|
D:ILE365
|
3.3
|
33.1
|
1.0
|
C
|
D:ALA699
|
3.4
|
31.2
|
1.0
|
OD2
|
D:ASP360
|
3.4
|
42.0
|
1.0
|
CG
|
D:ASP360
|
3.5
|
36.5
|
1.0
|
CG
|
D:ASN700
|
3.6
|
31.8
|
1.0
|
N
|
D:ILE365
|
3.9
|
38.0
|
1.0
|
CA
|
D:ASN700
|
3.9
|
35.8
|
1.0
|
CA
|
D:ILE365
|
4.0
|
30.8
|
1.0
|
N
|
D:PRO363
|
4.0
|
33.2
|
1.0
|
CA
|
D:PRO363
|
4.0
|
37.1
|
1.0
|
N
|
D:ASN700
|
4.0
|
34.3
|
1.0
|
CA
|
D:ALA362
|
4.0
|
43.3
|
1.0
|
CB
|
D:ALA362
|
4.1
|
30.1
|
1.0
|
CB
|
D:ILE365
|
4.1
|
33.2
|
1.0
|
C
|
D:PRO363
|
4.2
|
40.7
|
1.0
|
N
|
D:ALA362
|
4.2
|
54.5
|
1.0
|
CB
|
D:ALA699
|
4.4
|
38.5
|
1.0
|
O
|
D:PRO363
|
4.4
|
40.5
|
1.0
|
CA
|
D:ALA699
|
4.4
|
27.7
|
1.0
|
CB
|
D:ASN700
|
4.4
|
37.6
|
1.0
|
N
|
D:GLU366
|
4.4
|
35.0
|
1.0
|
ND2
|
D:ASN700
|
4.6
|
37.1
|
1.0
|
CA
|
D:GLU366
|
4.7
|
28.5
|
1.0
|
N
|
D:GLN364
|
4.8
|
34.4
|
1.0
|
CD
|
D:PRO367
|
4.8
|
35.1
|
1.0
|
CG2
|
D:ILE365
|
4.8
|
25.6
|
1.0
|
CB
|
D:ASP360
|
5.0
|
38.9
|
1.0
|
|
Reference:
K.J.Mamounis,
E.T.Yukl,
V.L.Davidson.
Roles of Active Site Residues in Catalysis, Substrate Binding, Cooperativity and the Reaction Mechanism of the Quinoprotein Glycine Oxidase J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
Page generated: Tue Oct 1 22:07:56 2024
|