Magnesium in PDB 8yzy: Stc Syda Mutant - W297Y
Protein crystallography data
The structure of Stc Syda Mutant - W297Y, PDB code: 8yzy
was solved by
A.Fan,
S.Fan,
M.Wu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
27.30 /
1.73
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.892,
127.635,
89.143,
90,
93.47,
90
|
|
R / Rfree (%)
|
15.5 /
19.2
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Stc Syda Mutant - W297Y
(pdb code 8yzy). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Stc Syda Mutant - W297Y, PDB code: 8yzy:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 8yzy
Go back to
Magnesium Binding Sites List in 8yzy
Magnesium binding site 1 out
of 8 in the Stc Syda Mutant - W297Y
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Stc Syda Mutant - W297Y within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:22.5
occ:1.00
|
O5
|
A:POP401
|
2.1
|
19.1
|
1.0
|
|
O1
|
A:POP401
|
2.2
|
21.6
|
1.0
|
|
OD2
|
A:ASP106
|
2.4
|
31.3
|
1.0
|
|
P2
|
A:POP401
|
3.2
|
18.3
|
1.0
|
|
P1
|
A:POP401
|
3.4
|
16.2
|
1.0
|
|
CG
|
A:ASP106
|
3.4
|
46.5
|
1.0
|
|
O
|
A:POP401
|
3.5
|
15.2
|
1.0
|
|
OD1
|
A:ASP106
|
3.7
|
38.1
|
1.0
|
|
O4
|
A:POP401
|
3.8
|
18.1
|
1.0
|
|
NZ
|
A:LYS239
|
3.8
|
20.0
|
1.0
|
|
NH2
|
A:ARG311
|
4.1
|
29.8
|
1.0
|
|
O2
|
A:POP401
|
4.3
|
15.3
|
1.0
|
|
OE2
|
A:GLU240
|
4.3
|
18.9
|
1.0
|
|
O
|
A:HOH510
|
4.4
|
33.5
|
1.0
|
|
O6
|
A:POP401
|
4.5
|
18.7
|
1.0
|
|
O
|
A:HOH617
|
4.5
|
31.0
|
1.0
|
|
O3
|
A:POP401
|
4.5
|
17.3
|
1.0
|
|
OE1
|
A:GLU246
|
4.6
|
39.2
|
1.0
|
|
O
|
A:HOH556
|
4.6
|
28.4
|
1.0
|
|
O
|
A:HOH551
|
4.6
|
21.5
|
1.0
|
|
CB
|
A:ASP106
|
4.8
|
30.2
|
1.0
|
|
MG
|
A:MG403
|
4.9
|
16.3
|
1.0
|
|
OE2
|
A:GLU246
|
4.9
|
43.3
|
1.0
|
|
CE
|
A:LYS239
|
5.0
|
18.2
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 8yzy
Go back to
Magnesium Binding Sites List in 8yzy
Magnesium binding site 2 out
of 8 in the Stc Syda Mutant - W297Y
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Stc Syda Mutant - W297Y within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:16.3
occ:1.00
|
O4
|
A:POP401
|
2.0
|
18.1
|
1.0
|
|
O2
|
A:POP401
|
2.1
|
15.3
|
1.0
|
|
OD1
|
A:ASN232
|
2.1
|
16.1
|
1.0
|
|
OE2
|
A:GLU240
|
2.2
|
18.9
|
1.0
|
|
OG
|
A:SER236
|
2.3
|
15.2
|
1.0
|
|
CG
|
A:ASN232
|
3.1
|
16.6
|
1.0
|
|
CD
|
A:GLU240
|
3.1
|
25.0
|
1.0
|
|
P1
|
A:POP401
|
3.2
|
16.2
|
1.0
|
|
P2
|
A:POP401
|
3.2
|
18.3
|
1.0
|
|
CB
|
A:SER236
|
3.2
|
15.3
|
1.0
|
|
O
|
A:POP401
|
3.4
|
15.2
|
1.0
|
|
ND2
|
A:ASN232
|
3.5
|
14.2
|
1.0
|
|
OE1
|
A:GLU240
|
3.5
|
19.7
|
1.0
|
|
O
|
A:HOH551
|
3.9
|
21.5
|
1.0
|
|
O1
|
A:POP401
|
3.9
|
21.6
|
1.0
|
|
O
|
A:ASN232
|
4.0
|
14.9
|
1.0
|
|
NH2
|
A:ARG189
|
4.1
|
18.2
|
1.0
|
|
O6
|
A:POP401
|
4.2
|
18.7
|
1.0
|
|
O5
|
A:POP401
|
4.2
|
19.1
|
1.0
|
|
C
|
A:ASN232
|
4.3
|
16.5
|
1.0
|
|
CG
|
A:GLU240
|
4.4
|
22.6
|
1.0
|
|
O3
|
A:POP401
|
4.4
|
17.3
|
1.0
|
|
CB
|
A:ASN232
|
4.4
|
16.8
|
1.0
|
|
OD1
|
A:ASP233
|
4.6
|
19.1
|
1.0
|
|
CA
|
A:SER236
|
4.6
|
19.8
|
1.0
|
|
N
|
A:ASP233
|
4.7
|
14.3
|
1.0
|
|
CA
|
A:ASP233
|
4.8
|
16.5
|
1.0
|
|
MG
|
A:MG402
|
4.9
|
22.5
|
1.0
|
|
CZ
|
A:ARG189
|
4.9
|
21.6
|
1.0
|
|
CE
|
A:LYS239
|
4.9
|
18.2
|
1.0
|
|
O
|
A:HOH576
|
4.9
|
18.1
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 8yzy
Go back to
Magnesium Binding Sites List in 8yzy
Magnesium binding site 3 out
of 8 in the Stc Syda Mutant - W297Y
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Stc Syda Mutant - W297Y within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:17.3
occ:1.00
|
O2
|
B:POP401
|
2.0
|
18.2
|
1.0
|
|
O4
|
B:POP401
|
2.1
|
17.6
|
1.0
|
|
OE2
|
B:GLU240
|
2.1
|
17.3
|
1.0
|
|
OD1
|
B:ASN232
|
2.2
|
17.6
|
1.0
|
|
OG
|
B:SER236
|
2.2
|
14.6
|
1.0
|
|
CD
|
B:GLU240
|
3.1
|
20.4
|
1.0
|
|
CG
|
B:ASN232
|
3.2
|
14.7
|
1.0
|
|
CB
|
B:SER236
|
3.2
|
15.4
|
1.0
|
|
P1
|
B:POP401
|
3.2
|
20.0
|
1.0
|
|
P2
|
B:POP401
|
3.2
|
18.7
|
1.0
|
|
O
|
B:POP401
|
3.4
|
19.0
|
1.0
|
|
ND2
|
B:ASN232
|
3.5
|
14.7
|
1.0
|
|
OE1
|
B:GLU240
|
3.5
|
21.5
|
1.0
|
|
O6
|
B:POP401
|
3.9
|
18.5
|
1.0
|
|
O
|
B:ASN232
|
4.0
|
17.1
|
1.0
|
|
O
|
B:HOH605
|
4.0
|
22.8
|
1.0
|
|
O3
|
B:POP401
|
4.2
|
22.6
|
1.0
|
|
NH2
|
B:ARG189
|
4.2
|
17.7
|
1.0
|
|
O1
|
B:POP401
|
4.2
|
18.1
|
1.0
|
|
CG
|
B:GLU240
|
4.4
|
20.0
|
1.0
|
|
C
|
B:ASN232
|
4.4
|
17.5
|
1.0
|
|
O5
|
B:POP401
|
4.4
|
20.1
|
1.0
|
|
CB
|
B:ASN232
|
4.5
|
13.7
|
1.0
|
|
CA
|
B:SER236
|
4.6
|
15.6
|
1.0
|
|
MG
|
B:MG403
|
4.7
|
22.9
|
1.0
|
|
N
|
B:ASP233
|
4.8
|
13.7
|
1.0
|
|
OD1
|
B:ASP233
|
4.8
|
19.5
|
1.0
|
|
CA
|
B:ASP233
|
4.8
|
13.2
|
1.0
|
|
NH1
|
B:ARG189
|
4.9
|
19.8
|
1.0
|
|
CE
|
B:LYS239
|
4.9
|
19.0
|
1.0
|
|
CZ
|
B:ARG189
|
4.9
|
19.3
|
1.0
|
|
C
|
B:SER236
|
4.9
|
16.6
|
1.0
|
|
O
|
B:HOH641
|
4.9
|
29.6
|
1.0
|
|
O
|
B:HOH566
|
5.0
|
15.6
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 8yzy
Go back to
Magnesium Binding Sites List in 8yzy
Magnesium binding site 4 out
of 8 in the Stc Syda Mutant - W297Y
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Stc Syda Mutant - W297Y within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg403
b:22.9
occ:1.00
|
O3
|
B:POP401
|
2.1
|
22.6
|
1.0
|
|
O6
|
B:POP401
|
2.1
|
18.5
|
1.0
|
|
O
|
B:HOH658
|
2.3
|
28.0
|
1.0
|
|
P1
|
B:POP401
|
3.1
|
20.0
|
1.0
|
|
P2
|
B:POP401
|
3.3
|
18.7
|
1.0
|
|
O
|
B:POP401
|
3.4
|
19.0
|
1.0
|
|
O2
|
B:POP401
|
3.7
|
18.2
|
1.0
|
|
NZ
|
B:LYS239
|
3.8
|
23.5
|
1.0
|
|
NH2
|
B:ARG311
|
4.0
|
31.3
|
1.0
|
|
OD2
|
B:ASP106
|
4.1
|
64.7
|
1.0
|
|
O4
|
B:POP401
|
4.1
|
17.6
|
1.0
|
|
OE2
|
B:GLU240
|
4.2
|
17.3
|
1.0
|
|
O
|
B:HOH572
|
4.3
|
48.2
|
1.0
|
|
O1
|
B:POP401
|
4.4
|
18.1
|
1.0
|
|
O5
|
B:POP401
|
4.5
|
20.1
|
1.0
|
|
O
|
B:HOH580
|
4.5
|
46.2
|
1.0
|
|
O
|
B:HOH554
|
4.6
|
31.8
|
1.0
|
|
O
|
B:HOH552
|
4.6
|
32.2
|
1.0
|
|
O
|
B:HOH663
|
4.7
|
40.8
|
1.0
|
|
OD1
|
B:ASP106
|
4.7
|
58.0
|
1.0
|
|
O
|
B:HOH605
|
4.7
|
22.8
|
1.0
|
|
MG
|
B:MG402
|
4.7
|
17.3
|
1.0
|
|
CG
|
B:ASP106
|
4.8
|
54.1
|
1.0
|
|
OE1
|
B:GLU246
|
4.9
|
57.1
|
1.0
|
|
CE
|
B:LYS239
|
4.9
|
19.0
|
1.0
|
|
O
|
B:HOH587
|
5.0
|
42.5
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 8yzy
Go back to
Magnesium Binding Sites List in 8yzy
Magnesium binding site 5 out
of 8 in the Stc Syda Mutant - W297Y
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Stc Syda Mutant - W297Y within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg402
b:18.2
occ:1.00
|
O2
|
C:POP401
|
2.0
|
16.2
|
1.0
|
|
OE2
|
C:GLU240
|
2.0
|
22.8
|
1.0
|
|
OD1
|
C:ASN232
|
2.1
|
18.4
|
1.0
|
|
O4
|
C:POP401
|
2.1
|
17.7
|
1.0
|
|
OG
|
C:SER236
|
2.3
|
17.2
|
1.0
|
|
CD
|
C:GLU240
|
3.1
|
27.4
|
1.0
|
|
CG
|
C:ASN232
|
3.1
|
15.7
|
1.0
|
|
P2
|
C:POP401
|
3.2
|
19.5
|
1.0
|
|
P1
|
C:POP401
|
3.2
|
21.2
|
1.0
|
|
CB
|
C:SER236
|
3.3
|
18.7
|
1.0
|
|
O
|
C:POP401
|
3.4
|
19.9
|
1.0
|
|
OE1
|
C:GLU240
|
3.5
|
22.4
|
1.0
|
|
ND2
|
C:ASN232
|
3.5
|
16.9
|
1.0
|
|
O6
|
C:POP401
|
3.9
|
22.9
|
1.0
|
|
O
|
C:HOH583
|
4.0
|
20.0
|
1.0
|
|
O
|
C:ASN232
|
4.0
|
18.6
|
1.0
|
|
O3
|
C:POP401
|
4.2
|
20.8
|
1.0
|
|
NH2
|
C:ARG189
|
4.2
|
21.3
|
1.0
|
|
O1
|
C:POP401
|
4.2
|
18.3
|
1.0
|
|
CG
|
C:GLU240
|
4.3
|
24.2
|
1.0
|
|
C
|
C:ASN232
|
4.4
|
21.2
|
1.0
|
|
O5
|
C:POP401
|
4.4
|
20.9
|
1.0
|
|
CB
|
C:ASN232
|
4.5
|
16.0
|
1.0
|
|
CA
|
C:SER236
|
4.6
|
21.8
|
1.0
|
|
OD1
|
C:ASP233
|
4.7
|
20.4
|
1.0
|
|
MG
|
C:MG403
|
4.8
|
25.6
|
1.0
|
|
CE
|
C:LYS239
|
4.8
|
21.1
|
1.0
|
|
N
|
C:ASP233
|
4.8
|
24.7
|
1.0
|
|
CA
|
C:ASP233
|
4.8
|
17.7
|
1.0
|
|
CZ
|
C:ARG189
|
4.9
|
21.4
|
1.0
|
|
O
|
C:SER236
|
4.9
|
23.2
|
1.0
|
|
NH1
|
C:ARG189
|
4.9
|
20.7
|
1.0
|
|
C
|
C:SER236
|
4.9
|
24.0
|
1.0
|
|
O
|
C:HOH557
|
5.0
|
19.1
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 8yzy
Go back to
Magnesium Binding Sites List in 8yzy
Magnesium binding site 6 out
of 8 in the Stc Syda Mutant - W297Y
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Stc Syda Mutant - W297Y within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg403
b:25.6
occ:1.00
|
O3
|
C:POP401
|
2.1
|
20.8
|
1.0
|
|
O6
|
C:POP401
|
2.1
|
22.9
|
1.0
|
|
P1
|
C:POP401
|
3.1
|
21.2
|
1.0
|
|
P2
|
C:POP401
|
3.3
|
19.5
|
1.0
|
|
O
|
C:POP401
|
3.4
|
19.9
|
1.0
|
|
O2
|
C:POP401
|
3.7
|
16.2
|
1.0
|
|
NZ
|
C:LYS239
|
3.8
|
26.7
|
1.0
|
|
O
|
C:HOH660
|
3.9
|
38.4
|
1.0
|
|
NH2
|
C:ARG311
|
3.9
|
29.3
|
1.0
|
|
OD2
|
C:ASP106
|
4.1
|
43.4
|
1.0
|
|
O4
|
C:POP401
|
4.2
|
17.7
|
1.0
|
|
OE2
|
C:GLU240
|
4.3
|
22.8
|
1.0
|
|
O1
|
C:POP401
|
4.4
|
18.3
|
1.0
|
|
O5
|
C:POP401
|
4.5
|
20.9
|
1.0
|
|
OE1
|
C:GLU246
|
4.6
|
52.9
|
1.0
|
|
O
|
C:HOH618
|
4.7
|
36.8
|
1.0
|
|
O
|
C:HOH583
|
4.7
|
20.0
|
1.0
|
|
MG
|
C:MG402
|
4.8
|
18.2
|
1.0
|
|
CG
|
C:ASP106
|
4.8
|
43.9
|
1.0
|
|
CE
|
C:LYS239
|
4.9
|
21.1
|
1.0
|
|
OE2
|
C:GLU246
|
5.0
|
51.0
|
1.0
|
|
OD1
|
C:ASP106
|
5.0
|
46.0
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 8yzy
Go back to
Magnesium Binding Sites List in 8yzy
Magnesium binding site 7 out
of 8 in the Stc Syda Mutant - W297Y
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Stc Syda Mutant - W297Y within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg402
b:22.9
occ:1.00
|
O2
|
D:POP401
|
2.0
|
27.4
|
1.0
|
|
O4
|
D:POP401
|
2.1
|
33.8
|
1.0
|
|
OD1
|
D:ASN232
|
2.1
|
24.1
|
1.0
|
|
OE2
|
D:GLU240
|
2.2
|
29.4
|
1.0
|
|
OG
|
D:SER236
|
2.3
|
21.2
|
1.0
|
|
P1
|
D:POP401
|
3.1
|
28.8
|
1.0
|
|
CG
|
D:ASN232
|
3.1
|
18.8
|
1.0
|
|
CD
|
D:GLU240
|
3.1
|
27.5
|
1.0
|
|
P2
|
D:POP401
|
3.2
|
28.3
|
1.0
|
|
CB
|
D:SER236
|
3.3
|
21.8
|
1.0
|
|
O
|
D:POP401
|
3.3
|
23.1
|
1.0
|
|
ND2
|
D:ASN232
|
3.5
|
20.3
|
1.0
|
|
OE1
|
D:GLU240
|
3.6
|
27.1
|
1.0
|
|
O1
|
D:POP401
|
3.9
|
29.9
|
1.0
|
|
O
|
D:ASN232
|
4.0
|
18.8
|
1.0
|
|
O
|
D:HOH562
|
4.1
|
25.6
|
1.0
|
|
O6
|
D:POP401
|
4.2
|
25.7
|
1.0
|
|
NH2
|
D:ARG189
|
4.3
|
18.9
|
1.0
|
|
O3
|
D:POP401
|
4.3
|
26.0
|
1.0
|
|
O5
|
D:POP401
|
4.3
|
27.7
|
1.0
|
|
CG
|
D:GLU240
|
4.4
|
26.8
|
1.0
|
|
C
|
D:ASN232
|
4.4
|
18.2
|
1.0
|
|
CB
|
D:ASN232
|
4.5
|
19.0
|
1.0
|
|
CA
|
D:SER236
|
4.6
|
21.8
|
1.0
|
|
OD1
|
D:ASP233
|
4.7
|
20.5
|
1.0
|
|
N
|
D:ASP233
|
4.8
|
16.5
|
1.0
|
|
CA
|
D:ASP233
|
4.9
|
19.1
|
1.0
|
|
MG
|
D:MG403
|
4.9
|
29.5
|
1.0
|
|
NH1
|
D:ARG189
|
4.9
|
20.6
|
1.0
|
|
CE
|
D:LYS239
|
4.9
|
37.6
|
1.0
|
|
CZ
|
D:ARG189
|
4.9
|
20.9
|
1.0
|
|
O
|
D:HOH540
|
4.9
|
36.0
|
1.0
|
|
O
|
D:HOH573
|
5.0
|
20.8
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 8yzy
Go back to
Magnesium Binding Sites List in 8yzy
Magnesium binding site 8 out
of 8 in the Stc Syda Mutant - W297Y
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Stc Syda Mutant - W297Y within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg403
b:29.5
occ:1.00
|
O5
|
D:POP401
|
2.1
|
27.7
|
1.0
|
|
O1
|
D:POP401
|
2.1
|
29.9
|
1.0
|
|
P2
|
D:POP401
|
3.2
|
28.3
|
1.0
|
|
P1
|
D:POP401
|
3.4
|
28.8
|
1.0
|
|
O
|
D:POP401
|
3.4
|
23.1
|
1.0
|
|
O4
|
D:POP401
|
3.8
|
33.8
|
1.0
|
|
NH2
|
D:ARG311
|
4.0
|
45.9
|
1.0
|
|
NZ
|
D:LYS239
|
4.1
|
32.5
|
1.0
|
|
O
|
D:HOH641
|
4.3
|
36.6
|
1.0
|
|
O2
|
D:POP401
|
4.3
|
27.4
|
1.0
|
|
OE2
|
D:GLU240
|
4.4
|
29.4
|
1.0
|
|
O6
|
D:POP401
|
4.4
|
25.7
|
1.0
|
|
O3
|
D:POP401
|
4.6
|
26.0
|
1.0
|
|
O
|
D:HOH616
|
4.6
|
39.7
|
1.0
|
|
O
|
D:HOH516
|
4.6
|
33.9
|
1.0
|
|
O
|
D:HOH562
|
4.7
|
25.6
|
1.0
|
|
MG
|
D:MG402
|
4.9
|
22.9
|
1.0
|
|
Reference:
A.Fan,
S.Fan.
Stc Syda Mutant - W297Y To Be Published.
Page generated: Fri Aug 15 21:41:20 2025
|
