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Magnesium in PDB 2zm5: Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe)

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

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

Protein crystallography data

The structure of Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe), PDB code: 2zm5 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 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.200, 89.400, 150.800, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 27

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe) (pdb code 2zm5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe), PDB code: 2zm5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 2zm5

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Magnesium binding site 1 out of 7 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg77

b:25.8
occ:1.00
 OP1 C:G19 1.9 52.5 1.0
OP1 C:C17 2.2 38.5 1.0
P C:G19 3.2 46.9 1.0
O3' C:U16 3.4 38.1 1.0
P C:C17 3.4 39.9 1.0
OP2 C:G19 3.6 54.1 1.0
O3' C:G18 4.2 47.7 1.0
O5' C:G19 4.2 48.0 1.0
O2' C:U16 4.2 37.9 1.0
O5' C:C17 4.4 42.5 1.0
OP2 C:C17 4.4 41.1 1.0
C3' C:G18 4.6 47.4 1.0
C3' C:U16 4.7 36.8 1.0
C5 C:C17 4.8 43.9 1.0

Magnesium binding site 2 out of 7 in 2zm5

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Magnesium binding site 2 out of 7 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg78

b:33.5
occ:1.00
 O C:HOH101 2.4 42.0 1.0
N7 C:G27 2.7 42.3 1.0
O6 C:G27 2.7 45.7 1.0
C5 C:G27 3.3 41.7 1.0
C6 C:G27 3.3 41.7 1.0
O C:HOH111 3.3 43.0 1.0
C8 C:G27 3.9 42.3 1.0
OP2 C:A26 4.1 41.3 1.0
N7 C:A26 4.4 39.9 1.0
O6 C:G28 4.5 44.9 1.0
C4 C:G27 4.6 41.4 1.0
N1 C:G27 4.7 40.0 1.0
N7 C:G28 4.8 43.2 1.0
OP2 C:G27 4.8 41.4 1.0
C8 C:A26 4.8 40.1 1.0
N9 C:G27 4.9 41.0 1.0

Magnesium binding site 3 out of 7 in 2zm5

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Magnesium binding site 3 out of 7 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg79

b:31.8
occ:1.00
 OP1 C:A7 2.4 50.6 1.0
O C:HOH83 2.5 35.5 1.0
O4 C:U8 2.6 44.4 1.0
OP2 C:A14 2.6 49.0 1.0
O C:HOH106 2.8 43.4 1.0
C4 C:U8 3.5 42.7 1.0
P C:A7 3.8 48.2 1.0
P C:A14 3.9 51.0 1.0
C5 C:U8 4.1 41.2 1.0
N7 C:G15 4.3 37.6 1.0
O5' C:A14 4.3 49.7 1.0
O3' C:G6 4.3 50.5 1.0
OP2 C:A7 4.4 50.7 1.0
C5' C:A14 4.5 48.5 1.0
N3 C:U8 4.5 40.4 1.0
OP2 C:G15 4.6 45.5 1.0
OP1 C:A14 4.6 53.9 1.0
O C:HOH130 4.8 42.8 1.0
O6 C:G15 5.0 36.5 1.0
O5' C:A7 5.0 47.6 1.0

Magnesium binding site 4 out of 7 in 2zm5

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Magnesium binding site 4 out of 7 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg80

b:45.9
occ:1.00
 OP1 C:U60 2.3 40.3 1.0
P C:U60 3.6 41.6 1.0
O3' C:U59 3.7 43.8 1.0
O4 C:U50 3.9 61.3 1.0
O4 C:U51 4.1 56.8 1.0
C5' C:U60 4.3 45.3 1.0
O5' C:U60 4.4 43.4 1.0
N4 C:C62 4.4 64.3 1.0
OP2 C:U60 4.8 41.4 1.0
C4 C:U50 4.9 62.2 1.0

Magnesium binding site 5 out of 7 in 2zm5

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Magnesium binding site 5 out of 7 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg81

b:35.8
occ:1.00
 OP2 C:U59 2.2 50.7 1.0
O2' C:A58 2.6 53.9 1.0
C2' C:A58 3.3 49.4 1.0
P C:U59 3.7 47.8 1.0
C3' C:A58 4.0 50.4 1.0
OP2 C:U60 4.2 41.4 1.0
O3' C:A58 4.3 50.9 1.0
O5' C:U59 4.5 48.0 1.0
O6 C:G52 4.5 67.0 1.0
C5' C:U59 4.6 44.4 1.0
O6 C:G53 4.7 54.2 1.0
OP1 C:U59 4.7 50.2 1.0
C1' C:A58 4.8 51.0 1.0
O4 C:U51 5.0 56.8 1.0

Magnesium binding site 6 out of 7 in 2zm5

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Magnesium binding site 6 out of 7 in the Crystal Structure of Trna Modification Enzyme Miaa in the Complex with Trna(Phe)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg82

b:49.1
occ:1.00
 OP2 C:G22 2.4 59.7 1.0
O6 C:G46 2.5 52.1 1.0
C6 C:G46 3.5 51.6 1.0
OP2 C:U45 3.6 82.6 1.0
O2' C:G44 3.8 72.8 1.0
P C:G22 3.9 63.8 1.0
C5 C:G46 4.2 54.2 1.0
N7 C:G46 4.3 55.0 1.0
O5' C:U45 4.4 84.5 1.0
O5' C:G22 4.6 60.6 1.0
N1 C:G46 4.6 50.8 1.0
C3' C:A21 4.6 57.6 1.0
P C:U45 4.6 84.0 1.0
N1 C:A9 4.7 38.8 1.0
OP1 C:G22 4.8 63.8 1.0
C2' C:G44 4.8 70.2 1.0
C2' C:A21 4.8 54.8 1.0
O3' C:A21 4.8 61.1 1.0
C2 C:A9 4.8 38.5 1.0
C8 C:G22 4.9 42.5 1.0

Magnesium binding site 7 out of 7 in 2zm5

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


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg77

b:41.8
occ:1.00
 O6 D:G27 2.2 52.7 1.0
N7 D:G27 2.5 51.3 1.0
C6 D:G27 2.8 50.9 1.0
O D:HOH89 2.8 61.1 1.0
C5 D:G27 2.9 50.7 1.0
C8 D:G27 3.7 51.4 1.0
OP2 D:A26 3.9 56.2 1.0
N7 D:A26 4.1 45.8 1.0
N1 D:G27 4.2 50.5 1.0
OP2 D:G27 4.3 57.0 1.0
C4 D:G27 4.3 50.9 1.0
C8 D:A26 4.4 45.0 1.0
N9 D:G27 4.6 51.2 1.0
O6 D:G28 4.8 56.7 1.0
O5' D:A26 4.9 52.8 1.0
C5 D:A26 4.9 43.3 1.0
N7 D:G28 4.9 57.9 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 07:54:38 2024

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