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Magnesium in PDB 3eph: Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism

Enzymatic activity of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism

All present enzymatic activity of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism:
2.5.1.8;

Protein crystallography data

The structure of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism, PDB code: 3eph was solved by R.H.Huang, C.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 162.463, 211.596, 125.518, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.6

Other elements in 3eph:

The structure of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism (pdb code 3eph). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism, PDB code: 3eph:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3eph

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Magnesium binding site 1 out of 10 in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:47.0
occ:1.00
 O32 A:PPV422 2.0 94.4 1.0
O31 A:PPV422 2.2 95.0 1.0
OG A:SER28 2.5 64.7 1.0
P2 A:PPV422 3.1 94.3 1.0
OPP A:PPV422 3.2 95.7 1.0
P1 A:PPV422 3.3 96.5 1.0
NE2 A:GLN49 3.7 76.3 1.0
CB A:SER28 3.8 67.6 1.0
O21 A:PPV422 4.0 96.8 1.0
O A:HOH489 4.0 56.0 1.0
O12 A:PPV422 4.2 94.9 1.0
ND2 A:ASN59 4.2 77.5 1.0
O A:ASN59 4.2 77.4 1.0
O22 A:PPV422 4.3 93.9 1.0
O A:HOH427 4.3 44.6 1.0
N A:SER28 4.4 66.8 1.0
O11 A:PPV422 4.5 94.9 1.0
CA A:SER28 4.7 67.3 1.0
CD A:GLN49 4.7 76.5 1.0
OE1 A:GLN49 4.8 77.2 1.0

Magnesium binding site 2 out of 10 in 3eph

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Magnesium binding site 2 out of 10 in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4

b:64.4
occ:1.00
 O A:HOH481 2.6 31.9 1.0
NZ A:LYS298 3.7 44.0 1.0
CE A:LYS294 3.8 53.3 1.0
CB A:LYS294 3.8 57.9 1.0
OP2 E:C28 3.9 59.6 1.0
CE A:LYS298 4.3 43.4 1.0
CD A:LYS294 4.4 54.7 1.0
CG A:LYS294 4.7 58.1 1.0
NZ A:LYS294 4.7 50.0 1.0
O A:GLN291 4.7 69.9 1.0
OP2 E:A29 4.8 59.3 1.0
N A:ARG295 4.9 60.5 1.0
CD A:LYS298 4.9 42.1 1.0
C A:LYS294 5.0 60.6 1.0
CG A:ARG295 5.0 64.8 1.0

Magnesium binding site 3 out of 10 in 3eph

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Magnesium binding site 3 out of 10 in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg6

b:74.7
occ:1.00
 OE1 A:GLN29 2.2 90.2 1.0
CD A:GLN29 3.3 87.6 1.0
O A:HOH487 3.4 63.9 1.0
O A:HOH488 3.5 59.8 1.0
O A:HOH425 3.9 46.0 1.0
CG A:GLN29 4.1 81.2 1.0
CE2 A:TRP323 4.1 59.5 1.0
NE1 A:TRP323 4.2 61.1 1.0
CD2 A:TRP323 4.2 60.3 1.0
CD1 A:TRP323 4.3 64.1 1.0
CG A:TRP323 4.3 63.9 1.0
NE2 A:GLN29 4.4 88.6 1.0
CZ2 A:TRP323 4.6 58.3 1.0
CE3 A:TRP323 4.7 58.8 1.0
CB A:GLN29 4.8 74.3 1.0

Magnesium binding site 4 out of 10 in 3eph

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Magnesium binding site 4 out of 10 in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7

b:95.0
occ:1.00
 O A:HOH449 2.4 82.6 1.0
CD2 A:TRP79 3.4 79.1 1.0
CG A:TRP79 3.5 79.2 1.0
CE2 A:TRP79 3.6 80.5 1.0
CD1 A:TRP79 3.7 81.0 1.0
NE1 A:TRP79 3.7 81.4 1.0
CE3 A:TRP79 3.9 79.0 1.0
CB A:TRP79 4.1 79.0 1.0
CE1 A:TYR239 4.2 90.5 1.0
CZ2 A:TRP79 4.2 80.5 1.0
OD1 A:ASP78 4.4 89.1 1.0
CD1 A:TYR239 4.5 91.6 1.0
N A:TRP79 4.5 81.4 1.0
CZ3 A:TRP79 4.5 80.0 1.0
CH2 A:TRP79 4.6 80.0 1.0
OD2 A:ASP53 4.7 96.0 1.0
CB A:LYS52 4.8 85.4 1.0
CA A:TRP79 5.0 80.0 1.0
CG A:ASP78 5.0 89.0 1.0
CD A:LYS52 5.0 84.0 1.0

Magnesium binding site 5 out of 10 in 3eph

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Magnesium binding site 5 out of 10 in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg72

b:71.2
occ:1.00
 OP2 E:G12 2.3 0.1 1.0
P E:G12 3.5 0.3 1.0
O5' E:G12 3.6 96.4 1.0
C8 E:G12 3.8 83.0 1.0
N7 E:G12 3.8 81.6 1.0
OP2 E:C13 4.5 96.0 1.0
OP1 E:G12 4.5 100.0 1.0
O3' E:C11 4.6 98.3 1.0
C3' E:C11 4.6 94.7 1.0
C5 E:C13 4.7 83.5 1.0
OP2 E:G9 4.8 99.4 1.0
N9 E:G12 4.9 84.5 1.0
C5' E:G12 5.0 92.8 1.0
C5 E:G12 5.0 82.3 1.0

Magnesium binding site 6 out of 10 in 3eph

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Magnesium binding site 6 out of 10 in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg73

b:76.7
occ:1.00
 O E:HOH104 2.7 65.1 1.0
O E:HOH116 3.1 62.2 1.0
OP1 E:G57 4.1 87.5 1.0
OP2 E:G57 4.2 87.2 1.0
C5 E:U55 4.2 84.7 1.0
OP2 E:U55 4.4 91.7 1.0
P E:G57 4.6 88.1 1.0
C6 E:U55 4.6 85.0 1.0
OP2 E:C56 4.8 84.3 1.0
OP2 E:U54 4.8 0.7 1.0
C4 E:U55 5.0 85.8 1.0

Magnesium binding site 7 out of 10 in 3eph

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Magnesium binding site 7 out of 10 in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2

b:50.0
occ:1.00
 OG B:SER28 2.0 67.3 1.0
O21 B:PPV422 2.1 92.5 1.0
O B:HOH481 2.2 64.0 1.0
O32 B:PPV422 2.3 92.6 1.0
O B:HOH504 2.5 49.6 1.0
O B:HOH482 3.3 58.8 1.0
CB B:SER28 3.4 66.2 1.0
P2 B:PPV422 3.4 93.2 1.0
P1 B:PPV422 3.5 93.9 1.0
OPP B:PPV422 3.6 93.9 1.0
O B:HOH428 3.8 54.6 1.0
N B:SER28 4.0 67.4 1.0
NE2 B:GLN49 4.0 74.4 1.0
O B:HOH522 4.1 88.3 1.0
O11 B:PPV422 4.1 91.9 1.0
CA B:SER28 4.2 66.7 1.0
O12 B:PPV422 4.4 92.4 1.0
O B:HOH427 4.5 44.0 1.0
O B:ASN59 4.5 75.5 1.0
ND2 B:ASN59 4.5 76.6 1.0
O22 B:PPV422 4.6 92.2 1.0
O31 B:PPV422 4.7 92.8 1.0
OE1 B:GLN49 4.9 72.5 1.0
CD B:GLN49 4.9 73.3 1.0
CB B:LYS27 5.0 62.8 1.0

Magnesium binding site 8 out of 10 in 3eph

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Magnesium binding site 8 out of 10 in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4

b:68.9
occ:1.00
 OE1 B:GLN29 2.7 79.6 1.0
CD B:GLN29 3.9 78.7 1.0
CG B:TRP323 4.6 68.8 1.0
CD2 B:TRP323 4.6 67.8 1.0
CG B:GLN29 4.6 75.2 1.0
CD1 B:TRP323 4.6 67.1 1.0
CE2 B:TRP323 4.6 67.1 1.0
NE1 B:TRP323 4.6 65.4 1.0
NE2 B:GLN29 4.9 79.1 1.0
CD2 B:LEU320 5.0 61.4 1.0

Magnesium binding site 9 out of 10 in 3eph

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Magnesium binding site 9 out of 10 in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5

b:69.2
occ:1.00
 O B:HOH458 2.5 62.7 1.0
O B:HOH486 2.8 67.1 1.0
OD1 B:ASP78 4.0 87.4 1.0
CE1 B:TYR239 4.1 90.8 1.0
CD2 B:TRP79 4.2 79.0 1.0
CG B:TRP79 4.2 78.8 1.0
CD1 B:TRP79 4.4 79.3 1.0
CE2 B:TRP79 4.4 79.8 1.0
CD1 B:TYR239 4.5 92.7 1.0
CB B:TRP79 4.5 77.8 1.0
NE1 B:TRP79 4.6 80.8 1.0
CE3 B:TRP79 4.6 78.3 1.0
CG B:ASP78 4.6 87.5 1.0
N B:TRP79 4.7 79.9 1.0
OD2 B:ASP78 4.8 88.4 1.0
CD B:LYS52 5.0 87.4 1.0

Magnesium binding site 10 out of 10 in 3eph

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Magnesium binding site 10 out of 10 in the Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg72

b:92.3
occ:1.00
 O6 F:G53 3.5 0.5 1.0
N7 F:G53 3.7 0.4 1.0
O4 F:U54 4.1 0.0 1.0
C6 F:G53 4.2 0.4 1.0
C5 F:G53 4.3 0.8 1.0
O5' F:A58 4.6 0.4 1.0
C8 F:G53 4.8 0.8 1.0

Reference:

C.Zhou, R.H.Huang. Crystallographic Snapshots of Eukaryotic Dimethylallyltransferase Acting on Trna: Insight Into Trna Recognition and Reaction Mechanism. Proc.Natl.Acad.Sci.Usa V. 105 16142 2008.
ISSN: ISSN 0027-8424
PubMed: 18852462
DOI: 10.1073/PNAS.0805680105
Page generated: Wed Aug 14 13:08:58 2024

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