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Magnesium in PDB 1l8v: Crystal Structure of A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia

Protein crystallography data

The structure of Crystal Structure of A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia, PDB code: 1l8v was solved by D.J.Battle, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.72 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.455, 129.918, 144.686, 90.00, 90.00, 90.00
R / Rfree (%) 29 / 29.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia (pdb code 1l8v). 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 A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia, PDB code: 1l8v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 1l8v

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Magnesium binding site 1 out of 10 in the Crystal Structure of A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia


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 A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:82.1
occ:1.00
 O6 A:G188 2.9 91.5 1.0
OP1 A:C166 3.4 78.3 1.0
OP2 A:C166 3.5 78.3 1.0
P A:C166 3.9 77.4 1.0
OP1 A:U168 3.9 81.0 1.0
C6 A:G188 4.0 89.8 1.0
OP2 A:U168 4.0 80.2 1.0
O3' A:U167 4.1 83.0 1.0
N7 A:G188 4.2 87.7 1.0
P A:U168 4.2 81.8 1.0
OP1 A:U182 4.2 74.0 1.0
C5 A:G188 4.5 88.8 1.0
C5' A:C165 4.5 75.8 1.0
O3' A:C165 4.6 76.0 1.0
OP1 A:C165 4.7 80.0 1.0
C5 A:U168 4.8 84.8 1.0
N7 A:A183 4.8 88.8 1.0

Magnesium binding site 2 out of 10 in 1l8v

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Magnesium binding site 2 out of 10 in the Crystal Structure of A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia


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 A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg307

b:70.0
occ:1.00
 OP1 A:A184 1.9 86.9 1.0
OP2 A:A187 2.1 86.8 1.0
OP1 A:A186 2.5 89.1 1.0
OP2 A:G188 2.9 89.5 1.0
OP2 A:A186 3.1 90.5 1.0
P A:A186 3.2 88.3 1.0
P A:A184 3.3 86.8 1.0
P A:A187 3.3 82.2 1.0
OP1 A:A187 3.7 82.2 1.0
O5' A:A184 4.0 86.4 1.0
O3' A:A183 4.2 87.3 1.0
P A:G188 4.2 93.0 1.0
OP2 A:A184 4.3 89.6 1.0
C4' A:U185 4.3 94.4 1.0
C5' A:U185 4.3 93.2 1.0
O5' A:A186 4.4 85.5 1.0
O3' A:A186 4.4 80.1 1.0
C3' A:A186 4.4 78.5 1.0
O3' A:U185 4.4 92.3 1.0
O5' A:A187 4.4 83.4 1.0
C5' A:A184 4.5 87.2 1.0
C5' A:A187 4.5 85.1 1.0
C5' A:A186 4.6 80.6 1.0
OP1 A:G188 4.7 94.7 1.0
C3' A:U185 4.9 94.5 1.0
OP1 A:A183 4.9 83.5 1.0

Magnesium binding site 3 out of 10 in 1l8v

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Magnesium binding site 3 out of 10 in the Crystal Structure of A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia


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 A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg308

b:78.4
occ:1.00
 OP2 A:A171 2.3 80.0 1.0
O2' A:U167 2.8 89.1 1.0
OP2 A:C165 3.6 84.5 1.0
P A:A171 3.7 78.1 1.0
O5' A:A171 4.1 78.5 1.0
N7 A:A171 4.1 91.2 1.0
C2' A:U167 4.2 84.8 1.0
C8 A:A171 4.2 87.5 1.0
O2 A:U167 4.3 84.5 1.0
OP1 A:A171 4.5 80.7 1.0
O3' A:C170 4.8 78.2 1.0
O3' A:U167 4.8 83.0 1.0
OP2 A:U168 4.8 80.2 1.0
C1' A:U167 4.9 84.2 1.0
OP2 A:C170 5.0 83.3 1.0
C3' A:C170 5.0 80.3 1.0

Magnesium binding site 4 out of 10 in 1l8v

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Magnesium binding site 4 out of 10 in the Crystal Structure of A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia


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 A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg309

b:86.2
occ:1.00
 OP2 A:A173 2.4 89.9 1.0
O A:HOH410 3.6 0.2 1.0
P A:A173 3.7 87.5 1.0
N7 A:G174 3.7 89.9 1.0
O6 A:G174 3.9 91.0 1.0
O5' A:A173 4.0 87.2 1.0
N7 A:A173 4.1 98.1 1.0
C8 A:A173 4.2 96.2 1.0
C5 A:G174 4.5 89.2 1.0
OP1 A:A173 4.6 87.6 1.0
C6 A:G174 4.6 89.8 1.0
O5' A:A172 4.8 81.3 1.0
O3' A:A172 4.8 84.2 1.0
C8 A:G174 4.8 88.7 1.0
C3' A:A172 4.8 82.8 1.0
O3' A:A171 4.8 80.7 1.0
O2' A:A171 4.9 84.6 1.0
O6 A:G175 4.9 89.8 1.0

Magnesium binding site 5 out of 10 in 1l8v

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Magnesium binding site 5 out of 10 in the Crystal Structure of A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia


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 A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg310

b:70.1
occ:1.00
 OP2 A:A184 2.4 89.6 1.0
OP2 A:A186 2.6 90.5 1.0
OP1 A:A183 2.9 83.5 1.0
O3' A:U185 3.0 92.3 1.0
P A:A186 3.4 88.3 1.0
P A:A183 3.6 82.2 1.0
O5' A:A183 3.7 84.2 1.0
P A:A184 3.7 86.8 1.0
OP2 A:A183 3.8 82.3 1.0
C8 A:A186 4.1 71.1 1.0
OP1 A:A184 4.1 86.9 1.0
O5' A:A186 4.2 85.5 1.0
C3' A:U185 4.2 94.5 1.0
O A:HOH404 4.2 0.8 1.0
N7 A:A186 4.2 70.7 1.0
OP1 A:A186 4.7 89.1 1.0
O5' A:A184 4.7 86.4 1.0
C3' A:A183 4.7 85.7 1.0
O3' A:A183 4.8 87.3 1.0
N3 A:A139 4.9 79.2 1.0
N7 A:A184 4.9 91.8 1.0
C5' A:A183 4.9 84.5 1.0

Magnesium binding site 6 out of 10 in 1l8v

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Magnesium binding site 6 out of 10 in the Crystal Structure of A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia


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 A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:76.3
occ:1.00
 OP1 B:A184 2.0 84.0 1.0
OP2 B:A187 2.0 94.7 1.0
OP1 B:A186 2.3 90.0 1.0
OP2 B:G188 3.0 0.7 1.0
OP2 B:A186 3.0 91.6 1.0
P B:A186 3.1 88.7 1.0
P B:A187 3.2 90.2 1.0
O B:HOH348 3.4 0.4 1.0
P B:A184 3.4 83.8 1.0
OP1 B:A187 3.5 92.4 1.0
O5' B:A184 4.1 84.7 1.0
O5' B:A186 4.1 89.4 1.0
C3' B:A186 4.2 84.1 1.0
O3' B:A186 4.2 87.5 1.0
C4' B:U185 4.3 98.5 1.0
O5' B:A187 4.3 90.4 1.0
O3' B:U185 4.3 96.0 1.0
O3' B:A183 4.3 82.8 1.0
C5' B:A186 4.3 86.4 1.0
C5' B:U185 4.3 97.7 1.0
OP2 B:A184 4.4 82.4 1.0
P B:G188 4.4 0.8 1.0
C5' B:A187 4.5 92.8 1.0
C5' B:A184 4.6 88.5 1.0
C4' B:A186 4.9 83.9 1.0
C3' B:U185 4.9 98.7 1.0
OP1 B:G188 4.9 0.3 1.0
OP1 B:A183 4.9 85.7 1.0

Magnesium binding site 7 out of 10 in 1l8v

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Magnesium binding site 7 out of 10 in the Crystal Structure of A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia


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 A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg311

b:60.6
occ:1.00
 OP2 B:A173 2.5 82.4 1.0
O B:HOH342 2.8 94.6 1.0
N7 B:G174 3.7 81.2 1.0
O6 B:G174 3.7 84.1 1.0
P B:A173 3.9 82.2 1.0
N7 B:A173 3.9 74.8 1.0
C8 B:A173 4.1 75.7 1.0
O5' B:A173 4.1 83.1 1.0
O B:HOH347 4.1 89.3 1.0
C6 B:G174 4.5 81.7 1.0
C5 B:G174 4.5 81.1 1.0
O3' B:A171 4.5 82.8 1.0
O2' B:A171 4.5 87.8 1.0
O5' B:A172 4.6 81.7 1.0
C3' B:A172 4.8 78.7 1.0
C8 B:G174 4.8 83.3 1.0
C5 B:A173 4.8 73.1 1.0
OP1 B:A173 4.9 80.7 1.0
O3' B:A172 4.9 79.6 1.0
O6 B:G175 4.9 80.3 1.0

Magnesium binding site 8 out of 10 in 1l8v

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Magnesium binding site 8 out of 10 in the Crystal Structure of A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia


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 A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg312

b:76.5
occ:1.00
 OP2 B:A184 2.4 82.4 1.0
OP2 B:A186 2.6 91.6 1.0
OP1 B:A183 2.8 85.7 1.0
O3' B:U185 3.1 96.0 1.0
P B:A183 3.5 83.1 1.0
P B:A186 3.5 88.7 1.0
O5' B:A183 3.6 82.3 1.0
OP2 B:A183 3.6 84.4 1.0
P B:A184 3.7 83.8 1.0
C8 B:A186 3.9 85.9 1.0
N7 B:A186 4.0 85.7 1.0
OP1 B:A184 4.1 84.0 1.0
O5' B:A186 4.3 89.4 1.0
C3' B:U185 4.3 98.7 1.0
C3' B:A183 4.7 83.4 1.0
O5' B:A184 4.7 84.7 1.0
O3' B:A183 4.7 82.8 1.0
OP1 B:A186 4.7 90.0 1.0
C5' B:A183 4.8 82.4 1.0
N7 B:A184 4.9 96.0 1.0
N3 B:A139 5.0 88.8 1.0
C8 B:A184 5.0 94.7 1.0

Magnesium binding site 9 out of 10 in 1l8v

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Magnesium binding site 9 out of 10 in the Crystal Structure of A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia


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 A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg313

b:81.5
occ:1.00
 O6 B:G188 2.4 96.4 1.0
C6 B:G188 3.4 95.3 1.0
OP1 B:C166 3.7 76.1 1.0
N7 B:G188 3.8 95.3 1.0
C5 B:G188 4.0 96.4 1.0
OP2 B:C166 4.0 78.4 1.0
OP1 B:U168 4.1 85.0 1.0
OP2 B:U168 4.2 82.2 1.0
OP1 B:U182 4.2 87.4 1.0
P B:C166 4.3 76.7 1.0
C5 B:U168 4.4 98.9 1.0
P B:U168 4.4 85.5 1.0
N7 B:A183 4.5 86.8 1.0
O3' B:U167 4.5 82.7 1.0
C8 B:A183 4.6 85.7 1.0
N1 B:G188 4.6 94.3 1.0
OP2 B:A183 4.8 84.4 1.0
C6 B:U168 4.9 99.0 1.0
OP1 B:C165 4.9 75.2 1.0
C5' B:C165 4.9 76.4 1.0
O3' B:C165 4.9 76.6 1.0

Magnesium binding site 10 out of 10 in 1l8v

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Magnesium binding site 10 out of 10 in the Crystal Structure of A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia


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 A Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron From Tetrahymena Thermophilia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg314

b:91.3
occ:1.00
 OP2 B:A171 2.4 79.7 1.0
O2' B:U167 2.8 84.0 1.0
N7 B:A171 3.7 82.3 1.0
P B:A171 3.8 78.9 1.0
OP2 B:C170 3.9 83.6 1.0
C8 B:A171 4.0 81.8 1.0
OP2 B:U168 4.2 82.2 1.0
OP1 B:C170 4.2 88.1 1.0
C2' B:U167 4.2 80.9 1.0
P B:C170 4.3 85.7 1.0
O5' B:C170 4.3 83.9 1.0
O5' B:A171 4.4 79.4 1.0
OP2 B:C165 4.5 83.8 1.0
C5' B:U168 4.5 93.3 1.0
O3' B:U167 4.5 82.7 1.0
O3' B:C170 4.6 78.6 1.0
C3' B:C170 4.6 78.8 1.0
O2 B:U167 4.6 81.1 1.0
C5 B:A171 4.8 80.4 1.0
C1' B:U167 4.9 79.6 1.0
OP1 B:A171 4.9 82.9 1.0
P B:U168 4.9 85.5 1.0
C5' B:C170 5.0 80.6 1.0

Reference:

D.J.Battle, J.A.Doudna. Specificity of Rna-Rna Helix Recognition Proc.Natl.Acad.Sci.Usa V. 99 11676 2002.
ISSN: ISSN 0027-8424
PubMed: 12189204
DOI: 10.1073/PNAS.182221799
Page generated: Tue Aug 13 08:27:51 2024

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