Magnesium in PDB 7kpf: NME2 Bound to Myristoyl-Coa
Enzymatic activity of NME2 Bound to Myristoyl-Coa
All present enzymatic activity of NME2 Bound to Myristoyl-Coa:
2.7.13.3;
2.7.4.6;
Protein crystallography data
The structure of NME2 Bound to Myristoyl-Coa, PDB code: 7kpf
was solved by
I.R.Price,
H.Lin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
78.56 /
2.23
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.727,
107.515,
115.08,
90,
90,
90
|
|
R / Rfree (%)
|
19 /
22.9
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the NME2 Bound to Myristoyl-Coa
(pdb code 7kpf). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
NME2 Bound to Myristoyl-Coa, PDB code: 7kpf:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 7kpf
Go back to
Magnesium Binding Sites List in 7kpf
Magnesium binding site 1 out
of 7 in the NME2 Bound to Myristoyl-Coa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of NME2 Bound to Myristoyl-Coa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg202
b:73.9
occ:1.00
|
HZ3
|
B:LYS12
|
2.4
|
61.3
|
1.0
|
|
HZ2
|
B:LYS12
|
2.7
|
61.3
|
1.0
|
|
NZ
|
B:LYS12
|
2.9
|
53.2
|
1.0
|
|
HD13
|
B:LEU64
|
2.9
|
74.0
|
1.0
|
|
HZ1
|
B:LYS12
|
3.0
|
61.3
|
1.0
|
|
O
|
B:VAL112
|
3.1
|
51.4
|
1.0
|
|
N3A
|
B:WYV201
|
3.2
|
63.2
|
1.0
|
|
HO2A
|
B:WYV201
|
3.2
|
104.3
|
1.0
|
|
O2B
|
B:WYV201
|
3.2
|
74.5
|
1.0
|
|
OD1
|
B:ASN115
|
3.3
|
45.7
|
1.0
|
|
HD11
|
B:LEU64
|
3.4
|
74.0
|
1.0
|
|
HE2
|
B:TYR67
|
3.5
|
78.9
|
1.0
|
|
HA2
|
B:GLY113
|
3.5
|
57.9
|
1.0
|
|
CD1
|
B:LEU64
|
3.5
|
63.3
|
1.0
|
|
H9
|
B:WYV201
|
3.5
|
99.5
|
1.0
|
|
HD21
|
B:ASN115
|
3.8
|
61.1
|
1.0
|
|
C4A
|
B:WYV201
|
3.8
|
65.0
|
1.0
|
|
HD12
|
B:LEU64
|
3.9
|
74.0
|
1.0
|
|
C2A
|
B:WYV201
|
3.9
|
66.7
|
1.0
|
|
H2A
|
B:WYV201
|
3.9
|
94.2
|
1.0
|
|
CG
|
B:ASN115
|
3.9
|
47.1
|
1.0
|
|
N9A
|
B:WYV201
|
4.0
|
67.1
|
1.0
|
|
ND2
|
B:ASN115
|
4.1
|
53.9
|
1.0
|
|
C1B
|
B:WYV201
|
4.1
|
71.4
|
1.0
|
|
HG22
|
B:VAL112
|
4.1
|
72.2
|
1.0
|
|
C
|
B:VAL112
|
4.2
|
51.0
|
1.0
|
|
C2B
|
B:WYV201
|
4.2
|
70.7
|
1.0
|
|
CE
|
B:LYS12
|
4.3
|
53.0
|
1.0
|
|
O7A
|
B:WYV201
|
4.3
|
65.4
|
1.0
|
|
H
|
B:ASN115
|
4.3
|
59.0
|
1.0
|
|
CA
|
B:GLY113
|
4.3
|
49.4
|
1.0
|
|
CE2
|
B:TYR67
|
4.3
|
67.8
|
1.0
|
|
HD3
|
B:LYS12
|
4.4
|
51.3
|
1.0
|
|
C
|
B:GLY113
|
4.6
|
55.4
|
1.0
|
|
O3B
|
B:WYV201
|
4.6
|
70.8
|
1.0
|
|
HE2
|
B:LYS12
|
4.6
|
61.4
|
1.0
|
|
O
|
B:GLY113
|
4.7
|
42.4
|
1.0
|
|
HD22
|
B:LEU64
|
4.7
|
76.6
|
1.0
|
|
HD2
|
B:LYS12
|
4.7
|
51.3
|
1.0
|
|
CD
|
B:LYS12
|
4.7
|
44.2
|
1.0
|
|
N
|
B:GLY113
|
4.8
|
52.7
|
1.0
|
|
HD22
|
B:ASN115
|
4.8
|
61.1
|
1.0
|
|
H10
|
B:WYV201
|
4.8
|
99.0
|
1.0
|
|
HE3
|
B:LYS12
|
4.8
|
61.4
|
1.0
|
|
CG
|
B:LEU64
|
4.9
|
60.5
|
1.0
|
|
C5A
|
B:WYV201
|
4.9
|
65.0
|
1.0
|
|
HD2
|
B:TYR67
|
4.9
|
76.1
|
1.0
|
|
N1A
|
B:WYV201
|
4.9
|
62.4
|
1.0
|
|
P3B
|
B:WYV201
|
4.9
|
71.5
|
1.0
|
|
HD21
|
B:LEU64
|
4.9
|
76.6
|
1.0
|
|
OH
|
B:TYR67
|
5.0
|
60.1
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 7kpf
Go back to
Magnesium Binding Sites List in 7kpf
Magnesium binding site 2 out
of 7 in the NME2 Bound to Myristoyl-Coa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of NME2 Bound to Myristoyl-Coa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg202
b:80.3
occ:1.00
|
O
|
C:HOH301
|
2.5
|
71.7
|
1.0
|
|
O4A
|
C:WYV201
|
3.9
|
80.3
|
1.0
|
|
O3A
|
C:WYV201
|
4.2
|
81.7
|
1.0
|
|
HH21
|
C:ARG58
|
4.4
|
94.8
|
1.0
|
|
O2A
|
C:WYV201
|
4.4
|
69.3
|
1.0
|
|
HH22
|
C:ARG58
|
4.6
|
94.8
|
1.0
|
|
P2A
|
C:WYV201
|
4.7
|
77.8
|
1.0
|
|
NH2
|
C:ARG58
|
4.8
|
79.0
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 7kpf
Go back to
Magnesium Binding Sites List in 7kpf
Magnesium binding site 3 out
of 7 in the NME2 Bound to Myristoyl-Coa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of NME2 Bound to Myristoyl-Coa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg202
b:48.5
occ:1.00
|
HZ1
|
D:LYS12
|
2.5
|
60.5
|
1.0
|
|
HD1
|
D:HIS118
|
2.9
|
55.2
|
1.0
|
|
HD21
|
D:ASN115
|
3.4
|
46.9
|
1.0
|
|
HB2
|
D:HIS118
|
3.4
|
46.7
|
1.0
|
|
NZ
|
D:LYS12
|
3.4
|
53.0
|
1.0
|
|
HG23
|
D:THR94
|
3.6
|
52.8
|
1.0
|
|
NZ
|
D:LYS49
|
3.7
|
57.0
|
1.0
|
|
HZ2
|
D:LYS12
|
3.7
|
60.5
|
1.0
|
|
ND1
|
D:HIS118
|
3.7
|
48.6
|
1.0
|
|
HZ3
|
D:LYS12
|
3.9
|
60.5
|
1.0
|
|
O
|
D:HOH323
|
3.9
|
43.1
|
1.0
|
|
HA
|
D:HIS118
|
3.9
|
50.1
|
1.0
|
|
HE3
|
D:LYS12
|
4.0
|
62.2
|
1.0
|
|
HG21
|
D:THR94
|
4.1
|
52.8
|
1.0
|
|
CE
|
D:LYS12
|
4.1
|
54.3
|
1.0
|
|
HE2
|
D:LYS12
|
4.2
|
62.2
|
1.0
|
|
CB
|
D:HIS118
|
4.2
|
41.0
|
1.0
|
|
HH21
|
D:ARG105
|
4.2
|
43.2
|
1.0
|
|
ND2
|
D:ASN115
|
4.2
|
40.0
|
1.0
|
|
CG2
|
D:THR94
|
4.3
|
46.4
|
1.0
|
|
HH22
|
D:ARG105
|
4.3
|
43.2
|
1.0
|
|
O
|
D:ILE117
|
4.4
|
36.2
|
1.0
|
|
CG
|
D:HIS118
|
4.4
|
39.5
|
1.0
|
|
NH2
|
D:ARG105
|
4.5
|
37.6
|
1.0
|
|
CA
|
D:HIS118
|
4.6
|
43.3
|
1.0
|
|
HG22
|
D:THR94
|
4.6
|
52.8
|
1.0
|
|
CE
|
D:LYS49
|
4.7
|
72.0
|
1.0
|
|
HD22
|
D:ASN115
|
4.7
|
46.9
|
1.0
|
|
HH22
|
D:ARG88
|
4.7
|
70.0
|
1.0
|
|
O
|
D:HOH326
|
4.8
|
55.5
|
1.0
|
|
CE1
|
D:HIS118
|
4.8
|
44.3
|
1.0
|
|
OD1
|
D:ASN115
|
4.8
|
43.3
|
1.0
|
|
OE1
|
D:GLU45
|
4.8
|
64.8
|
1.0
|
|
HE1
|
D:HIS118
|
5.0
|
49.6
|
1.0
|
|
HB3
|
D:HIS118
|
5.0
|
46.7
|
1.0
|
|
CG
|
D:ASN115
|
5.0
|
41.1
|
1.0
|
|
HH21
|
D:ARG88
|
5.0
|
70.0
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 7kpf
Go back to
Magnesium Binding Sites List in 7kpf
Magnesium binding site 4 out
of 7 in the NME2 Bound to Myristoyl-Coa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of NME2 Bound to Myristoyl-Coa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg201
b:62.9
occ:1.00
|
O
|
E:HOH320
|
2.2
|
49.7
|
1.0
|
|
HZ1
|
E:LYS12
|
2.7
|
64.1
|
1.0
|
|
HD21
|
E:ASN115
|
2.8
|
57.4
|
1.0
|
|
HG23
|
E:THR94
|
3.3
|
53.3
|
1.0
|
|
NZ
|
E:LYS12
|
3.6
|
55.7
|
1.0
|
|
NZ
|
E:LYS49
|
3.7
|
80.3
|
1.0
|
|
ND2
|
E:ASN115
|
3.7
|
49.2
|
1.0
|
|
HG21
|
E:THR94
|
3.7
|
53.3
|
1.0
|
|
HZ2
|
E:LYS12
|
3.9
|
64.1
|
1.0
|
|
CG2
|
E:THR94
|
3.9
|
46.0
|
1.0
|
|
HB2
|
E:HIS118
|
4.0
|
57.2
|
1.0
|
|
HZ3
|
E:LYS12
|
4.1
|
64.1
|
1.0
|
|
HD22
|
E:ASN115
|
4.2
|
57.4
|
1.0
|
|
ND1
|
E:HIS118
|
4.2
|
46.1
|
1.0
|
|
HG22
|
E:THR94
|
4.2
|
53.3
|
1.0
|
|
HE3
|
E:LYS12
|
4.2
|
53.6
|
1.0
|
|
HH21
|
E:ARG105
|
4.2
|
54.7
|
1.0
|
|
O
|
E:HOH327
|
4.3
|
36.9
|
1.0
|
|
HA
|
E:HIS118
|
4.3
|
49.1
|
1.0
|
|
CE
|
E:LYS12
|
4.4
|
46.8
|
1.0
|
|
HH22
|
E:ARG105
|
4.4
|
54.7
|
1.0
|
|
CE
|
E:LYS49
|
4.4
|
79.1
|
1.0
|
|
HE2
|
E:LYS12
|
4.4
|
53.6
|
1.0
|
|
OD1
|
E:ASN115
|
4.5
|
43.1
|
1.0
|
|
NH2
|
E:ARG105
|
4.5
|
46.9
|
1.0
|
|
CG
|
E:ASN115
|
4.5
|
46.1
|
1.0
|
|
O
|
E:ILE117
|
4.6
|
40.0
|
1.0
|
|
O
|
E:HOH318
|
4.7
|
51.0
|
1.0
|
|
CB
|
E:HIS118
|
4.7
|
47.4
|
1.0
|
|
CG
|
E:HIS118
|
4.9
|
49.3
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 7kpf
Go back to
Magnesium Binding Sites List in 7kpf
Magnesium binding site 5 out
of 7 in the NME2 Bound to Myristoyl-Coa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of NME2 Bound to Myristoyl-Coa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg201
b:51.4
occ:1.00
|
H
|
F:LYS100
|
2.3
|
58.0
|
1.0
|
|
O
|
F:HOH317
|
2.4
|
62.2
|
1.0
|
|
H
|
F:GLU93
|
2.6
|
66.4
|
1.0
|
|
HG2
|
F:LYS100
|
2.7
|
66.8
|
1.0
|
|
HA
|
F:SER99
|
2.8
|
76.0
|
1.0
|
|
HG2
|
F:GLU93
|
2.8
|
69.2
|
1.0
|
|
HA2
|
F:GLY92
|
2.8
|
68.2
|
1.0
|
|
HG21
|
F:THR103
|
2.9
|
61.3
|
1.0
|
|
N
|
F:LYS100
|
3.1
|
50.3
|
1.0
|
|
N
|
F:GLU93
|
3.3
|
55.4
|
1.0
|
|
HB2
|
F:LYS100
|
3.5
|
65.0
|
1.0
|
|
CA
|
F:GLY92
|
3.6
|
56.5
|
1.0
|
|
CG
|
F:LYS100
|
3.6
|
58.0
|
1.0
|
|
HA3
|
F:GLY92
|
3.6
|
68.2
|
1.0
|
|
CA
|
F:SER99
|
3.7
|
67.1
|
1.0
|
|
CG
|
F:GLU93
|
3.8
|
58.7
|
1.0
|
|
CG2
|
F:THR103
|
3.8
|
53.1
|
1.0
|
|
CB
|
F:LYS100
|
3.9
|
55.9
|
1.0
|
|
C
|
F:SER99
|
3.9
|
56.2
|
1.0
|
|
HG3
|
F:LYS100
|
3.9
|
66.8
|
1.0
|
|
C
|
F:GLY92
|
3.9
|
56.5
|
1.0
|
|
HG23
|
F:THR103
|
4.0
|
61.3
|
1.0
|
|
CA
|
F:LYS100
|
4.1
|
52.5
|
1.0
|
|
O
|
F:ASP98
|
4.1
|
63.7
|
1.0
|
|
HB3
|
F:SER99
|
4.1
|
66.8
|
1.0
|
|
HG3
|
F:GLU93
|
4.2
|
69.2
|
1.0
|
|
HG
|
F:SER99
|
4.2
|
70.9
|
1.0
|
|
HB2
|
F:GLU93
|
4.2
|
68.8
|
1.0
|
|
OG1
|
F:THR103
|
4.3
|
45.1
|
1.0
|
|
CB
|
F:GLU93
|
4.4
|
58.3
|
1.0
|
|
CB
|
F:SER99
|
4.4
|
59.1
|
1.0
|
|
CA
|
F:GLU93
|
4.4
|
57.4
|
1.0
|
|
HG22
|
F:THR103
|
4.4
|
61.3
|
1.0
|
|
HG1
|
F:THR103
|
4.5
|
51.9
|
1.0
|
|
OE2
|
F:GLU93
|
4.6
|
71.9
|
1.0
|
|
HE2
|
F:LYS100
|
4.6
|
83.1
|
1.0
|
|
CB
|
F:THR103
|
4.6
|
48.6
|
1.0
|
|
HD3
|
F:LYS100
|
4.6
|
71.9
|
1.0
|
|
CD
|
F:GLU93
|
4.6
|
68.1
|
1.0
|
|
CD
|
F:LYS100
|
4.7
|
62.5
|
1.0
|
|
N
|
F:SER99
|
4.7
|
59.7
|
1.0
|
|
HA
|
F:LYS100
|
4.7
|
61.0
|
1.0
|
|
OG
|
F:SER99
|
4.8
|
62.8
|
1.0
|
|
HB
|
F:THR103
|
4.8
|
56.3
|
1.0
|
|
HB3
|
F:LYS100
|
4.8
|
65.0
|
1.0
|
|
HA
|
F:GLU93
|
4.8
|
68.1
|
1.0
|
|
C
|
F:ASP98
|
4.8
|
63.4
|
1.0
|
|
N
|
F:GLY92
|
4.8
|
57.2
|
1.0
|
|
O
|
F:LYS100
|
4.9
|
45.9
|
1.0
|
|
H
|
F:GLY92
|
4.9
|
69.3
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 7kpf
Go back to
Magnesium Binding Sites List in 7kpf
Magnesium binding site 6 out
of 7 in the NME2 Bound to Myristoyl-Coa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of NME2 Bound to Myristoyl-Coa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg202
b:89.3
occ:1.00
|
O
|
C:HOH330
|
2.0
|
65.2
|
1.0
|
|
HH22
|
F:ARG42
|
2.0
|
83.0
|
1.0
|
|
NH2
|
F:ARG42
|
2.8
|
71.1
|
1.0
|
|
HH21
|
F:ARG42
|
3.1
|
83.0
|
1.0
|
|
HA
|
C:TYR142
|
3.2
|
72.7
|
1.0
|
|
HH12
|
F:ARG42
|
3.5
|
101.6
|
1.0
|
|
HB2
|
C:TYR142
|
3.7
|
61.2
|
1.0
|
|
CZ
|
F:ARG42
|
3.7
|
77.5
|
1.0
|
|
O
|
F:SER70
|
3.8
|
86.4
|
1.0
|
|
H
|
C:LYS143
|
3.8
|
59.3
|
1.0
|
|
HB3
|
C:TYR142
|
3.9
|
61.2
|
1.0
|
|
NH1
|
F:ARG42
|
4.0
|
87.4
|
1.0
|
|
CA
|
C:TYR142
|
4.1
|
62.9
|
1.0
|
|
CB
|
C:TYR142
|
4.1
|
53.2
|
1.0
|
|
N
|
C:LYS143
|
4.6
|
52.0
|
1.0
|
|
O
|
C:ASP141
|
4.6
|
69.3
|
1.0
|
|
HA2
|
F:GLY71
|
4.6
|
87.8
|
1.0
|
|
HH11
|
F:ARG42
|
4.8
|
101.6
|
1.0
|
|
C
|
F:SER70
|
4.8
|
87.0
|
1.0
|
|
C
|
C:TYR142
|
4.9
|
50.3
|
1.0
|
|
NE
|
F:ARG42
|
4.9
|
71.8
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 7kpf
Go back to
Magnesium Binding Sites List in 7kpf
Magnesium binding site 7 out
of 7 in the NME2 Bound to Myristoyl-Coa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of NME2 Bound to Myristoyl-Coa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg203
b:71.8
occ:1.00
|
ND1
|
F:HIS118
|
2.8
|
62.0
|
1.0
|
|
HB2
|
F:HIS118
|
3.3
|
70.9
|
1.0
|
|
HA
|
F:HIS118
|
3.4
|
60.5
|
1.0
|
|
HH22
|
F:ARG88
|
3.5
|
63.8
|
1.0
|
|
CG
|
F:HIS118
|
3.7
|
59.8
|
1.0
|
|
HG23
|
F:THR94
|
3.8
|
76.3
|
1.0
|
|
HH21
|
F:ARG88
|
3.8
|
63.8
|
1.0
|
|
HZ1
|
F:LYS12
|
3.8
|
75.4
|
1.0
|
|
CE1
|
F:HIS118
|
3.8
|
54.9
|
1.0
|
|
CB
|
F:HIS118
|
3.8
|
60.4
|
1.0
|
|
HH22
|
F:ARG105
|
3.8
|
55.5
|
1.0
|
|
NH2
|
F:ARG88
|
3.9
|
57.8
|
1.0
|
|
HE1
|
F:HIS118
|
3.9
|
62.4
|
1.0
|
|
H
|
F:GLY119
|
4.0
|
55.7
|
1.0
|
|
CA
|
F:HIS118
|
4.1
|
51.2
|
1.0
|
|
HH21
|
F:ARG105
|
4.1
|
55.5
|
1.0
|
|
HD21
|
F:ASN115
|
4.1
|
63.7
|
1.0
|
|
HG21
|
F:THR94
|
4.2
|
76.3
|
1.0
|
|
NH2
|
F:ARG105
|
4.2
|
48.8
|
1.0
|
|
CG2
|
F:THR94
|
4.5
|
66.6
|
1.0
|
|
O
|
F:ILE117
|
4.6
|
51.4
|
1.0
|
|
NZ
|
F:LYS12
|
4.6
|
64.2
|
1.0
|
|
N
|
F:GLY119
|
4.6
|
48.4
|
1.0
|
|
HE3
|
F:LYS12
|
4.7
|
64.8
|
1.0
|
|
HB3
|
F:HIS118
|
4.8
|
70.9
|
1.0
|
|
O
|
F:GLY119
|
4.8
|
55.5
|
1.0
|
|
HG1
|
F:THR94
|
4.8
|
70.6
|
1.0
|
|
HZ2
|
F:LYS12
|
4.9
|
75.4
|
1.0
|
|
ND2
|
F:ASN115
|
4.9
|
56.7
|
1.0
|
|
C
|
F:HIS118
|
4.9
|
56.8
|
1.0
|
|
CD2
|
F:HIS118
|
4.9
|
51.2
|
1.0
|
|
NE2
|
F:HIS118
|
4.9
|
61.9
|
1.0
|
|
CZ
|
F:ARG88
|
5.0
|
66.5
|
1.0
|
|
Reference:
S.Zhang,
O.D.Nelson,
I.R.Price,
C.Zhu,
I.R.Fernandez,
X.Lu,
R.S.Weiss,
H.Lin.
A Chemical Proteomic Approach Reveals the Regulation of NME1/2 and Cancer Metastasis By Long-Chain Fatty Acyl Coenzyme A To Be Published.
Page generated: Wed Oct 2 22:33:18 2024
|
