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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

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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

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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

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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

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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

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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

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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

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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.
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