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Magnesium in PDB 1ehz: The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution

Protein crystallography data

The structure of The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution, PDB code: 1ehz was solved by H.Shi, P.B.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.981, 33.389, 61.921, 90.00, 90.20, 90.00
R / Rfree (%) 23.3 / 25.3

Other elements in 1ehz:

The structure of The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution (pdb code 1ehz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution, PDB code: 1ehz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1ehz

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Magnesium binding site 1 out of 6 in the The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg590

b:65.4
occ:1.00
OP2 A:YYG37 2.5 99.2 1.0
N6 A:A38 3.0 80.4 1.0
N7 A:A38 3.1 82.6 1.0
N7 A:YYG37 3.3 89.9 1.0
C8 A:YYG37 3.5 89.8 1.0
O5' A:YYG37 3.7 97.0 1.0
P A:YYG37 3.7 99.0 1.0
C5 A:A38 3.8 82.7 1.0
C6 A:A38 3.8 81.7 1.0
O2 A:OMC32 4.2 63.7 1.0
O2 A:PSU39 4.2 75.8 1.0
C8 A:A38 4.3 83.8 1.0
C5 A:YYG37 4.4 89.9 1.0
OP2 A:A38 4.5 96.1 1.0
N9 A:YYG37 4.5 90.9 1.0
N1 A:A31 4.6 54.0 1.0
C3' A:A36 4.6 92.8 1.0
O3' A:A36 4.7 97.1 1.0
OP1 A:YYG37 4.8 99.3 1.0
C2' A:A36 4.8 91.1 1.0
C2 A:PSU39 4.9 75.6 1.0
N3 A:OMC32 4.9 62.0 1.0
C3' A:YYG37 5.0 94.7 1.0
C2 A:OMC32 5.0 63.9 1.0

Magnesium binding site 2 out of 6 in 1ehz

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Magnesium binding site 2 out of 6 in the The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg510

b:62.8
occ:1.00
O A:HOH713 2.0 62.4 1.0
O A:HOH712 2.0 61.1 1.0
O A:HOH714 2.0 62.2 1.0
O A:HOH715 2.0 63.7 1.0
O A:HOH716 2.0 64.7 1.0
O6 A:G3 3.9 53.3 1.0
O4 A:U69 4.0 37.6 1.0
O4 A:U68 4.3 38.5 1.0
O A:HOH626 4.4 57.7 1.0
O A:HOH707 4.6 56.9 1.0
N7 A:G3 4.6 63.0 1.0
O6 A:G4 4.7 42.5 1.0
C6 A:G3 4.8 55.6 1.0
N6 A:A5 4.9 32.7 1.0

Magnesium binding site 3 out of 6 in 1ehz

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Magnesium binding site 3 out of 6 in the The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg540

b:40.1
occ:1.00
O A:HOH723 2.0 42.8 1.0
O A:HOH722 2.0 42.3 1.0
O A:HOH724 2.0 43.7 1.0
OP1 A:G20 2.1 37.5 1.0
OP2 A:A21 2.1 35.5 1.0
P A:G20 3.4 37.6 1.0
P A:A21 3.5 36.0 1.0
O A:HOH602 4.1 57.4 1.0
OP1 A:A21 4.1 35.1 1.0
OP2 A:G20 4.1 34.9 1.0
O5' A:G20 4.2 35.3 1.0
C5' A:G20 4.2 34.8 1.0
O A:HOH152 4.4 44.5 1.0
O5' A:A21 4.4 34.6 1.0
O3' A:G20 4.4 32.1 1.0
O A:HOH166 4.5 45.1 1.0
O3' A:G19 4.5 33.8 1.0
C3' A:G20 4.9 34.5 1.0

Magnesium binding site 4 out of 6 in 1ehz

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Magnesium binding site 4 out of 6 in the The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg560

b:47.0
occ:1.00
O A:HOH728 2.0 43.7 1.0
O A:HOH730 2.0 46.3 1.0
O A:HOH727 2.0 44.7 1.0
O A:HOH726 2.0 41.9 1.0
O A:HOH725 2.0 43.5 1.0
O A:HOH729 2.0 41.7 1.0
OP2 A:U12 3.7 59.7 1.0
OP2 A:U8 3.7 38.7 1.0
OP1 A:U8 4.0 39.0 1.0
OP2 A:A9 4.1 31.3 1.0
O A:HOH206 4.1 53.1 1.0
O A:HOH226 4.2 34.0 1.0
OP2 A:C11 4.2 44.9 1.0
O A:HOH101 4.3 30.0 1.0
OP1 A:A9 4.3 36.5 1.0
P A:U8 4.4 36.8 1.0
O A:HOH139 4.5 49.2 1.0
C5 A:U12 4.6 40.1 1.0
P A:A9 4.8 32.0 1.0
O5' A:C11 4.9 49.6 1.0
P A:C11 4.9 50.8 1.0
O A:HOH141 4.9 37.3 1.0

Magnesium binding site 5 out of 6 in 1ehz

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Magnesium binding site 5 out of 6 in the The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg570

b:50.4
occ:1.00
O A:HOH735 2.0 47.0 1.0
O A:HOH736 2.0 47.7 1.0
O A:HOH731 2.0 50.2 1.0
O A:HOH734 2.0 48.1 1.0
O A:HOH733 2.0 51.5 1.0
O A:HOH732 2.0 49.4 1.0
O A:HOH196 3.7 46.2 1.0
O A:HOH690 4.0 58.3 1.0
O6 A:G42 4.1 41.5 1.0
O A:HOH148 4.3 52.8 1.0
OP2 A:C25 4.3 47.8 1.0
O A:HOH219 4.5 52.1 1.0
O4 A:U41 4.5 49.2 1.0
N7 A:G42 4.5 41.6 1.0
O A:HOH147 4.5 53.7 1.0
C4 A:U41 4.9 40.8 1.0
C6 A:G42 5.0 39.6 1.0
C5 A:U41 5.0 43.7 1.0

Magnesium binding site 6 out of 6 in 1ehz

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Magnesium binding site 6 out of 6 in the The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg580

b:61.7
occ:1.00
OP2 A:A14 1.9 54.4 1.0
O A:HOH737 2.0 46.5 1.0
OP1 A:U7 2.6 48.1 1.0
O A:HOH611 2.8 59.1 1.0
O A:HOH740 3.2 61.5 1.0
P A:A14 3.3 52.7 1.0
C3' A:C13 3.9 46.0 1.0
P A:U7 3.9 44.4 1.0
OP1 A:A14 4.0 56.8 1.0
O3' A:C13 4.0 49.1 1.0
O4 A:U8 4.0 32.6 1.0
O A:HOH141 4.0 37.3 1.0
O3' A:U6 4.1 45.8 1.0
O5' A:A14 4.4 52.4 1.0
O A:HOH742 4.5 61.0 1.0
C5 A:U8 4.6 29.6 1.0
C5' A:A14 4.6 44.6 1.0
C4 A:U8 4.6 27.4 1.0
O A:HOH738 4.6 58.5 1.0
C5' A:U7 4.7 37.9 1.0
C5' A:C13 4.7 46.6 1.0
O5' A:U7 4.8 40.9 1.0
MN A:MN550 4.8 56.5 1.0
C2' A:C13 4.9 42.8 1.0
C4' A:C13 4.9 43.5 1.0

Reference:

H.Shi, P.B.Moore. The Crystal Structure of Yeast Phenylalanine Trna at 1.93 A Resolution: A Classic Structure Revisited Rna V. 6 1091 2000.
ISSN: ISSN 1355-8382
PubMed: 10943889
DOI: 10.1017/S1355838200000364
Page generated: Mon Dec 14 05:52:08 2020

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