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Magnesium in PDB 2zxu: Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp

Enzymatic activity of Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp

All present enzymatic activity of Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp:
2.5.1.8;

Protein crystallography data

The structure of Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp, PDB code: 2zxu was solved by J.Sakai, M.Yao, S.Chimnaronk, I.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.300, 90.000, 150.500, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 28.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp (pdb code 2zxu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp, PDB code: 2zxu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 2zxu

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Magnesium binding site 1 out of 10 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp


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 Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg318

b:52.3
occ:1.00
 OG1 A:THR24 2.1 36.0 1.0
O7 A:DST317 2.1 52.8 1.0
O5 A:DST317 2.3 47.5 1.0
CB A:THR24 3.4 34.6 1.0
P3 A:DST317 3.5 51.9 1.0
P1 A:DST317 3.6 45.0 1.0
O A:ALA55 3.9 20.1 1.0
O2 A:DST317 3.9 49.0 1.0
O4 A:DST317 4.2 45.7 1.0
CG2 A:THR24 4.2 34.7 1.0
O8 A:DST317 4.3 51.6 1.0
N A:THR24 4.3 31.6 1.0
CA A:THR24 4.4 32.9 1.0
O A:HOH366 4.7 31.9 1.0
O6 A:DST317 4.7 44.4 1.0
O A:HOH371 4.9 37.1 1.0
NZ A:LYS23 4.9 35.1 1.0
C A:ALA55 4.9 17.6 1.0
S9 A:DST317 5.0 56.7 1.0
NH2 A:ARG217 5.0 51.0 1.0
CD1 A:LEU45 5.0 15.0 1.0
CB A:ALA55 5.0 18.0 1.0

Magnesium binding site 2 out of 10 in 2zxu

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Magnesium binding site 2 out of 10 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp


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 Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg318

b:63.9
occ:1.00
 O7 B:DST317 2.0 82.5 1.0
O5 B:DST317 2.0 75.2 1.0
OG1 B:THR24 2.1 36.4 1.0
P3 B:DST317 3.3 81.5 1.0
CB B:THR24 3.4 33.7 1.0
P1 B:DST317 3.4 73.5 1.0
O B:ALA55 3.7 21.1 1.0
O2 B:DST317 3.7 78.1 1.0
O8 B:DST317 4.1 81.0 1.0
CG2 B:THR24 4.1 33.1 1.0
O6 B:DST317 4.3 74.0 1.0
N B:THR24 4.3 31.9 1.0
O4 B:DST317 4.4 74.0 1.0
CA B:THR24 4.4 33.5 1.0
CB B:ALA55 4.8 20.6 1.0
C B:ALA55 4.8 20.8 1.0
S9 B:DST317 4.9 83.2 1.0
CG B:LYS23 5.0 30.7 1.0

Magnesium binding site 3 out of 10 in 2zxu

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Magnesium binding site 3 out of 10 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp


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 Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg77

b:10.0
occ:1.00
 OP1 C:G19 2.1 31.3 1.0
OP1 C:C17 2.4 23.2 1.0
P C:G19 3.3 26.4 1.0
O3' C:U16 3.4 19.5 1.0
P C:C17 3.5 22.0 1.0
OP2 C:G19 3.7 32.6 1.0
O2' C:U16 4.3 20.8 1.0
O5' C:G19 4.3 30.1 1.0
O3' C:G18 4.4 29.2 1.0
O5' C:C17 4.5 25.8 1.0
OP2 C:C17 4.7 23.9 1.0
C3' C:G18 4.7 28.7 1.0
C5 C:C17 4.7 26.7 1.0
C3' C:U16 4.8 18.9 1.0

Magnesium binding site 4 out of 10 in 2zxu

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Magnesium binding site 4 out of 10 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp


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 Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg78

b:16.7
occ:1.00
 N7 C:G27 2.5 24.2 1.0
O C:HOH108 2.5 22.2 1.0
O6 C:G27 2.6 25.2 1.0
C5 C:G27 3.1 23.0 1.0
C6 C:G27 3.1 21.7 1.0
O C:HOH110 3.6 20.0 1.0
C8 C:G27 3.7 23.7 1.0
O C:HOH109 4.0 25.8 1.0
OP2 C:A26 4.3 25.5 1.0
N7 C:A26 4.3 22.0 1.0
N7 C:G28 4.4 23.7 1.0
C4 C:G27 4.4 23.4 1.0
O C:HOH161 4.4 30.0 1.0
O6 C:G28 4.5 27.0 1.0
N1 C:G27 4.5 21.5 1.0
N9 C:G27 4.7 22.9 1.0
OP2 C:G27 4.7 21.6 1.0
C8 C:A26 4.8 20.4 1.0
N4 C:C43 4.9 24.4 1.0

Magnesium binding site 5 out of 10 in 2zxu

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Magnesium binding site 5 out of 10 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg79

b:23.2
occ:1.00
 O C:HOH112 2.0 22.6 1.0
OP1 C:A7 2.1 31.4 1.0
O4 C:U8 2.2 29.6 1.0
OP2 C:A14 2.5 25.8 1.0
O C:HOH113 2.6 20.6 1.0
C4 C:U8 3.2 29.0 1.0
P C:A7 3.5 29.3 1.0
O C:HOH147 3.8 23.5 1.0
C5 C:U8 3.8 26.3 1.0
P C:A14 3.9 27.9 1.0
O3' C:G6 4.2 32.1 1.0
OP2 C:A7 4.2 30.1 1.0
N3 C:U8 4.3 28.3 1.0
O5' C:A14 4.5 29.3 1.0
OP1 C:A14 4.6 31.9 1.0
O5' C:A7 4.6 30.1 1.0
N7 C:G15 4.6 23.2 1.0
C5' C:A14 4.8 30.1 1.0

Magnesium binding site 6 out of 10 in 2zxu

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Magnesium binding site 6 out of 10 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg80

b:29.6
occ:1.00
 OP1 C:U60 2.1 19.9 1.0
P C:U60 3.4 21.4 1.0
O3' C:U59 3.5 22.2 1.0
O4 C:U51 4.0 41.5 1.0
O4 C:U50 4.2 42.2 1.0
O5' C:U60 4.3 23.0 1.0
C5' C:U60 4.3 22.9 1.0
OP2 C:U60 4.5 17.3 1.0
N4 C:C62 4.5 39.0 1.0
C3' C:U59 4.9 20.5 1.0

Magnesium binding site 7 out of 10 in 2zxu

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Magnesium binding site 7 out of 10 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg81

b:29.1
occ:1.00
 OP2 C:U59 2.1 31.4 1.0
O2' C:A58 3.5 37.8 1.0
C2' C:A58 3.5 31.6 1.0
P C:U59 3.6 29.1 1.0
OP2 C:U60 4.1 17.3 1.0
C3' C:A58 4.1 31.9 1.0
O5' C:U59 4.2 26.3 1.0
C5' C:U59 4.3 23.3 1.0
O3' C:A58 4.4 32.9 1.0
O6 C:G52 4.6 48.4 1.0
OP1 C:U59 4.7 31.8 1.0
O6 C:G53 4.8 38.0 1.0
C1' C:A58 4.9 33.1 1.0
O4 C:U51 5.0 41.5 1.0

Magnesium binding site 8 out of 10 in 2zxu

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Magnesium binding site 8 out of 10 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg82

b:36.1
occ:1.00
 OP2 C:G22 2.2 42.5 1.0
O6 C:G46 2.3 34.1 1.0
O C:HOH195 2.5 40.3 1.0
C6 C:G46 3.2 33.8 1.0
OP2 C:U45 3.3 62.9 1.0
P C:G22 3.7 46.0 1.0
C5 C:G46 4.0 35.7 1.0
N7 C:G46 4.1 37.4 1.0
N1 C:G46 4.3 31.2 1.0
O5' C:G22 4.3 43.0 1.0
O2' C:G44 4.3 50.7 1.0
N1 C:A9 4.4 19.7 1.0
C3' C:A21 4.5 40.4 1.0
C2 C:A9 4.5 20.0 1.0
P C:U45 4.6 64.7 1.0
OP1 C:G22 4.6 43.6 1.0
O3' C:A21 4.6 43.3 1.0
C2' C:A21 4.6 38.2 1.0
C8 C:G22 4.7 23.8 1.0
O5' C:U45 4.7 65.2 1.0
C8 C:A21 4.8 25.9 1.0
C2' C:G44 4.9 47.8 1.0

Magnesium binding site 9 out of 10 in 2zxu

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Magnesium binding site 9 out of 10 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg83

b:32.0
occ:1.00
 OP2 C:U12 2.2 32.2 1.0
P C:U12 3.6 31.4 1.0
OP2 C:U8 3.9 27.2 1.0
OP1 C:U8 4.2 25.9 1.0
OP1 C:U12 4.2 29.1 1.0
O3' C:C11 4.3 28.0 1.0
OP2 C:C11 4.5 34.2 1.0
P C:U8 4.6 25.4 1.0
O5' C:C11 4.6 31.0 1.0
C3' C:C11 4.6 28.0 1.0
O5' C:U12 4.6 29.3 1.0
OP1 C:C11 4.7 34.6 1.0
OP1 C:A9 4.7 28.2 1.0
P C:C11 4.8 33.5 1.0
OP2 C:A9 4.9 26.5 1.0

Magnesium binding site 10 out of 10 in 2zxu

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Magnesium binding site 10 out of 10 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) and Dmaspp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg77

b:28.4
occ:1.00
 O6 D:G27 2.2 29.9 1.0
N7 D:G27 2.3 31.0 1.0
C6 D:G27 2.7 30.0 1.0
C5 D:G27 2.7 30.5 1.0
O D:HOH142 2.8 31.0 1.0
C8 D:G27 3.5 31.2 1.0
N7 D:A26 4.0 31.6 1.0
OP2 D:A26 4.0 33.2 1.0
C4 D:G27 4.1 30.7 1.0
N1 D:G27 4.1 29.2 1.0
N9 D:G27 4.5 30.1 1.0
C8 D:A26 4.5 30.7 1.0
OP2 D:G27 4.5 30.9 1.0
N7 D:G28 4.5 41.5 1.0
C5 D:A26 4.7 29.8 1.0
O6 D:G28 4.8 43.4 1.0

Reference:

S.Chimnaronk, F.Forouhar, J.Sakai, M.Yao, C.M.Tron, M.Atta, M.Fontecave, J.F.Hunt, I.Tanaka. Snapshots of Dynamics in Synthesizing N(6)-Isopentenyladenosine at the Trna Anticodon Biochemistry V. 48 5057 2009.
ISSN: ISSN 0006-2960
PubMed: 19435325
DOI: 10.1021/BI900337D
Page generated: Wed Aug 14 08:06:15 2024

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