Atomistry » Magnesium » PDB 1e9b-1enn » 1ehz
Atomistry »
  Magnesium »
    PDB 1e9b-1enn »
      1ehz »

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

Go back to Magnesium Binding Sites List in 1ehz
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

Go back to Magnesium Binding Sites List in 1ehz
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

Go back to Magnesium Binding Sites List in 1ehz
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

Go back to Magnesium Binding Sites List in 1ehz
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

Go back to Magnesium Binding Sites List in 1ehz
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

Go back to Magnesium Binding Sites List in 1ehz
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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy