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Magnesium in PDB 5dhc: Cooperativity and Downstream Binding in Rna Replication

Protein crystallography data

The structure of Cooperativity and Downstream Binding in Rna Replication, PDB code: 5dhc was solved by W.Zhang, A.C.Fahrenbach, C.P.Tam, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.55
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 43.107, 43.107, 83.245, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 19.5

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the Cooperativity and Downstream Binding in Rna Replication (pdb code 5dhc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the Cooperativity and Downstream Binding in Rna Replication, PDB code: 5dhc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in 5dhc

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Magnesium binding site 1 out of 15 in the Cooperativity and Downstream Binding in Rna Replication


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cooperativity and Downstream Binding in Rna Replication within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:15.4
occ:1.00
 O B:HOH267 2.1 13.7 1.0
O B:HOH240 2.1 14.3 1.0
O A:HOH232 2.1 15.7 1.0
O A:HOH206 2.1 17.2 1.0
O B:HOH249 2.2 17.4 1.0
OP2 A:A5 4.1 14.9 1.0
O B:HOH229 4.2 15.6 1.0
O B:HOH270 4.3 30.5 1.0
O A:HOH261 4.3 26.4 1.0
OP2 B:U7 4.4 13.4 1.0
OP1 A:A5 4.4 15.0 1.0
OP1 A:LCG4 4.4 15.1 1.0
O A:HOH214 4.5 24.4 1.0
OP1 B:C6 4.5 14.0 1.0
O B:HOH265 4.6 24.3 1.0
P A:A5 4.7 14.4 1.0
OP1 B:U7 5.0 15.8 1.0

Magnesium binding site 2 out of 15 in 5dhc

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Magnesium binding site 2 out of 15 in the Cooperativity and Downstream Binding in Rna Replication


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cooperativity and Downstream Binding in Rna Replication within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:21.9
occ:1.00
 O A:HOH245 2.1 19.1 1.0
O B:HOH201 2.1 30.8 1.0
O A:HOH230 2.1 23.5 1.0
O A:HOH263 2.1 26.1 1.0
O B:HOH220 2.2 20.1 1.0
O B:HOH271 2.2 19.7 1.0
O4 B:U8 4.1 18.6 1.0
O B:HOH265 4.2 24.3 1.0
O A:HOH256 4.2 25.2 1.0
O4 A:U7 4.3 16.2 1.0
O4 B:U7 4.4 14.0 1.0
O B:HOH257 4.4 23.2 1.0
O4 A:U8 4.5 16.0 1.0
O B:HOH256 4.5 27.7 1.0
O A:HOH252 4.5 19.9 1.0
O B:HOH263 4.5 27.1 1.0
N6 A:A9 4.7 17.4 1.0
N6 B:A9 5.0 14.5 1.0

Magnesium binding site 3 out of 15 in 5dhc

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Magnesium binding site 3 out of 15 in the Cooperativity and Downstream Binding in Rna Replication


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cooperativity and Downstream Binding in Rna Replication within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:15.1
occ:0.50
 O A:HOH266 2.0 22.4 0.5
O A:HOH265 2.0 18.8 0.5
O A:HOH241 2.0 11.7 0.5
O A:HOH262 2.1 24.1 0.5
O A:HOH212 2.1 21.4 0.5
O A:HOH239 2.2 14.3 0.5
O A:HOH248 4.0 22.4 1.0
O A:HOH221 4.0 28.4 1.0
N7 A:LCA3 4.1 15.7 1.0
O A:HOH253 4.3 20.2 1.0
O B:HOH225 4.3 20.0 1.0
N6 A:LCA3 4.3 17.9 1.0
O6 A:LCG4 4.5 15.9 1.0
N7 A:LCG4 4.5 13.8 1.0
O B:HOH273 4.5 35.6 1.0
C5 A:LCA3 4.8 15.2 1.0
O B:HOH272 4.9 25.0 1.0
N4 A:LCC2 5.0 19.0 1.0

Magnesium binding site 4 out of 15 in 5dhc

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Magnesium binding site 4 out of 15 in the Cooperativity and Downstream Binding in Rna Replication


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cooperativity and Downstream Binding in Rna Replication within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:17.9
occ:1.00
 O A:HOH259 2.0 15.0 1.0
O A:HOH247 2.0 21.3 1.0
O B:HOH237 2.1 20.7 1.0
O A:HOH257 2.1 24.0 1.0
O B:HOH208 2.1 26.6 1.0
O A:HOH209 4.1 13.8 1.0
OP2 B:A5 4.1 15.9 1.0
O A:HOH216 4.2 14.4 1.0
OP1 B:A5 4.3 17.3 1.0
OP2 A:U7 4.3 14.0 1.0
O B:HOH269 4.3 25.8 1.0
OP1 B:LCG4 4.4 16.7 1.0
OP1 A:C6 4.7 13.4 1.0
P B:A5 4.7 16.1 1.0
O B:HOH207 4.7 35.4 1.0
OP2 B:LCG4 4.9 16.6 1.0
OP1 A:U7 4.9 16.2 1.0
P B:LCG4 5.0 15.6 1.0

Magnesium binding site 5 out of 15 in 5dhc

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Magnesium binding site 5 out of 15 in the Cooperativity and Downstream Binding in Rna Replication


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cooperativity and Downstream Binding in Rna Replication within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:17.2
occ:0.33
 OP1 B:G11 2.1 20.9 1.0
O B:HOH251 2.3 25.6 1.0
P B:G11 3.5 20.8 1.0
O B:HOH224 3.5 8.4 0.3
O5' B:G11 3.7 19.9 1.0
O B:HOH253 4.1 35.1 1.0
O3' B:A10 4.3 19.2 1.0
C5' B:G11 4.3 16.4 1.0
OP2 B:G11 4.6 20.4 1.0
C4' B:G11 4.9 15.1 1.0

Magnesium binding site 6 out of 15 in 5dhc

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Magnesium binding site 6 out of 15 in the Cooperativity and Downstream Binding in Rna Replication


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cooperativity and Downstream Binding in Rna Replication within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg103

b:29.8
occ:1.00
 O B:HOH272 1.7 25.0 1.0
O B:HOH268 1.8 28.5 1.0
O B:HOH227 2.0 20.5 1.0
O B:HOH273 2.2 35.6 1.0
O B:HOH260 2.3 22.8 1.0
O B:HOH210 2.3 20.6 1.0
O B:HOH213 3.6 21.2 1.0
O B:HOH211 3.8 25.3 1.0
O A:HOH262 4.1 24.1 0.5
N7 B:A10 4.1 15.3 1.0
O B:HOH225 4.2 20.0 1.0
O B:HOH202 4.5 28.1 1.0
N7 B:G11 4.5 13.2 1.0
OP2 B:A10 4.7 19.9 1.0
O B:HOH235 4.7 18.4 1.0
C8 B:A10 4.8 15.4 1.0

Magnesium binding site 7 out of 15 in 5dhc

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Magnesium binding site 7 out of 15 in the Cooperativity and Downstream Binding in Rna Replication


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cooperativity and Downstream Binding in Rna Replication within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg104

b:30.3
occ:0.33
 O2' A:5GP104 2.4 24.1 1.0
O3' A:5GP104 2.5 28.6 1.0
C3' A:5GP104 3.4 27.2 1.0
C2' A:5GP104 3.4 24.0 1.0
C4' A:5GP104 3.7 30.1 1.0
O A:HOH203 4.3 34.5 1.0
C1' A:5GP104 4.5 21.0 1.0
O4' A:5GP104 4.7 23.7 1.0
O A:HOH220 4.7 29.1 1.0
C5' A:5GP104 4.7 33.5 1.0

Magnesium binding site 8 out of 15 in 5dhc

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Magnesium binding site 8 out of 15 in the Cooperativity and Downstream Binding in Rna Replication


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cooperativity and Downstream Binding in Rna Replication within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:15.3
occ:1.00
 O D:HOH268 2.1 13.6 1.0
O C:HOH206 2.1 16.5 1.0
O D:HOH248 2.1 14.6 1.0
O C:HOH225 2.1 16.8 1.0
O D:HOH254 2.2 16.2 1.0
OP2 C:A5 4.1 14.6 1.0
O D:HOH228 4.2 14.9 1.0
O D:HOH272 4.2 29.2 1.0
O C:HOH261 4.3 26.1 1.0
OP2 D:U7 4.4 13.8 1.0
OP1 C:LCG4 4.4 15.2 1.0
OP1 C:A5 4.4 15.5 1.0
O D:HOH267 4.5 23.7 1.0
OP1 D:C6 4.5 13.9 1.0
O C:HOH218 4.6 25.1 1.0
P C:A5 4.7 14.5 1.0

Magnesium binding site 9 out of 15 in 5dhc

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Magnesium binding site 9 out of 15 in the Cooperativity and Downstream Binding in Rna Replication


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cooperativity and Downstream Binding in Rna Replication within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:21.1
occ:1.00
 O C:HOH249 2.0 18.9 1.0
O C:HOH264 2.0 26.2 1.0
O D:HOH201 2.0 31.2 1.0
O C:HOH233 2.0 22.9 1.0
O D:HOH273 2.2 20.7 1.0
O D:HOH224 2.2 20.1 1.0
O4 D:U8 4.1 17.9 1.0
O D:HOH267 4.2 23.7 1.0
O C:HOH259 4.2 26.2 1.0
O4 C:U7 4.3 16.6 1.0
O4 D:U7 4.4 13.5 1.0
O D:HOH255 4.4 23.3 1.0
O4 C:U8 4.5 16.1 1.0
O C:HOH252 4.5 19.7 1.0
O D:HOH265 4.5 27.2 1.0
O D:HOH259 4.5 27.6 1.0
N6 C:A9 4.7 17.5 1.0
N6 D:A9 5.0 14.4 1.0

Magnesium binding site 10 out of 15 in 5dhc

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Magnesium binding site 10 out of 15 in the Cooperativity and Downstream Binding in Rna Replication


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cooperativity and Downstream Binding in Rna Replication within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg103

b:14.3
occ:0.50
 O C:HOH248 1.9 18.5 0.5
O C:HOH266 2.0 16.7 0.5
O C:HOH262 2.0 23.7 0.5
O C:HOH267 2.1 22.1 0.5
O C:HOH224 2.1 11.7 0.5
O C:HOH230 2.2 13.4 0.5
O C:HOH244 4.0 21.9 1.0
N7 C:LCA3 4.1 15.4 1.0
O C:HOH216 4.2 28.7 1.0
O C:HOH255 4.2 18.6 1.0
O D:HOH226 4.3 19.5 1.0
N6 C:LCA3 4.3 17.1 1.0
O6 C:LCG4 4.4 16.0 1.0
N7 C:LCG4 4.4 12.8 1.0
O D:HOH276 4.6 34.2 1.0
C5 C:LCA3 4.8 14.6 1.0
O D:HOH275 4.8 25.3 1.0

Reference:

W.Zhang, C.P.Tam, J.Wang, J.W.Szostak. Unusual Base-Pairing Interactions in Monomer-Template Complexes. Acs Cent Sci V. 2 916 2016.
ISSN: ESSN 2374-7943
PubMed: 28058281
DOI: 10.1021/ACSCENTSCI.6B00278
Page generated: Sun Sep 29 02:48:02 2024

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