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Magnesium in PDB 1evv: Crystal Structure of Yeast Phenylalanine Transfer Rna at 2.0 A Resolution

Protein crystallography data

The structure of Crystal Structure of Yeast Phenylalanine Transfer Rna at 2.0 A Resolution, PDB code: 1evv was solved by L.Jovine, S.Djordjevic, D.Rhodes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.79 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.252, 32.988, 61.882, 90.00, 90.38, 90.00
R / Rfree (%) 22.7 / 26.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Yeast Phenylalanine Transfer Rna at 2.0 A Resolution (pdb code 1evv). 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 Yeast Phenylalanine Transfer Rna at 2.0 A Resolution, PDB code: 1evv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 1evv

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Magnesium binding site 1 out of 10 in the Crystal Structure of Yeast Phenylalanine Transfer Rna at 2.0 A Resolution


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 Yeast Phenylalanine Transfer Rna at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:51.4
occ:1.00
 O A:HOH985 2.5 33.2 0.9
O A:HOH986 2.6 50.2 1.0
O A:HOH988 2.7 32.1 0.7
O A:HOH987 2.8 49.3 1.0
OP2 A:U12 3.0 47.0 1.0
C5 A:U12 3.9 44.5 1.0
P A:U12 4.3 46.1 1.0
C6 A:U12 4.3 43.1 1.0
OP2 A:U8 4.3 34.6 1.0
O5' A:U12 4.4 52.5 1.0
OP2 A:C11 4.6 43.5 1.0
C5 A:C13 4.6 31.8 1.0
O A:HOH989 4.7 41.1 0.9
OP2 A:A9 4.7 27.3 1.0
C3' A:C11 4.8 46.3 1.0
O5' A:C11 4.8 46.4 1.0
C4 A:U12 4.9 46.0 1.0

Magnesium binding site 2 out of 10 in 1evv

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Magnesium binding site 2 out of 10 in the Crystal Structure of Yeast Phenylalanine Transfer Rna at 2.0 A Resolution


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 Yeast Phenylalanine Transfer Rna at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:48.7
occ:0.94
 OP1 A:G20 1.9 37.9 1.0
O A:HOH1105 1.9 48.1 1.0
OP2 A:A21 2.0 32.4 1.0
O A:HOH1114 2.2 38.0 0.8
P A:G20 3.1 34.1 1.0
P A:A21 3.4 35.5 1.0
OP2 A:G20 3.6 31.1 1.0
O5' A:G20 3.7 35.0 1.0
O A:HOH1123 3.9 71.1 1.0
C5' A:G20 4.1 31.7 1.0
OP1 A:A21 4.1 39.1 1.0
O3' A:G20 4.3 33.5 1.0
O3' A:G19 4.4 31.5 1.0
O A:HOH1122 4.5 59.1 1.0
O5' A:A21 4.6 37.9 1.0
C3' A:G20 4.6 34.0 1.0
C5' A:A21 4.7 33.0 1.0
C4' A:G20 4.9 33.1 1.0

Magnesium binding site 3 out of 10 in 1evv

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Magnesium binding site 3 out of 10 in the Crystal Structure of Yeast Phenylalanine Transfer Rna at 2.0 A Resolution


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 Yeast Phenylalanine Transfer Rna at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:29.6
occ:1.00
 O A:HOH918 1.8 38.3 1.0
O A:HOH922 1.9 31.7 0.9
OP1 A:G19 2.0 32.3 1.0
O A:HOH920 2.1 26.2 0.8
O A:HOH921 2.1 34.2 0.9
O A:HOH919 2.2 31.7 1.0
P A:G19 3.3 30.8 1.0
OP2 A:G19 3.7 37.4 1.0
O5' A:G19 3.9 29.5 1.0
O4 A:U59 3.9 36.2 1.0
N4 A:C60 4.0 37.8 1.0
C5' A:G19 4.2 34.5 1.0
N7 A:G20 4.2 25.4 1.0
O6 A:G20 4.3 27.2 1.0
N3 A:C60 4.3 33.9 1.0
O A:HOH1021 4.3 35.4 0.9
O3' A:G18 4.6 31.9 1.0
C4 A:C60 4.7 35.6 1.0
C4 A:U59 4.9 36.6 1.0

Magnesium binding site 4 out of 10 in 1evv

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Magnesium binding site 4 out of 10 in the Crystal Structure of Yeast Phenylalanine Transfer Rna at 2.0 A Resolution


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 Yeast Phenylalanine Transfer Rna at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg904

b:44.5
occ:1.00
 O A:HOH938 1.8 50.6 1.0
O A:HOH937 1.9 36.8 1.0
O A:HOH939 2.0 38.3 0.9
O A:HOH941 2.0 57.0 1.0
O A:HOH940 2.1 40.7 1.0
O A:HOH936 2.1 50.8 1.0
O A:HOH974 3.7 45.7 0.9
O A:HOH929 4.1 48.0 1.0
O4 A:U41 4.2 51.9 1.0
OP2 A:C25 4.3 48.2 1.0
O6 A:G42 4.4 47.7 1.0
N7 A:G42 4.4 41.1 1.0
C4 A:U41 4.8 49.0 1.0
C5 A:U41 5.0 43.2 1.0

Magnesium binding site 5 out of 10 in 1evv

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Magnesium binding site 5 out of 10 in the Crystal Structure of Yeast Phenylalanine Transfer Rna at 2.0 A Resolution


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 Yeast Phenylalanine Transfer Rna at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg905

b:60.7
occ:0.84
 OP1 A:C11 2.0 39.6 1.0
P A:C11 2.3 43.2 1.0
OP2 A:C11 2.3 43.5 1.0
O3' A:2MG10 2.9 41.8 1.0
O A:HOH977 3.0 44.6 1.0
O A:HOH1034 3.1 70.6 1.0
O5' A:C11 3.8 46.4 1.0
C3' A:2MG10 3.9 40.0 1.0
O A:HOH1045 3.9 67.5 1.0
C5' A:2MG10 4.2 39.6 1.0
C4' A:2MG10 4.4 37.1 1.0
O A:HOH987 4.5 49.3 1.0
O A:HOH985 4.6 33.2 0.9
C5' A:C11 4.6 48.1 1.0
O5' A:2MG10 4.8 30.1 1.0

Magnesium binding site 6 out of 10 in 1evv

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Magnesium binding site 6 out of 10 in the Crystal Structure of Yeast Phenylalanine Transfer Rna at 2.0 A Resolution


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 Yeast Phenylalanine Transfer Rna at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg906

b:89.4
occ:1.00
 OP1 A:A36 1.8 0.9 1.0
P A:A36 2.8 0.1 1.0
O3' A:A35 2.8 0.4 1.0
OP2 A:A36 3.8 0.1 1.0
O5' A:A36 3.9 0.2 1.0
C5' A:A36 4.0 1.0 1.0
C3' A:A35 4.2 97.0 1.0
O5' A:A35 4.4 99.0 1.0
C4' A:A35 4.6 96.8 1.0
O A:HOH932 4.8 55.1 0.8
O2' A:A35 4.9 95.4 1.0

Magnesium binding site 7 out of 10 in 1evv

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Magnesium binding site 7 out of 10 in the Crystal Structure of Yeast Phenylalanine Transfer Rna at 2.0 A Resolution


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 Yeast Phenylalanine Transfer Rna at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg907

b:32.5
occ:0.32
 O A:HOH971 2.1 55.4 1.0
OP2 A:G43 2.2 49.0 1.0
P A:G43 3.5 52.5 1.0
O5' A:G42 4.0 52.9 1.0
O A:HOH1075 4.1 61.1 0.9
O A:HOH1033 4.1 50.2 1.0
O A:HOH1032 4.1 66.4 1.0
C3' A:G42 4.1 49.7 1.0
O3' A:G42 4.2 53.9 1.0
OP1 A:G43 4.2 55.4 1.0
O5' A:G43 4.6 53.5 1.0
OP1 A:G42 4.7 62.2 1.0
P A:G42 4.7 58.3 1.0
OP2 A:G42 4.7 56.8 1.0
C5' A:G42 4.7 44.5 1.0

Magnesium binding site 8 out of 10 in 1evv

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Magnesium binding site 8 out of 10 in the Crystal Structure of Yeast Phenylalanine Transfer Rna at 2.0 A Resolution


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 Yeast Phenylalanine Transfer Rna at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg908

b:69.3
occ:0.66
 O3' A:G71 2.0 68.2 1.0
P A:C72 2.2 69.8 1.0
OP2 A:C72 2.3 72.6 1.0
OP1 A:C72 2.5 73.8 1.0
C3' A:G71 3.1 64.3 1.0
O5' A:C72 3.7 70.3 1.0
C4' A:G71 3.7 60.4 1.0
C5' A:G71 3.8 57.1 1.0
C2' A:G71 4.3 63.7 1.0
O5' A:G71 4.3 53.5 1.0
O A:HOH1103 4.4 66.9 1.0
C5' A:C72 4.6 69.3 1.0
O2' A:G71 4.7 65.0 1.0

Magnesium binding site 9 out of 10 in 1evv

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Magnesium binding site 9 out of 10 in the Crystal Structure of Yeast Phenylalanine Transfer Rna at 2.0 A Resolution


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 Yeast Phenylalanine Transfer Rna at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg909

b:63.7
occ:0.53
 O A:HOH1062 2.1 81.9 1.0
O A:HOH1043 2.1 56.2 0.8
OP1 A:U52 2.2 42.9 1.0
P A:U52 3.5 45.2 1.0
O5' A:U52 3.9 39.9 1.0
C5' A:U52 4.1 44.3 1.0
OP2 A:U52 4.2 41.3 1.0
O A:HOH1044 4.3 44.2 0.6
O3' A:G51 4.7 43.6 1.0
OP2 A:G53 5.0 36.6 1.0

Magnesium binding site 10 out of 10 in 1evv

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Magnesium binding site 10 out of 10 in the Crystal Structure of Yeast Phenylalanine Transfer Rna at 2.0 A Resolution


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 Yeast Phenylalanine Transfer Rna at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg910

b:0.7
occ:0.77
 OP1 A:G30 1.8 69.7 1.0
P A:G30 3.1 68.3 1.0
O3' A:A29 3.6 66.4 1.0
OP2 A:G30 3.7 59.5 1.0
O5' A:G30 4.3 65.9 1.0
C5' A:G30 4.8 65.0 1.0
C3' A:A29 4.9 64.6 1.0

Reference:

L.Jovine, S.Djordjevic, D.Rhodes. The Crystal Structure of Yeast Phenylalanine Trna at 2.0 A Resolution: Cleavage By Mg(2+) in 15-Year Old Crystals. J.Mol.Biol. V. 301 401 2000.
ISSN: ISSN 0022-2836
PubMed: 10926517
DOI: 10.1006/JMBI.2000.3950
Page generated: Mon Dec 14 05:52:47 2020

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