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Magnesium in PDB 1f7y: The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability

Protein crystallography data

The structure of The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability, PDB code: 1f7y was solved by E.Ennifar, A.Nikouline, A.Serganov, S.Tishchenko, N.Nevskaya, M.Garber, B.Ehresmann, C.Ehresmann, S.Nikonov, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.80
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.800, 128.800, 65.100, 90.00, 90.00, 120.00
R / Rfree (%) 22.2 / 28.9

Other elements in 1f7y:

The structure of The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability also contains other interesting chemical elements:

Potassium (K) 1 atom
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability (pdb code 1f7y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability, PDB code: 1f7y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 1f7y

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Magnesium binding site 1 out of 9 in the The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability


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 Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:66.8
occ:1.00
 N7 B:G13 4.0 49.9 1.0
N7 B:G14 4.1 51.0 1.0
O B:HOH1031 4.3 81.1 1.0
C8 B:G13 4.6 38.1 1.0
C5 B:G13 4.6 37.4 1.0
MG B:MG1004 4.7 54.8 1.0
O6 B:G13 4.8 55.9 1.0
OP2 B:G14 4.8 59.8 1.0
C6 B:G13 4.9 42.2 1.0
C8 B:G14 4.9 51.3 1.0

Magnesium binding site 2 out of 9 in 1f7y

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Magnesium binding site 2 out of 9 in the The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability


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 Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:72.7
occ:1.00
 OP2 B:G26 3.6 67.4 1.0
N7 B:G25 4.3 49.8 1.0
N7 B:G26 4.3 58.6 1.0
C8 B:G25 4.5 39.5 1.0
C8 B:G26 4.7 55.4 1.0

Magnesium binding site 3 out of 9 in 1f7y

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Magnesium binding site 3 out of 9 in the The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability


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 Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:68.7
occ:0.98
 N7 B:G49 3.1 47.6 1.0
C4 B:C48 3.5 37.9 1.0
N4 B:C48 3.5 37.3 1.0
C5 B:C48 3.7 29.8 1.0
O6 B:G49 4.0 36.8 1.0
O B:HOH1014 4.0 47.2 1.0
C8 B:G49 4.0 36.3 1.0
N3 B:C48 4.1 27.6 1.0
C5 B:G49 4.1 41.8 1.0
C6 B:C48 4.3 29.8 1.0
C6 B:G49 4.4 44.8 1.0
OP2 B:C48 4.6 79.7 1.0
C2 B:C48 4.7 38.4 1.0
N1 B:C48 4.7 42.8 1.0
OP2 B:G49 4.9 41.6 1.0

Magnesium binding site 4 out of 9 in 1f7y

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Magnesium binding site 4 out of 9 in the The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability


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 Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1004

b:54.8
occ:1.00
 MG B:MG1001 4.7 66.8 1.0
OP1 B:G51 4.8 45.1 1.0
C3' B:G51 4.8 33.3 1.0

Magnesium binding site 5 out of 9 in 1f7y

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Magnesium binding site 5 out of 9 in the The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability


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 Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability within 5.0Å range:

Magnesium binding site 6 out of 9 in 1f7y

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Magnesium binding site 6 out of 9 in the The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability


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 Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1006

b:82.3
occ:1.00
 O4 B:U39 3.7 69.1 1.0
O B:HOH1023 3.7 67.0 1.0
C4 B:U39 3.8 61.9 1.0
C5 B:U39 4.2 53.7 1.0
N3 B:U39 4.2 51.1 1.0
N7 B:G40 4.2 36.8 1.0
O6 B:G40 4.4 50.3 1.0
C6 B:U39 4.8 49.6 1.0
C2 B:U39 4.9 53.3 1.0

Magnesium binding site 7 out of 9 in 1f7y

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Magnesium binding site 7 out of 9 in the The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1007

b:66.7
occ:0.97
 O B:HOH1022 4.8 39.5 0.9

Magnesium binding site 8 out of 9 in 1f7y

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Magnesium binding site 8 out of 9 in the The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1008

b:60.1
occ:0.97
 OP1 B:G21 3.6 50.9 1.0
OP2 B:G21 3.6 49.5 1.0
OP2 B:U42 3.9 24.7 1.0
P B:G21 4.0 49.0 1.0
OP1 B:C20 4.4 48.8 1.0
O3' B:C20 4.6 49.6 1.0
C5' B:C20 5.0 31.6 1.0

Magnesium binding site 9 out of 9 in 1f7y

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Magnesium binding site 9 out of 9 in the The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Crystal Structure of Two Uucg Loops Highlights the Role Played By 2'-Hydroxyl Groups in Its Unusual Stability within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1009

b:65.0
occ:1.00
 O2' B:A52 3.4 47.8 1.0
N1 B:G5 3.8 37.5 1.0
C2 B:G5 4.0 35.4 1.0
O B:HOH1017 4.1 69.6 0.9
C6 B:G5 4.2 40.2 1.0
O3' B:A52 4.3 48.8 1.0
N2 B:G5 4.3 33.2 1.0
OP2 B:C53 4.3 40.5 1.0
N3 B:G5 4.5 39.7 1.0
C2' B:A52 4.6 43.6 1.0
O6 B:G5 4.6 51.5 1.0
C5 B:G5 4.6 39.6 1.0
P B:C53 4.7 55.1 1.0
C4 B:G5 4.7 47.1 1.0
OP1 B:C53 4.8 61.2 1.0
C3' B:A52 4.8 40.6 1.0
N7 B:G6 4.9 38.5 1.0

Reference:

E.Ennifar, A.Nikulin, S.Tishchenko, A.Serganov, N.Nevskaya, M.Garber, B.Ehresmann, C.Ehresmann, S.Nikonov, P.Dumas. The Crystal Structure of Uucg Tetraloop. J.Mol.Biol. V. 304 35 2000.
ISSN: ISSN 0022-2836
PubMed: 11071808
DOI: 10.1006/JMBI.2000.4204
Page generated: Tue Aug 13 03:11:39 2024

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