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Magnesium in PDB 6d8n: Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA

Protein crystallography data

The structure of Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA, PDB code: 6d8n was solved by G.M.Shoffner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.14 / 3.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.650, 130.880, 146.430, 90.00, 90.00, 90.00
R / Rfree (%) 24.6 / 26.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA (pdb code 6d8n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA, PDB code: 6d8n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6d8n

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Magnesium binding site 1 out of 9 in the Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:0.5
occ:1.00
 O4' A:A187 1.7 0.9 1.0
C1' A:A187 2.2 0.3 1.0
OP1 A:A184 2.3 0.5 1.0
OP1 A:A186 2.4 0.4 1.0
C4' A:A187 2.9 0.9 1.0
O3' A:A186 3.1 0.8 1.0
O2' A:A186 3.1 0.4 1.0
N9 A:A187 3.3 0.8 1.0
C2' A:A187 3.3 0.1 1.0
O2' A:A187 3.4 0.1 1.0
P A:A184 3.4 0.4 1.0
OP2 A:A184 3.7 0.8 1.0
C8 A:A187 3.7 0.3 1.0
C3' A:A187 3.8 0.0 1.0
P A:A186 3.8 0.9 1.0
C3' A:A186 3.8 0.3 1.0
C5' A:A187 3.9 0.4 1.0
C4' A:A186 4.0 0.1 1.0
C2' A:A186 4.0 0.4 1.0
O5' A:A187 4.1 0.4 1.0
C4' A:A185 4.1 0.1 1.0
P A:A187 4.2 0.6 1.0
O5' A:A183 4.3 0.9 1.0
OP1 A:A183 4.4 0.3 1.0
O5' A:A186 4.4 0.6 1.0
O3' A:A183 4.5 0.9 1.0
C4 A:A187 4.5 0.5 1.0
O5' A:A184 4.6 0.8 1.0
OP2 A:A186 4.6 0.7 1.0
OP1 A:A187 4.6 0.8 1.0
C5' A:A185 4.7 0.9 1.0
O4' A:A185 4.7 0.0 1.0
O3' A:A187 4.8 0.6 1.0
P A:A183 4.9 0.5 1.0
C5' A:A186 4.9 0.0 1.0
O3' A:A185 4.9 0.6 1.0
O3' A:U182 4.9 0.2 1.0
O4' A:A186 5.0 0.8 1.0
N7 A:A187 5.0 0.7 1.0

Magnesium binding site 2 out of 9 in 6d8n

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Magnesium binding site 2 out of 9 in the Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:0.9
occ:1.00
 O6 A:G189 2.5 0.2 1.0
OP2 A:U168 3.4 0.3 1.0
C6 A:G189 3.7 0.7 1.0
OP1 A:U168 3.8 0.0 1.0
OP1 A:C165 3.8 0.3 1.0
OP2 A:C166 4.1 0.6 1.0
P A:U168 4.1 0.3 1.0
OP1 A:C166 4.2 0.5 1.0
N7 A:A183 4.2 0.9 1.0
P A:C166 4.6 0.0 1.0
N1 A:G189 4.6 0.1 1.0
OP2 A:A183 4.6 0.4 1.0
OP1 A:U182 4.6 0.6 1.0
C8 A:A183 4.7 0.6 1.0
C5 A:G189 4.7 0.2 1.0
C5' A:C165 4.7 0.3 1.0
P A:C165 4.9 0.1 1.0
C5 A:U168 4.9 0.9 1.0
O5' A:C165 4.9 0.9 1.0
N7 A:G189 4.9 1.0 1.0

Magnesium binding site 3 out of 9 in 6d8n

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Magnesium binding site 3 out of 9 in the Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:0.6
occ:1.00
 O4' A:U182 3.1 0.2 1.0
OP1 A:A187 3.2 0.8 1.0
C4' A:U182 3.5 0.3 1.0
C1' A:U182 4.1 0.1 1.0
N2 A:G164 4.1 0.8 1.0
C5' A:U182 4.3 0.8 1.0
N3 A:G164 4.4 0.2 1.0
O2' A:G181 4.4 0.4 1.0
C5 A:A139 4.5 0.9 1.0
C6 A:A139 4.5 0.6 1.0
O3' A:U182 4.6 0.2 1.0
N2 A:G181 4.6 0.2 1.0
P A:A187 4.6 0.6 1.0
C3' A:U182 4.6 0.5 1.0
C2 A:G164 4.7 0.5 1.0
C4 A:A139 4.7 0.1 1.0
N7 A:A139 4.8 0.2 1.0
N1 A:A139 4.8 0.7 1.0
N3 A:G181 4.8 0.0 1.0
N1 A:U182 4.9 0.3 1.0
N6 A:A139 4.9 0.2 1.0
OP1 A:A183 5.0 0.3 1.0

Magnesium binding site 4 out of 9 in 6d8n

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Magnesium binding site 4 out of 9 in the Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:0.8
occ:1.00
 OP2 A:A171 2.2 0.8 1.0
P A:A171 3.0 0.1 1.0
OP1 A:A171 3.3 0.0 1.0
O3' A:C170 3.5 0.1 1.0
OP1 A:C170 3.8 0.9 1.0
C3' A:C170 4.0 0.5 1.0
O5' A:C170 4.1 0.7 1.0
P A:C170 4.3 0.0 1.0
OP2 A:U168 4.4 0.3 1.0
OP2 A:C170 4.5 0.3 1.0
O5' A:A171 4.5 0.9 1.0
C5' A:C170 4.5 0.9 1.0
C8 A:A171 4.5 0.3 1.0
N7 A:A171 4.8 0.2 1.0
C4' A:C170 4.8 1.0 1.0
O3' A:U167 4.9 0.6 1.0

Magnesium binding site 5 out of 9 in 6d8n

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Magnesium binding site 5 out of 9 in the Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:0.3
occ:1.00
 N4 B:C205 4.3 0.9 1.0
O4 B:U206 4.6 0.3 1.0
O6 B:G117 4.6 0.7 1.0
O6 B:G116 4.6 0.0 1.0
OP2 B:A114 4.8 0.6 1.0
N7 B:G116 5.0 0.7 1.0

Magnesium binding site 6 out of 9 in 6d8n

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Magnesium binding site 6 out of 9 in the Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:0.7
occ:1.00
 OP1 B:A183 2.2 0.8 1.0
OP2 B:A184 2.3 0.4 1.0
OP2 B:A186 2.5 0.2 1.0
P B:A183 3.3 0.9 1.0
P B:A186 3.5 0.8 1.0
OP2 B:A183 3.6 0.7 1.0
P B:A184 3.8 0.3 1.0
O5' B:A186 3.8 0.4 1.0
N3 B:A186 3.8 0.8 1.0
C2 B:A186 3.8 0.4 1.0
OP1 B:A186 3.9 0.6 1.0
O5' B:A183 4.2 0.6 1.0
O3' B:U182 4.5 0.9 1.0
C2 B:A139 4.5 0.6 1.0
C2' B:A186 4.5 0.1 1.0
OP1 B:A184 4.5 0.6 1.0
O3' B:A183 4.6 0.4 1.0
C3' B:A183 4.6 0.6 1.0
O5' B:A184 4.6 0.5 1.0
N3 B:A139 4.7 0.4 1.0
MG B:MG303 4.8 0.8 1.0
O2' B:A186 4.9 0.4 1.0
C3' B:A186 4.9 0.3 1.0
O3' B:A185 4.9 0.8 1.0
C5' B:A183 5.0 0.5 1.0

Magnesium binding site 7 out of 9 in 6d8n

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Magnesium binding site 7 out of 9 in the Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:0.8
occ:1.00
 O3' B:A186 1.7 0.6 1.0
C3' B:A186 2.1 0.3 1.0
OP1 B:A186 2.2 0.6 1.0
OP1 B:A184 2.4 0.6 1.0
P B:A187 3.2 0.6 1.0
C2' B:A186 3.2 0.1 1.0
C4' B:A186 3.4 0.5 1.0
O2' B:A186 3.4 0.4 1.0
P B:A184 3.4 0.3 1.0
P B:A186 3.5 0.8 1.0
OP2 B:A187 3.6 0.6 1.0
O5' B:A187 3.7 0.1 1.0
O5' B:A186 3.8 0.4 1.0
OP2 B:A184 3.8 0.4 1.0
C5' B:A186 4.0 0.7 1.0
O3' B:A183 4.0 0.4 1.0
OP2 B:A188 4.3 0.2 1.0
OP1 B:A187 4.3 0.3 1.0
OP1 B:A183 4.3 0.8 1.0
C1' B:A186 4.4 0.2 1.0
OP2 B:A186 4.5 0.2 1.0
O4' B:A186 4.5 0.5 1.0
O3' B:A185 4.6 0.8 1.0
O5' B:A184 4.8 0.5 1.0
MG B:MG302 4.8 0.7 1.0

Magnesium binding site 8 out of 9 in 6d8n

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Magnesium binding site 8 out of 9 in the Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:0.5
occ:1.00
 O6 B:G189 2.1 0.5 1.0
C6 B:G189 3.2 0.9 1.0
OP1 B:U168 3.8 0.9 1.0
N7 B:A183 3.9 0.4 1.0
OP2 B:U168 3.9 0.8 1.0
N1 B:G189 4.0 0.3 1.0
OP1 B:C165 4.0 0.5 1.0
OP1 B:C166 4.1 0.6 1.0
C8 B:A183 4.2 0.8 1.0
OP2 B:C166 4.2 0.6 1.0
P B:U168 4.4 0.9 1.0
C5 B:G189 4.4 0.1 1.0
P B:C166 4.6 0.3 1.0
OP2 B:A183 4.7 0.7 1.0
C5' B:C165 4.8 0.9 1.0
N7 B:G189 4.9 0.1 1.0
C5 B:A183 4.9 0.4 1.0
OP1 B:U182 5.0 0.3 1.0

Magnesium binding site 9 out of 9 in 6d8n

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Magnesium binding site 9 out of 9 in the Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Group I Self-Splicing Intron P4-P6 Domain Mutant G134A/U185AA within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:0.2
occ:1.00
 OP2 B:A171 2.1 0.1 1.0
P B:A171 3.4 0.9 1.0
OP2 B:U168 3.9 0.8 1.0
O3' B:U167 4.0 0.6 1.0
O5' B:A171 4.1 0.7 1.0
C8 B:A171 4.1 0.5 1.0
OP1 B:A171 4.1 0.5 1.0
N7 B:A171 4.2 0.6 1.0
O2' B:U167 4.2 0.7 1.0
O2 B:U167 4.3 0.1 1.0
OP1 B:C170 4.4 0.7 1.0
O5' B:C170 4.6 0.9 1.0
O3' B:C170 4.6 0.8 1.0
P B:U168 4.6 0.9 1.0
OP2 B:C165 4.7 0.0 1.0
OP2 B:C170 4.7 0.7 1.0
P B:C170 4.8 0.3 1.0
C1' B:U167 4.8 0.9 1.0
C3' B:C170 4.9 0.9 1.0
C2' B:U167 4.9 0.2 1.0

Reference:

G.M.Shoffner, R.Wang, E.Podell, T.R.Cech, F.Guo. In Crystallo Selection to Establish New Rna Crystal Contacts. Structure V. 26 1275 2018.
ISSN: ISSN 1878-4186
PubMed: 29910185
DOI: 10.1016/J.STR.2018.05.005
Page generated: Wed Aug 13 05:00:08 2025

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