Magnesium in PDB 9fvt: Crystal Structure of Marine Sulfatase (OPSULF1) From Ochrovirga Pacifica
Protein crystallography data
The structure of Crystal Structure of Marine Sulfatase (OPSULF1) From Ochrovirga Pacifica, PDB code: 9fvt
was solved by
V.A.Solanki,
J.Krull,
J.H.Hehemann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.33 /
1.49
|
|
Space group
|
P 43
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
115.268,
115.268,
169.831,
90,
90,
90
|
|
R / Rfree (%)
|
16.6 /
19.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Marine Sulfatase (OPSULF1) From Ochrovirga Pacifica
(pdb code 9fvt). 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 Marine Sulfatase (OPSULF1) From Ochrovirga Pacifica, PDB code: 9fvt:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 9fvt
Go back to
Magnesium Binding Sites List in 9fvt
Magnesium binding site 1 out
of 4 in the Crystal Structure of Marine Sulfatase (OPSULF1) From Ochrovirga Pacifica
 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 Marine Sulfatase (OPSULF1) From Ochrovirga Pacifica within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:30.0
occ:1.00
|
OD1
|
A:ASP28
|
2.2
|
15.8
|
1.0
|
|
OD1
|
A:ASP27
|
2.2
|
18.1
|
1.0
|
|
HE2
|
A:HIS336
|
2.2
|
12.5
|
0.0
|
|
OD2
|
A:ASP335
|
2.4
|
13.5
|
1.0
|
|
NE2
|
A:HIS336
|
2.7
|
12.4
|
1.0
|
|
HB2
|
A:CYS79
|
2.7
|
19.1
|
1.0
|
|
OD1
|
A:ASP335
|
2.9
|
12.3
|
1.0
|
|
CG
|
A:ASP335
|
3.0
|
12.5
|
1.0
|
|
HZ1
|
A:LYS141
|
3.2
|
16.1
|
1.0
|
|
HD2
|
A:HIS248
|
3.2
|
15.6
|
1.0
|
|
H
|
A:ASP28
|
3.4
|
12.7
|
1.0
|
|
HH21
|
A:ARG83
|
3.4
|
14.6
|
1.0
|
|
CE1
|
A:HIS336
|
3.4
|
13.4
|
1.0
|
|
HA
|
A:CYS79
|
3.4
|
14.3
|
1.0
|
|
CG
|
A:ASP28
|
3.4
|
13.8
|
1.0
|
|
CD2
|
A:HIS336
|
3.4
|
11.3
|
1.0
|
|
CG
|
A:ASP27
|
3.4
|
16.0
|
1.0
|
|
CB
|
A:CYS79
|
3.5
|
20.3
|
1.0
|
|
HE1
|
A:HIS336
|
3.6
|
13.2
|
1.0
|
|
HD2
|
A:HIS336
|
3.6
|
11.8
|
1.0
|
|
N
|
A:ASP28
|
3.7
|
12.2
|
1.0
|
|
HA
|
A:ASP27
|
3.7
|
13.5
|
1.0
|
|
H
|
A:CYS79
|
3.8
|
12.7
|
1.0
|
|
HG
|
A:CYS79
|
3.8
|
26.1
|
0.0
|
|
CA
|
A:CYS79
|
3.9
|
13.0
|
1.0
|
|
HE
|
A:ARG83
|
3.9
|
14.5
|
1.0
|
|
SG
|
A:CYS79
|
4.0
|
26.1
|
1.0
|
|
NZ
|
A:LYS141
|
4.0
|
16.0
|
1.0
|
|
HE3
|
A:LYS343
|
4.0
|
14.8
|
1.0
|
|
HA
|
A:ASP28
|
4.1
|
12.4
|
1.0
|
|
N
|
A:CYS79
|
4.1
|
12.9
|
1.0
|
|
CD2
|
A:HIS248
|
4.1
|
15.4
|
1.0
|
|
C
|
A:ASP27
|
4.2
|
14.4
|
1.0
|
|
HZ2
|
A:LYS141
|
4.2
|
16.1
|
1.0
|
|
OD2
|
A:ASP27
|
4.2
|
16.8
|
1.0
|
|
HZ3
|
A:LYS141
|
4.2
|
16.1
|
1.0
|
|
NH2
|
A:ARG83
|
4.2
|
14.5
|
1.0
|
|
OD2
|
A:ASP28
|
4.2
|
17.7
|
1.0
|
|
CA
|
A:ASP27
|
4.2
|
13.4
|
1.0
|
|
CA
|
A:ASP28
|
4.3
|
12.1
|
1.0
|
|
CB
|
A:ASP28
|
4.3
|
12.4
|
1.0
|
|
HB3
|
A:CYS79
|
4.3
|
19.1
|
1.0
|
|
HZ2
|
A:LYS343
|
4.3
|
15.8
|
1.0
|
|
ND1
|
A:HIS336
|
4.4
|
13.2
|
1.0
|
|
CG
|
A:HIS336
|
4.4
|
12.4
|
1.0
|
|
HZ3
|
A:LYS343
|
4.4
|
15.8
|
1.0
|
|
CB
|
A:ASP27
|
4.4
|
13.3
|
1.0
|
|
CB
|
A:ASP335
|
4.4
|
11.9
|
1.0
|
|
O
|
A:HOH1018
|
4.6
|
30.0
|
1.0
|
|
HB2
|
A:ASP28
|
4.6
|
12.7
|
1.0
|
|
HE2
|
A:HIS248
|
4.7
|
17.3
|
0.0
|
|
HB2
|
A:ASP335
|
4.7
|
12.0
|
1.0
|
|
NE
|
A:ARG83
|
4.7
|
14.5
|
1.0
|
|
NZ
|
A:LYS343
|
4.7
|
16.4
|
1.0
|
|
HH22
|
A:ARG83
|
4.8
|
14.6
|
1.0
|
|
CE
|
A:LYS343
|
4.8
|
14.7
|
1.0
|
|
NE2
|
A:HIS248
|
4.8
|
16.9
|
1.0
|
|
HB3
|
A:ASP335
|
4.9
|
12.0
|
1.0
|
|
CZ
|
A:ARG83
|
5.0
|
14.8
|
1.0
|
|
H
|
A:HIS336
|
5.0
|
11.1
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 9fvt
Go back to
Magnesium Binding Sites List in 9fvt
Magnesium binding site 2 out
of 4 in the Crystal Structure of Marine Sulfatase (OPSULF1) From Ochrovirga Pacifica
 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 Marine Sulfatase (OPSULF1) From Ochrovirga Pacifica within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:15.1
occ:1.00
|
HE2
|
B:HIS336
|
2.1
|
14.3
|
0.0
|
|
OD1
|
B:ASP28
|
2.2
|
18.0
|
1.0
|
|
OD1
|
B:ASP27
|
2.3
|
16.6
|
1.0
|
|
OD2
|
B:ASP335
|
2.3
|
13.5
|
1.0
|
|
NE2
|
B:HIS336
|
2.6
|
14.3
|
1.0
|
|
OD1
|
B:ASP335
|
2.8
|
12.8
|
1.0
|
|
CG
|
B:ASP335
|
2.8
|
12.3
|
1.0
|
|
HB2
|
B:CYS79
|
2.9
|
20.4
|
1.0
|
|
HG
|
B:CYS79
|
2.9
|
27.9
|
0.0
|
|
HA
|
B:CYS79
|
3.3
|
14.7
|
1.0
|
|
CD2
|
B:HIS336
|
3.3
|
13.2
|
1.0
|
|
H
|
B:ASP28
|
3.3
|
13.7
|
1.0
|
|
CE1
|
B:HIS336
|
3.4
|
15.7
|
1.0
|
|
HZ1
|
B:LYS141
|
3.4
|
16.6
|
1.0
|
|
HD1
|
B:HIS248
|
3.4
|
19.5
|
0.0
|
|
HH21
|
B:ARG83
|
3.4
|
15.6
|
1.0
|
|
CG
|
B:ASP28
|
3.5
|
16.2
|
1.0
|
|
HD2
|
B:HIS336
|
3.5
|
13.5
|
1.0
|
|
CG
|
B:ASP27
|
3.5
|
14.9
|
1.0
|
|
HE1
|
B:HIS336
|
3.6
|
14.6
|
1.0
|
|
CB
|
B:CYS79
|
3.6
|
22.1
|
1.0
|
|
N
|
B:ASP28
|
3.7
|
13.2
|
1.0
|
|
H
|
B:CYS79
|
3.7
|
13.2
|
1.0
|
|
HA
|
B:ASP27
|
3.8
|
13.4
|
1.0
|
|
CA
|
B:CYS79
|
3.8
|
13.6
|
1.0
|
|
HE
|
B:ARG83
|
3.9
|
14.6
|
1.0
|
|
HA
|
B:ASP28
|
4.0
|
14.2
|
1.0
|
|
SG
|
B:CYS79
|
4.0
|
27.9
|
1.0
|
|
N
|
B:CYS79
|
4.0
|
13.1
|
1.0
|
|
HE3
|
B:LYS343
|
4.1
|
16.9
|
1.0
|
|
NZ
|
B:LYS141
|
4.1
|
16.4
|
1.0
|
|
HZ3
|
B:LYS141
|
4.1
|
16.6
|
1.0
|
|
C
|
B:ASP27
|
4.2
|
14.5
|
1.0
|
|
CA
|
B:ASP28
|
4.2
|
14.4
|
1.0
|
|
ND1
|
B:HIS248
|
4.2
|
19.6
|
1.0
|
|
OD2
|
B:ASP27
|
4.3
|
17.4
|
1.0
|
|
HZ2
|
B:LYS343
|
4.3
|
17.9
|
1.0
|
|
ND1
|
B:HIS336
|
4.3
|
12.5
|
1.0
|
|
NH2
|
B:ARG83
|
4.3
|
15.5
|
1.0
|
|
HZ2
|
B:LYS141
|
4.3
|
16.6
|
1.0
|
|
OD2
|
B:ASP28
|
4.3
|
19.2
|
1.0
|
|
CG
|
B:HIS336
|
4.3
|
13.3
|
1.0
|
|
CA
|
B:ASP27
|
4.3
|
12.8
|
1.0
|
|
CB
|
B:ASP28
|
4.3
|
14.1
|
1.0
|
|
CB
|
B:ASP335
|
4.3
|
12.0
|
1.0
|
|
CB
|
B:ASP27
|
4.5
|
13.4
|
1.0
|
|
HB3
|
B:CYS79
|
4.5
|
20.5
|
1.0
|
|
HZ3
|
B:LYS343
|
4.6
|
17.9
|
1.0
|
|
HB2
|
B:ASP335
|
4.6
|
12.0
|
1.0
|
|
HE1
|
B:HIS248
|
4.6
|
18.6
|
1.0
|
|
NE
|
B:ARG83
|
4.7
|
14.6
|
1.0
|
|
HB2
|
B:ASP28
|
4.7
|
14.6
|
1.0
|
|
NZ
|
B:LYS343
|
4.7
|
18.6
|
1.0
|
|
HB3
|
B:ASP335
|
4.8
|
12.0
|
1.0
|
|
H
|
B:HIS336
|
4.8
|
12.0
|
1.0
|
|
O
|
B:HOH997
|
4.8
|
10.2
|
1.0
|
|
CE1
|
B:HIS248
|
4.8
|
16.9
|
1.0
|
|
HH22
|
B:ARG83
|
4.9
|
15.6
|
1.0
|
|
CE
|
B:LYS343
|
4.9
|
16.6
|
1.0
|
|
HA
|
B:VAL78
|
5.0
|
13.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 9fvt
Go back to
Magnesium Binding Sites List in 9fvt
Magnesium binding site 3 out
of 4 in the Crystal Structure of Marine Sulfatase (OPSULF1) From Ochrovirga Pacifica
 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 Marine Sulfatase (OPSULF1) From Ochrovirga Pacifica within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg601
b:14.4
occ:1.00
|
HE2
|
C:HIS336
|
2.1
|
13.4
|
0.0
|
|
OD1
|
C:ASP28
|
2.2
|
16.0
|
1.0
|
|
OD1
|
C:ASP27
|
2.3
|
17.5
|
1.0
|
|
OD2
|
C:ASP335
|
2.3
|
14.2
|
1.0
|
|
NE2
|
C:HIS336
|
2.6
|
13.7
|
1.0
|
|
HB2
|
C:CYS79
|
2.7
|
19.3
|
1.0
|
|
OD1
|
C:ASP335
|
2.8
|
13.0
|
1.0
|
|
CG
|
C:ASP335
|
2.9
|
13.8
|
1.0
|
|
H
|
C:ASP28
|
3.2
|
12.8
|
1.0
|
|
CD2
|
C:HIS336
|
3.3
|
12.7
|
1.0
|
|
HA
|
C:CYS79
|
3.3
|
15.0
|
1.0
|
|
HZ1
|
C:LYS141
|
3.3
|
29.7
|
1.0
|
|
HD2
|
C:HIS248
|
3.3
|
17.1
|
1.0
|
|
CE1
|
C:HIS336
|
3.3
|
14.2
|
1.0
|
|
HH21
|
C:ARG83
|
3.4
|
14.7
|
1.0
|
|
HD2
|
C:HIS336
|
3.4
|
12.9
|
1.0
|
|
CG
|
C:ASP28
|
3.4
|
14.4
|
1.0
|
|
CG
|
C:ASP27
|
3.5
|
15.5
|
1.0
|
|
CB
|
C:CYS79
|
3.6
|
19.4
|
1.0
|
|
HE1
|
C:HIS336
|
3.6
|
13.7
|
1.0
|
|
N
|
C:ASP28
|
3.6
|
12.4
|
1.0
|
|
HA
|
C:ASP27
|
3.7
|
12.8
|
1.0
|
|
CA
|
C:CYS79
|
3.8
|
14.3
|
1.0
|
|
HE
|
C:ARG83
|
3.9
|
14.5
|
1.0
|
|
HZ3
|
C:LYS141
|
3.9
|
29.8
|
1.0
|
|
H
|
C:CYS79
|
3.9
|
14.3
|
1.0
|
|
NZ
|
C:LYS141
|
3.9
|
36.1
|
1.0
|
|
HZ2
|
C:LYS141
|
4.0
|
29.6
|
1.0
|
|
HA
|
C:ASP28
|
4.1
|
13.1
|
1.0
|
|
N
|
C:CYS79
|
4.1
|
14.2
|
1.0
|
|
HE3
|
C:LYS343
|
4.1
|
17.8
|
1.0
|
|
C
|
C:ASP27
|
4.2
|
13.4
|
1.0
|
|
CD2
|
C:HIS248
|
4.2
|
18.2
|
1.0
|
|
SG
|
C:CYS79
|
4.2
|
28.0
|
1.0
|
|
CA
|
C:ASP28
|
4.2
|
13.1
|
1.0
|
|
NH2
|
C:ARG83
|
4.3
|
14.7
|
1.0
|
|
OD2
|
C:ASP28
|
4.3
|
17.2
|
1.0
|
|
CA
|
C:ASP27
|
4.3
|
12.6
|
1.0
|
|
CB
|
C:ASP28
|
4.3
|
12.9
|
1.0
|
|
CG
|
C:HIS336
|
4.3
|
12.6
|
1.0
|
|
ND1
|
C:HIS336
|
4.3
|
12.4
|
1.0
|
|
OD2
|
C:ASP27
|
4.3
|
16.3
|
1.0
|
|
HB3
|
C:CYS79
|
4.3
|
19.3
|
1.0
|
|
CB
|
C:ASP335
|
4.4
|
12.7
|
1.0
|
|
HZ2
|
C:LYS343
|
4.4
|
18.7
|
1.0
|
|
CB
|
C:ASP27
|
4.5
|
13.5
|
1.0
|
|
HZ3
|
C:LYS343
|
4.5
|
18.7
|
1.0
|
|
HB2
|
C:ASP335
|
4.6
|
13.1
|
1.0
|
|
HB2
|
C:ASP28
|
4.6
|
13.3
|
1.0
|
|
NE
|
C:ARG83
|
4.7
|
14.5
|
1.0
|
|
HE2
|
C:HIS248
|
4.7
|
16.6
|
0.0
|
|
HB3
|
C:ASP335
|
4.8
|
13.1
|
1.0
|
|
NZ
|
C:LYS343
|
4.8
|
19.3
|
1.0
|
|
O
|
C:HOH995
|
4.8
|
9.1
|
1.0
|
|
HH22
|
C:ARG83
|
4.8
|
14.7
|
1.0
|
|
H
|
C:HIS336
|
4.8
|
12.7
|
1.0
|
|
NE2
|
C:HIS248
|
4.9
|
16.8
|
1.0
|
|
CE
|
C:LYS343
|
4.9
|
17.6
|
1.0
|
|
CZ
|
C:ARG83
|
5.0
|
14.6
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 9fvt
Go back to
Magnesium Binding Sites List in 9fvt
Magnesium binding site 4 out
of 4 in the Crystal Structure of Marine Sulfatase (OPSULF1) From Ochrovirga Pacifica
 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 Marine Sulfatase (OPSULF1) From Ochrovirga Pacifica within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg601
b:30.0
occ:1.00
|
HE2
|
D:HIS336
|
2.1
|
13.6
|
0.0
|
|
OD1
|
D:ASP28
|
2.2
|
16.8
|
1.0
|
|
OD2
|
D:ASP335
|
2.3
|
13.6
|
1.0
|
|
OD1
|
D:ASP27
|
2.3
|
17.0
|
1.0
|
|
NE2
|
D:HIS336
|
2.5
|
13.7
|
1.0
|
|
OD1
|
D:ASP335
|
2.7
|
15.5
|
1.0
|
|
HB2
|
D:CYS79
|
2.7
|
21.1
|
1.0
|
|
CG
|
D:ASP335
|
2.8
|
15.1
|
1.0
|
|
CD2
|
D:HIS336
|
3.3
|
13.8
|
1.0
|
|
H
|
D:ASP28
|
3.3
|
15.0
|
1.0
|
|
CE1
|
D:HIS336
|
3.3
|
16.3
|
1.0
|
|
HZ1
|
D:LYS141
|
3.4
|
16.0
|
1.0
|
|
HA
|
D:CYS79
|
3.4
|
16.6
|
1.0
|
|
HH21
|
D:ARG83
|
3.4
|
16.2
|
1.0
|
|
HD2
|
D:HIS336
|
3.4
|
13.8
|
1.0
|
|
CG
|
D:ASP28
|
3.5
|
16.3
|
1.0
|
|
HD1
|
D:HIS248
|
3.5
|
19.8
|
0.0
|
|
CG
|
D:ASP27
|
3.5
|
18.6
|
1.0
|
|
CB
|
D:CYS79
|
3.5
|
20.8
|
1.0
|
|
HE1
|
D:HIS336
|
3.6
|
15.5
|
1.0
|
|
N
|
D:ASP28
|
3.7
|
15.2
|
1.0
|
|
HA
|
D:ASP27
|
3.8
|
15.1
|
1.0
|
|
HG
|
D:CYS79
|
3.8
|
31.1
|
0.0
|
|
HE
|
D:ARG83
|
3.8
|
15.9
|
1.0
|
|
CA
|
D:CYS79
|
3.9
|
16.1
|
1.0
|
|
SG
|
D:CYS79
|
4.0
|
30.8
|
1.0
|
|
H
|
D:CYS79
|
4.0
|
15.6
|
1.0
|
|
HA
|
D:ASP28
|
4.0
|
14.9
|
1.0
|
|
HE3
|
D:LYS343
|
4.0
|
18.5
|
1.0
|
|
NZ
|
D:LYS141
|
4.2
|
15.4
|
1.0
|
|
C
|
D:ASP27
|
4.2
|
15.2
|
1.0
|
|
N
|
D:CYS79
|
4.2
|
15.3
|
1.0
|
|
CA
|
D:ASP28
|
4.2
|
14.2
|
1.0
|
|
HZ3
|
D:LYS141
|
4.3
|
16.0
|
1.0
|
|
ND1
|
D:HIS336
|
4.3
|
15.3
|
1.0
|
|
CA
|
D:ASP27
|
4.3
|
15.1
|
1.0
|
|
CG
|
D:HIS336
|
4.3
|
13.9
|
1.0
|
|
OD2
|
D:ASP28
|
4.3
|
18.6
|
1.0
|
|
ND1
|
D:HIS248
|
4.3
|
19.7
|
1.0
|
|
CB
|
D:ASP28
|
4.3
|
15.9
|
1.0
|
|
NH2
|
D:ARG83
|
4.3
|
16.3
|
1.0
|
|
CB
|
D:ASP335
|
4.3
|
13.1
|
1.0
|
|
OD2
|
D:ASP27
|
4.3
|
18.7
|
1.0
|
|
HB3
|
D:CYS79
|
4.3
|
21.0
|
1.0
|
|
HZ2
|
D:LYS141
|
4.4
|
16.0
|
1.0
|
|
HZ2
|
D:LYS343
|
4.4
|
19.5
|
1.0
|
|
CB
|
D:ASP27
|
4.4
|
15.9
|
1.0
|
|
HB2
|
D:ASP335
|
4.5
|
13.4
|
1.0
|
|
HZ3
|
D:LYS343
|
4.6
|
19.5
|
1.0
|
|
NE
|
D:ARG83
|
4.6
|
16.3
|
1.0
|
|
HE1
|
D:HIS248
|
4.7
|
18.8
|
1.0
|
|
HB2
|
D:ASP28
|
4.7
|
15.6
|
1.0
|
|
HB3
|
D:ASP335
|
4.7
|
13.4
|
1.0
|
|
NZ
|
D:LYS343
|
4.8
|
19.9
|
1.0
|
|
CE
|
D:LYS343
|
4.8
|
18.6
|
1.0
|
|
H
|
D:HIS336
|
4.9
|
12.7
|
1.0
|
|
O
|
D:HOH984
|
4.9
|
12.2
|
1.0
|
|
HH22
|
D:ARG83
|
4.9
|
16.3
|
1.0
|
|
CE1
|
D:HIS248
|
4.9
|
17.7
|
1.0
|
|
CZ
|
D:ARG83
|
5.0
|
16.1
|
1.0
|
|
Reference:
V.A.Solanki,
J.Krull,
J.H.Hehemann.
Crystal Structure of Marine Sulfatase (OPSULF1) From Ochrovirga Pacifica To Be Published.
Page generated: Sat Oct 5 09:34:39 2024
|
