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Magnesium in PDB 3u2n: Crystal Structure of Dna(Cgcgaattcgcg)2 at 1.25 Angstroms

Protein crystallography data

The structure of Crystal Structure of Dna(Cgcgaattcgcg)2 at 1.25 Angstroms, PDB code: 3u2n was solved by D.G.Wei, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.26 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 23.920, 39.640, 65.390, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Dna(Cgcgaattcgcg)2 at 1.25 Angstroms (pdb code 3u2n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Dna(Cgcgaattcgcg)2 at 1.25 Angstroms, PDB code: 3u2n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3u2n

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Magnesium binding site 1 out of 9 in the Crystal Structure of Dna(Cgcgaattcgcg)2 at 1.25 Angstroms


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 Dna(Cgcgaattcgcg)2 at 1.25 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg13

b:10.5
occ:1.00
 O A:HOH20 2.0 13.0 1.0
O B:HOH11 2.1 11.5 1.0
O A:HOH37 2.1 11.8 1.0
O6 B:DG22 4.1 8.7 1.0
O B:HOH34 4.2 15.2 1.0
C5 A:DC1 4.2 14.9 1.0
O B:HOH10 4.3 13.1 1.0
O A:HOH92 4.3 21.5 1.0
N7 A:DG2 4.4 9.5 1.0
O6 A:DG2 4.5 10.3 1.0
C6 A:DC1 4.6 16.2 1.0

Magnesium binding site 2 out of 9 in 3u2n

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Magnesium binding site 2 out of 9 in the Crystal Structure of Dna(Cgcgaattcgcg)2 at 1.25 Angstroms


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 Dna(Cgcgaattcgcg)2 at 1.25 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg14

b:29.2
occ:1.00
 O A:HOH119 1.9 27.2 1.0
O A:HOH128 2.0 25.2 1.0
O B:HOH74 2.1 26.9 1.0
O A:HOH155 2.1 34.1 1.0
O B:HOH109 2.1 22.9 1.0
O A:HOH159 2.3 44.1 1.0
O A:HOH58 4.0 23.4 1.0
O B:HOH43 4.0 15.2 1.0
O A:HOH90 4.0 21.8 1.0
O B:HOH115 4.0 19.5 1.0
O A:HOH17 4.1 20.6 1.0
O B:HOH46 4.1 22.3 1.0
O B:HOH38 4.4 43.5 1.0
O A:HOH132 4.4 22.8 1.0
O B:HOH2 4.5 43.8 1.0
O4' A:DA5 4.7 15.9 1.0
N2 A:DG4 4.8 11.2 1.0
C4' A:DA5 4.9 14.8 1.0

Magnesium binding site 3 out of 9 in 3u2n

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Magnesium binding site 3 out of 9 in the Crystal Structure of Dna(Cgcgaattcgcg)2 at 1.25 Angstroms


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 Dna(Cgcgaattcgcg)2 at 1.25 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg15

b:25.8
occ:1.00
 O A:HOH158 1.8 28.8 1.0
O A:HOH135 1.9 20.5 1.0
O B:HOH70 2.3 27.8 1.0
OP1 A:DG10 3.9 18.0 1.0
O B:HOH55 4.1 21.1 1.0
O B:HOH157 4.3 33.0 1.0
OP2 A:DG10 4.4 16.8 1.0
O A:HOH211 4.5 37.6 1.0
P A:DG10 4.6 16.0 1.0
O A:HOH69 4.8 26.2 1.0

Magnesium binding site 4 out of 9 in 3u2n

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Magnesium binding site 4 out of 9 in the Crystal Structure of Dna(Cgcgaattcgcg)2 at 1.25 Angstroms


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 Dna(Cgcgaattcgcg)2 at 1.25 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg16

b:33.6
occ:1.00
 OP2 A:DG4 2.1 16.6 1.0
O A:HOH190 2.2 32.5 1.0
O A:HOH189 2.2 34.5 1.0
O A:HOH23 2.9 29.2 0.5
O A:HOH191 3.1 29.2 1.0
O A:HOH194 3.5 47.3 1.0
P A:DG4 3.5 15.2 1.0
C3' A:DC3 4.1 10.8 1.0
C8 A:DG4 4.2 14.1 1.0
O3' A:DC3 4.2 13.2 1.0
N7 A:DG4 4.3 13.5 1.0
O A:HOH192 4.3 31.1 1.0
O5' A:DG4 4.4 14.3 1.0
OP1 A:DG4 4.4 18.9 1.0
O A:HOH23 4.5 18.2 0.5
C2' A:DC3 4.7 15.5 1.0
O5' A:DC3 4.9 14.7 1.0

Magnesium binding site 5 out of 9 in 3u2n

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Magnesium binding site 5 out of 9 in the Crystal Structure of Dna(Cgcgaattcgcg)2 at 1.25 Angstroms


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 Dna(Cgcgaattcgcg)2 at 1.25 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:18.0
occ:1.00
 OP1 B:DT19 2.1 17.4 1.0
O B:HOH62 2.1 18.0 1.0
O B:HOH55 2.2 21.1 1.0
P B:DT19 3.4 16.4 1.0
O5' B:DT19 4.0 15.0 1.0
C5' B:DT19 4.0 14.2 1.0
O A:HOH35 4.3 16.9 1.0
O A:HOH135 4.3 20.5 1.0
O B:HOH172 4.3 30.9 1.0
OP2 B:DT19 4.4 19.2 1.0
O B:HOH36 4.4 21.4 1.0
O3' B:DA18 4.4 14.9 1.0
O B:HOH157 4.5 33.0 1.0

Magnesium binding site 6 out of 9 in 3u2n

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Magnesium binding site 6 out of 9 in the Crystal Structure of Dna(Cgcgaattcgcg)2 at 1.25 Angstroms


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 Dna(Cgcgaattcgcg)2 at 1.25 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg25

b:28.7
occ:1.00
 OP1 B:DA17 1.9 21.6 1.0
O B:HOH167 2.0 32.4 1.0
O B:HOH131 2.2 37.0 1.0
O B:HOH171 2.3 35.1 1.0
O B:HOH120 2.3 31.6 1.0
O B:HOH166 2.3 43.8 1.0
P B:DA17 3.3 18.3 1.0
O5' B:DA17 4.0 15.6 1.0
OP2 B:DA17 4.0 19.9 1.0
C5' B:DA17 4.2 14.0 1.0
O3' B:DG16 4.3 18.1 1.0
O B:HOH76 4.6 25.5 1.0

Magnesium binding site 7 out of 9 in 3u2n

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Magnesium binding site 7 out of 9 in the Crystal Structure of Dna(Cgcgaattcgcg)2 at 1.25 Angstroms


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 Dna(Cgcgaattcgcg)2 at 1.25 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg26

b:30.5
occ:1.00
 OP2 B:DG16 1.9 20.2 1.0
O B:HOH179 2.1 31.4 1.0
O B:HOH178 2.1 28.9 1.0
O B:HOH182 2.2 37.9 1.0
O B:HOH180 2.3 49.4 1.0
O B:HOH181 2.6 35.9 1.0
P B:DG16 3.3 18.5 1.0
OP1 B:DG16 4.1 23.2 1.0
C8 B:DG16 4.2 12.1 1.0
O5' B:DG16 4.2 17.2 1.0
O3' B:DC15 4.2 17.3 1.0
C3' B:DC15 4.3 15.7 1.0
O B:HOH4 4.3 49.4 1.0
O B:HOH143 4.3 30.1 1.0
N7 B:DG16 4.3 12.9 1.0
O B:HOH161 4.7 35.2 1.0
C2' B:DC15 4.7 18.7 1.0

Magnesium binding site 8 out of 9 in 3u2n

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Magnesium binding site 8 out of 9 in the Crystal Structure of Dna(Cgcgaattcgcg)2 at 1.25 Angstroms


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 Dna(Cgcgaattcgcg)2 at 1.25 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg27

b:27.9
occ:1.00
 O B:HOH187 1.8 21.8 1.0
O B:HOH188 2.0 26.1 1.0
O B:HOH197 2.0 15.6 0.3
O B:HOH196 2.2 34.5 1.0
OP1 B:DC21 2.2 21.4 1.0
O B:HOH195 2.3 39.9 1.0
O B:HOH198 3.2 15.6 0.3
P B:DC21 3.6 18.5 1.0
O5' B:DC21 4.1 15.8 1.0
C5' B:DC21 4.1 15.3 1.0
O B:HOH31 4.1 17.9 1.0
O B:HOH212 4.2 15.5 0.4
OP2 B:DC21 4.5 20.7 1.0
O A:HOH47 4.5 29.2 1.0
O3' B:DT20 4.6 16.0 1.0
O A:HOH116 4.9 30.5 1.0

Magnesium binding site 9 out of 9 in 3u2n

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Magnesium binding site 9 out of 9 in the Crystal Structure of Dna(Cgcgaattcgcg)2 at 1.25 Angstroms


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 Dna(Cgcgaattcgcg)2 at 1.25 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg28

b:39.1
occ:1.00
 O B:HOH201 2.0 34.5 1.0
O B:HOH85 2.0 27.6 1.0
O B:HOH203 2.1 40.5 1.0
O B:HOH202 2.3 31.8 1.0
O B:HOH118 2.7 39.9 1.0
O B:HOH83 4.2 31.6 1.0
O B:HOH103 4.2 31.7 1.0
OP2 B:DG24 4.4 19.3 1.0
N7 B:DG24 4.4 15.6 1.0
C2' B:DC23 4.5 15.2 1.0
C8 B:DG24 4.8 14.8 1.0

Reference:

D.Wei, W.D.Wilson, S.Neidle. Small-Molecule Binding to the Dna Minor Groove Is Mediated By A Conserved Water Cluster. J.Am.Chem.Soc. V. 135 1369 2013.
ISSN: ISSN 0002-7863
PubMed: 23276263
DOI: 10.1021/JA308952Y
Page generated: Thu Aug 15 12:19:39 2024

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