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Magnesium in PDB 8kda: Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas

Enzymatic activity of Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas

All present enzymatic activity of Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas:
3.1.26.5;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas (pdb code 8kda). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas, PDB code: 8kda:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8kda

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Magnesium binding site 1 out of 5 in the Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1001

b:27.0
occ:1.00
 OD2 E:ASP144 2.5 24.0 1.0
OD2 E:ASP162 2.7 19.2 1.0
OD1 E:ASP140 2.9 11.0 1.0
O5' T:A1 2.9 60.2 1.0
O3' T:A0 3.1 44.4 1.0
CG E:ASP144 3.5 19.8 1.0
P T:A1 3.7 70.7 1.0
MG E:MG1002 3.7 16.0 1.0
OD1 E:ASP144 3.7 13.9 1.0
CG E:ASP140 3.8 15.8 1.0
OD2 E:ASP140 3.9 21.9 1.0
CG E:ASP162 3.9 33.5 1.0
C5' T:A1 4.1 54.7 1.0
OP2 T:A1 4.3 60.2 1.0
OG E:SER141 4.4 18.9 1.0
O E:ILE138 4.6 25.0 1.0
OD1 E:ASP162 4.7 41.2 1.0
CB E:ASP162 4.7 30.6 1.0
CB E:ASP144 4.8 15.9 1.0
OP1 T:A1 4.9 60.8 1.0
N E:ASP140 5.0 14.6 1.0

Magnesium binding site 2 out of 5 in 8kda

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Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1002

b:16.0
occ:1.00
 O3' T:A0 2.1 44.4 1.0
OD1 E:ASP144 2.5 13.9 1.0
CG E:ASP144 3.5 19.8 1.0
P T:A1 3.6 70.7 1.0
MG E:MG1001 3.7 27.0 1.0
OG E:SER141 3.8 18.9 1.0
OD2 E:ASP144 3.8 24.0 1.0
OP2 T:A1 3.8 60.2 1.0
OE2 E:GLU51 3.9 27.4 1.0
OG1 E:THR8 4.3 25.1 1.0
CB E:GLU143 4.3 6.1 1.0
O5' T:A1 4.4 60.2 1.0
OP1 T:A1 4.5 60.8 1.0
N E:ASP144 4.7 12.2 1.0
OD2 E:ASP7 4.7 23.6 1.0
OD1 E:ASP7 4.8 28.4 1.0
CD E:GLU51 4.8 27.9 1.0
CB E:ASP144 4.9 15.9 1.0
CB E:SER141 4.9 18.7 1.0
OE1 E:GLU51 4.9 29.0 1.0

Magnesium binding site 3 out of 5 in 8kda

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Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1001

b:36.6
occ:1.00
 OD1 F:ASP144 2.1 26.1 1.0
CG F:ASP144 3.0 25.2 1.0
OD2 F:ASP144 3.3 32.9 1.0
O3' M:A0 3.7 46.2 1.0
OD2 F:ASP7 3.8 27.4 1.0
OD1 F:ASP7 3.9 27.9 1.0
OG F:SER141 4.1 14.4 1.0
CG F:ASP7 4.3 30.8 1.0
CB F:ASP144 4.3 16.8 1.0
OP1 M:A1 4.4 92.6 1.0
N F:ASP144 4.5 19.6 1.0
CA F:ASP144 4.5 6.1 1.0
P M:A1 4.7 97.0 1.0
OE2 F:GLU51 4.8 32.0 1.0

Magnesium binding site 4 out of 5 in 8kda

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Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg201

b:56.1
occ:1.00
 CB G:GLU143 3.6 7.5 1.0
OD1 G:ASP144 3.9 26.9 1.0
CG2 G:THR8 4.0 21.8 1.0
OG G:SER141 4.1 27.7 1.0
CG G:GLU143 4.3 19.1 1.0
OD1 G:ASP7 4.4 31.6 1.0
OE2 G:GLU51 4.5 22.7 1.0
CG G:GLU51 4.7 18.4 1.0
CG G:ASP144 4.8 25.2 1.0
N G:ASP144 4.8 9.4 1.0
CG1 G:VAL48 4.8 15.4 1.0
CA G:GLU143 4.9 8.4 1.0
CD G:GLU51 4.9 30.3 1.0
C G:GLU143 4.9 20.8 1.0
OD2 G:ASP7 5.0 29.9 1.0
CD G:GLU143 5.0 27.8 1.0

Magnesium binding site 5 out of 5 in 8kda

Go back to Magnesium Binding Sites List in 8kda
Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg201

b:33.9
occ:1.00
 OG I:SER141 3.4 21.4 1.0
OE1 I:GLU51 3.4 26.5 1.0
OE2 I:GLU51 3.5 25.2 1.0
OD2 I:ASP144 3.8 21.4 1.0
CD I:GLU51 3.8 28.1 1.0
OD1 I:ASP144 4.0 28.0 1.0
CG I:ASP144 4.1 23.6 1.0
OP1 N:A1 4.2 68.8 1.0
OE1 I:GLU143 4.2 29.1 1.0
CB I:SER141 4.6 25.6 1.0
CB I:GLU143 4.7 6.2 1.0
OG1 I:THR8 4.9 23.8 1.0
OD1 I:ASP140 5.0 21.3 1.0
N I:ASP144 5.0 7.9 1.0

Reference:

T.Teramoto, T.Koyasu, T.Yokogawa, N.Adachi, K.Mayanagi, T.Nakamura, T.Senda, Y.Kakuta. Cryo-Em Structure of Hydrogenobacter Thermophilus Minimal Protein-Only Rnase P (Harp) in Complex with Pre-Trnas To Be Published.
Page generated: Fri Oct 4 14:37:29 2024

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