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Magnesium in PDB 1gid: Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing

Protein crystallography data

The structure of Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing, PDB code: 1gid was solved by J.H.Cate, A.R.Gooding, E.Podell, K.Zhou, B.L.Golden, C.E.Kundrot, T.R.Cech, J.A.Doudna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.800, 128.700, 145.900, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 28.5

Other elements in 1gid:

The structure of Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing also contains other interesting chemical elements:

Cobalt (Co) 4 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing (pdb code 1gid). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing, PDB code: 1gid:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in 1gid

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Magnesium binding site 1 out of 24 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


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 Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg265

b:22.4
occ:1.00
O6 A:G188 2.0 31.9 1.0
C6 A:G188 3.3 24.9 1.0
OP1 A:U168 3.9 29.4 1.0
OP1 A:C165 4.1 24.3 1.0
N7 A:A183 4.1 22.1 1.0
OP2 A:C166 4.1 31.9 1.0
C5 A:G188 4.1 18.6 1.0
OP2 A:U168 4.2 19.6 1.0
N7 A:G188 4.2 26.5 1.0
C8 A:A183 4.3 18.5 1.0
OP1 A:U182 4.3 14.4 1.0
N1 A:G188 4.3 23.7 1.0
OP1 A:C166 4.4 24.1 1.0
OP2 A:A183 4.4 29.4 1.0
P A:U168 4.5 22.4 1.0
C5 A:U168 4.6 39.0 1.0
P A:C166 4.7 25.0 1.0
O5' A:A183 5.0 17.8 1.0

Magnesium binding site 2 out of 24 in 1gid

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Magnesium binding site 2 out of 24 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


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 Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg267

b:21.0
occ:1.00
OP1 A:A183 2.1 22.4 1.0
OP2 A:A184 2.3 28.8 1.0
OP2 A:A186 2.5 38.1 1.0
P A:A183 3.3 21.8 1.0
OP2 A:A183 3.7 29.4 1.0
P A:A184 3.8 25.7 1.0
P A:A186 4.0 33.5 1.0
N7 A:A186 4.1 31.4 1.0
O5' A:A183 4.2 17.8 1.0
N7 A:A184 4.3 24.4 1.0
C8 A:A186 4.4 26.4 1.0
C3' A:A183 4.5 18.4 1.0
O3' A:U182 4.5 16.2 1.0
OP1 A:A184 4.5 26.7 1.0
O3' A:A183 4.6 21.9 1.0
O5' A:A184 4.7 14.2 1.0
O5' A:A186 4.7 25.0 1.0
C8 A:A184 4.7 23.8 1.0
C3' A:U185 4.8 36.0 1.0
O3' A:U185 4.8 29.1 1.0
N3 A:A139 4.9 31.2 1.0
C2 A:A139 4.9 30.9 1.0
OP1 A:A186 4.9 38.7 1.0
C5' A:A183 4.9 19.1 1.0

Magnesium binding site 3 out of 24 in 1gid

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Magnesium binding site 3 out of 24 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


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 Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg268

b:25.1
occ:1.00
OP1 A:A184 2.1 26.7 1.0
OP2 A:A187 2.1 38.5 1.0
OP1 A:A186 2.3 38.7 1.0
P A:A184 3.2 25.7 1.0
P A:A186 3.5 33.5 1.0
O3' A:A183 3.6 21.9 1.0
P A:A187 3.6 38.7 1.0
OP2 A:A186 3.8 38.1 1.0
OP2 A:G188 3.8 55.2 1.0
OP2 A:A184 3.9 28.8 1.0
OP1 A:A187 4.4 42.5 1.0
C5' A:A187 4.4 36.1 1.0
OP1 A:A183 4.5 22.4 1.0
O5' A:A187 4.5 34.8 1.0
O5' A:A184 4.5 14.2 1.0
C3' A:A186 4.5 30.8 1.0
O3' A:A186 4.5 35.3 1.0
O3' A:U185 4.6 29.1 1.0
O5' A:A186 4.6 25.0 1.0
C3' A:A183 4.8 18.4 1.0
O5' A:G188 4.8 37.7 1.0
C5' A:A184 4.9 13.8 1.0
C5' A:A183 4.9 19.1 1.0
C3' A:U185 4.9 36.0 1.0
C4' A:U185 4.9 35.7 1.0
P A:G188 5.0 49.1 1.0

Magnesium binding site 4 out of 24 in 1gid

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Magnesium binding site 4 out of 24 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


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 Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg272

b:27.5
occ:1.00
O6 A:G164 2.1 34.4 1.0
N7 A:G163 2.6 39.4 1.0
C6 A:G164 3.2 32.6 1.0
C8 A:G163 3.3 38.9 1.0
C5 A:G163 3.7 38.2 1.0
N7 A:G164 3.9 29.3 1.0
C5 A:G164 3.9 28.8 1.0
OP2 A:G163 3.9 30.9 1.0
O6 A:G163 4.2 40.2 1.0
O2' A:U177 4.3 44.7 1.0
N7 A:A178 4.3 33.8 1.0
C6 A:G163 4.3 35.8 1.0
N1 A:G164 4.3 28.9 1.0
N6 A:A178 4.5 35.1 1.0
N9 A:G163 4.5 34.8 1.0
OP2 A:U162 4.6 41.5 1.0
O2 A:U177 4.7 55.0 1.0
C4 A:G163 4.8 37.1 1.0
C2' A:U177 5.0 43.1 1.0
O5' A:G163 5.0 23.1 1.0

Magnesium binding site 5 out of 24 in 1gid

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Magnesium binding site 5 out of 24 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


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 Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg274

b:31.0
occ:1.00
OP2 A:A171 2.3 38.3 1.0
P A:A171 3.7 33.2 1.0
OP2 A:U168 4.0 19.6 1.0
O3' A:U167 4.1 20.4 1.0
O2 A:U167 4.2 31.6 1.0
O2' A:U167 4.2 36.6 1.0
N7 A:A171 4.3 33.6 1.0
C8 A:A171 4.4 29.7 1.0
OP2 A:C165 4.4 21.1 1.0
OP1 A:A171 4.5 27.5 1.0
OP1 A:C170 4.5 31.3 1.0
OP2 A:C170 4.6 25.9 1.0
O5' A:A171 4.6 38.1 1.0
O3' A:C170 4.6 24.4 1.0
C1' A:U167 4.8 26.4 1.0
P A:U168 4.8 22.4 1.0
C5' A:A171 4.8 32.9 1.0
P A:C170 4.9 27.8 1.0

Magnesium binding site 6 out of 24 in 1gid

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Magnesium binding site 6 out of 24 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


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 Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg276

b:38.0
occ:1.00
OP2 A:A173 2.4 40.0 1.0
P A:A173 3.8 35.3 1.0
N3 A:NCO262 3.9 37.7 0.5
O6 A:G174 4.0 39.3 1.0
N7 A:A173 4.1 40.3 1.0
N7 A:G174 4.1 32.4 1.0
O5' A:A173 4.2 33.1 1.0
C8 A:A173 4.3 39.9 1.0
OP2 A:A172 4.4 18.4 1.0
O2' A:A171 4.6 34.1 1.0
O5' A:A172 4.7 36.0 1.0
O3' A:A172 4.7 30.0 1.0
C3' A:A172 4.7 27.6 1.0
O3' A:A171 4.8 30.1 1.0
C6 A:G174 4.8 34.6 1.0
OP1 A:A173 4.8 33.7 1.0
C5 A:G174 4.9 30.5 1.0
P A:A172 5.0 31.2 1.0
C5 A:A173 5.0 36.6 1.0

Magnesium binding site 7 out of 24 in 1gid

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Magnesium binding site 7 out of 24 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


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 Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg277

b:51.0
occ:1.00
OP1 A:C213 3.6 19.2 1.0
OP1 A:C255 3.7 53.0 1.0
OP2 A:A214 4.1 32.6 1.0
OP1 A:A171 4.8 27.5 1.0
OP1 A:A214 4.8 33.4 1.0
C5' A:C255 4.9 56.4 1.0
P A:C213 4.9 22.1 1.0
P A:A214 4.9 35.1 1.0

Magnesium binding site 8 out of 24 in 1gid

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Magnesium binding site 8 out of 24 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


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 Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg278

b:54.5
occ:1.00
O3' A:C127 4.2 44.7 1.0
OP2 A:A113 4.2 26.4 1.0
OP1 A:U202 4.3 40.1 1.0
OP1 A:C128 4.3 46.8 1.0
OP1 A:C203 4.5 24.0 1.0
O2' A:C127 4.6 56.5 1.0
OP2 A:C203 4.6 30.9 1.0
P A:C203 4.9 35.4 1.0
P A:C128 4.9 46.0 1.0

Magnesium binding site 9 out of 24 in 1gid

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Magnesium binding site 9 out of 24 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


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 Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg282

b:50.1
occ:1.00
OP2 A:G250 2.3 36.6 1.0
O2' A:A248 3.3 40.9 1.0
OP2 A:U249 3.6 43.8 1.0
P A:G250 3.7 25.8 1.0
O5' A:U249 3.8 36.7 1.0
P A:U249 4.4 39.0 1.0
OP1 A:G250 4.5 30.4 1.0
N7 A:G250 4.5 27.7 1.0
O5' A:G250 4.5 21.8 1.0
C2' A:A248 4.5 25.9 1.0
O3' A:U249 4.7 32.7 1.0
C8 A:G250 4.9 29.0 1.0
O3' A:A248 4.9 33.3 1.0
C3' A:U249 4.9 32.2 1.0
C5' A:U249 4.9 35.0 1.0
N7 A:G251 5.0 28.1 1.0

Magnesium binding site 10 out of 24 in 1gid

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Magnesium binding site 10 out of 24 in the Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing


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 Group I Ribozyme Domain: Principles of Rna Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg284

b:64.0
occ:1.00
OP1 A:U155 3.2 29.8 1.0
OP1 A:U142 3.9 40.3 1.0
OP1 A:U253 4.2 35.2 1.0
P A:U155 4.2 30.6 1.0
OP2 A:U155 4.3 31.0 1.0
O3' A:A252 4.6 23.8 1.0

Reference:

J.H.Cate, A.R.Gooding, E.Podell, K.Zhou, B.L.Golden, C.E.Kundrot, T.R.Cech, J.A.Doudna. Crystal Structure of A Group I Ribozyme Domain: Principles of Rna Packing. Science V. 273 1678 1996.
ISSN: ISSN 0036-8075
PubMed: 8781224
Page generated: Mon Dec 14 05:57:50 2020

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