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Magnesium in PDB 4kwx: Linear Structure of the Holliday Junction Sequence (Tcggcgccga)

Protein crystallography data

The structure of Linear Structure of the Holliday Junction Sequence (Tcggcgccga), PDB code: 4kwx was solved by G.Skamrova, I.Laponogov, N.Campbell, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.30 / 1.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 34.410, 34.490, 34.690, 101.28, 103.21, 103.81
R / Rfree (%) 17.3 / 18.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Linear Structure of the Holliday Junction Sequence (Tcggcgccga) (pdb code 4kwx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Linear Structure of the Holliday Junction Sequence (Tcggcgccga), PDB code: 4kwx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 4kwx

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Magnesium binding site 1 out of 10 in the Linear Structure of the Holliday Junction Sequence (Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Linear Structure of the Holliday Junction Sequence (Tcggcgccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:15.6
occ:1.00
 O C:HOH101 2.1 15.9 1.0
O C:HOH102 2.1 18.0 1.0
O A:HOH202 2.1 15.2 1.0
O B:HOH201 2.1 17.2 1.0
O A:HOH201 2.2 17.7 1.0
O B:HOH202 2.2 18.1 1.0
O C:HOH105 4.0 21.9 1.0
O2 B:DC7 4.1 12.8 1.0
OP1 C:DG4 4.2 17.9 1.0
O4' A:DG6 4.2 13.7 1.0
O C:HOH112 4.2 25.5 1.0
O A:HOH252 4.2 46.8 1.0
O A:HOH241 4.2 28.2 1.0
O A:HOH210 4.3 17.6 1.0
O A:HOH226 4.4 27.8 1.0
C4' A:DG6 4.4 14.9 1.0
O B:HOH231 4.4 26.5 1.0
OP2 C:DG4 4.4 17.6 1.0
O2 A:DC5 4.6 14.0 1.0
N2 B:DG6 4.6 13.2 1.0
O4' B:DC8 4.6 17.3 1.0
C5' A:DG6 4.7 16.1 1.0
C4' B:DC8 4.7 16.9 1.0
P C:DG4 4.7 17.1 1.0
C5' B:DC8 4.7 15.0 1.0
N2 A:DG4 4.8 12.9 1.0

Magnesium binding site 2 out of 10 in 4kwx

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Magnesium binding site 2 out of 10 in the Linear Structure of the Holliday Junction Sequence (Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Linear Structure of the Holliday Junction Sequence (Tcggcgccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:16.4
occ:1.00
 OP2 A:DC5 2.0 13.9 1.0
O E:HOH205 2.1 18.6 1.0
O E:HOH201 2.1 19.4 1.0
O A:HOH205 2.1 18.6 1.0
O E:HOH204 2.2 16.4 1.0
O A:HOH255 2.2 17.0 1.0
P A:DC5 3.5 14.2 1.0
O6 E:DG9 4.0 12.7 1.0
O5' A:DC5 4.1 14.7 1.0
N7 E:DG9 4.2 13.2 1.0
O A:HOH237 4.3 26.0 1.0
O E:HOH249 4.3 23.2 1.0
O E:HOH246 4.3 21.3 1.0
O D:HOH234 4.3 23.9 1.0
OP1 A:DC5 4.3 15.0 1.0
O E:HOH233 4.4 18.9 1.0
C3' A:DG4 4.4 13.8 1.0
C2' A:DG4 4.4 12.9 1.0
O A:HOH235 4.4 27.3 1.0
O3' A:DG4 4.5 13.8 1.0
O4 F:DT1 4.5 13.1 1.0
O A:HOH209 4.7 14.9 1.0
C6 E:DG9 4.8 11.9 1.0
C5 E:DG9 4.9 12.3 1.0
C7 F:DT1 5.0 15.1 1.0

Magnesium binding site 3 out of 10 in 4kwx

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Magnesium binding site 3 out of 10 in the Linear Structure of the Holliday Junction Sequence (Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Linear Structure of the Holliday Junction Sequence (Tcggcgccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:24.1
occ:1.00
 O E:HOH215 2.1 26.0 1.0
O B:HOH206 2.2 19.6 1.0
O D:HOH208 2.2 25.6 1.0
O B:HOH208 2.2 26.3 1.0
O B:HOH207 2.2 27.6 1.0
O D:HOH209 2.2 25.9 1.0
O A:HOH232 3.9 29.2 1.0
OP1 E:DC8 4.0 24.8 1.0
O6 B:DG3 4.2 13.8 1.0
N7 B:DG3 4.3 16.1 1.0
O B:HOH213 4.3 28.9 1.0
N4 A:DC7 4.3 18.3 1.0
OP2 D:DG4 4.4 16.8 1.0
O D:HOH218 4.4 21.5 1.0
OP1 D:DG4 4.4 20.7 1.0
O5' D:DG3 4.5 26.1 1.0
O6 B:DG4 4.6 23.0 1.0
C5 B:DC2 4.8 20.8 1.0
C3' D:DG3 4.8 21.5 1.0
P D:DG4 4.8 18.1 1.0
C5' D:DG3 4.9 24.8 1.0
C6 B:DG3 5.0 13.8 1.0
C5 B:DG3 5.0 14.4 1.0
OP2 E:DC8 5.0 27.3 1.0

Magnesium binding site 4 out of 10 in 4kwx

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Magnesium binding site 4 out of 10 in the Linear Structure of the Holliday Junction Sequence (Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Linear Structure of the Holliday Junction Sequence (Tcggcgccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:22.4
occ:1.00
 OP2 D:DC2 2.1 19.8 1.0
O D:HOH204 2.2 25.1 1.0
O D:HOH201 2.2 25.1 1.0
O D:HOH202 2.2 25.0 1.0
O D:HOH205 2.2 21.7 1.0
O D:HOH203 2.2 24.4 1.0
P D:DC2 3.4 20.1 1.0
O5' D:DC2 3.7 20.8 1.0
O D:HOH233 4.1 27.3 1.0
O D:HOH239 4.2 28.1 1.0
O E:HOH246 4.3 21.3 1.0
C3' D:DT1 4.3 18.9 1.0
O A:HOH235 4.4 27.3 1.0
O3' D:DT1 4.4 20.4 1.0
O D:HOH234 4.4 23.9 1.0
OP1 D:DC2 4.5 21.8 1.0
C2' D:DC2 4.9 23.5 1.0
O A:HOH223 5.0 25.2 1.0

Magnesium binding site 5 out of 10 in 4kwx

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Magnesium binding site 5 out of 10 in the Linear Structure of the Holliday Junction Sequence (Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Linear Structure of the Holliday Junction Sequence (Tcggcgccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg102

b:14.1
occ:1.00
 OP2 D:DC5 2.0 13.9 1.0
O A:HOH206 2.1 17.1 1.0
O A:HOH207 2.1 15.6 1.0
O D:HOH207 2.1 16.7 1.0
O B:HOH205 2.2 15.9 1.0
O D:HOH206 2.2 15.3 1.0
P D:DC5 3.4 13.8 1.0
O5' D:DC5 4.1 14.7 1.0
O D:HOH210 4.1 19.0 1.0
O6 A:DG9 4.1 14.9 1.0
O D:HOH224 4.2 21.5 1.0
OP1 D:DC5 4.3 14.7 1.0
N7 A:DG9 4.3 16.7 1.0
O A:HOH220 4.4 25.1 1.0
C3' D:DG4 4.4 13.3 1.0
O3' D:DG4 4.5 14.1 1.0
O D:HOH220 4.5 26.4 1.0
O A:HOH219 4.5 21.8 1.0
O D:HOH212 4.5 16.0 1.0
C2' D:DG4 4.6 13.9 1.0
O4 B:DT1 4.6 13.6 1.0
O A:HOH212 4.7 16.6 1.0
C7 B:DT1 4.8 16.5 1.0
C6 A:DG9 4.9 13.8 1.0
C5 A:DC8 5.0 14.1 1.0
C5 A:DG9 5.0 15.3 1.0

Magnesium binding site 6 out of 10 in 4kwx

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Magnesium binding site 6 out of 10 in the Linear Structure of the Holliday Junction Sequence (Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Linear Structure of the Holliday Junction Sequence (Tcggcgccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg101

b:18.9
occ:1.00
 O B:HOH204 2.1 18.0 1.0
O A:HOH204 2.1 20.1 1.0
O A:HOH203 2.2 22.0 1.0
O B:HOH203 2.2 19.7 1.0
O E:HOH203 2.2 21.2 1.0
O E:HOH202 2.2 19.4 1.0
O6 B:DG6 4.1 14.4 1.0
OP1 E:DG6 4.2 21.1 1.0
N7 B:DG6 4.2 15.4 1.0
O B:HOH224 4.2 36.0 1.0
O A:HOH227 4.2 25.6 1.0
O E:HOH225 4.3 17.0 1.0
O B:HOH218 4.3 26.4 1.0
O B:HOH217 4.4 28.5 1.0
OP1 E:DC7 4.5 14.2 1.0
O5' E:DG6 4.6 17.8 1.0
O6 A:DG4 4.6 14.1 1.0
C6 B:DG6 4.8 13.7 1.0
P E:DG6 4.8 17.5 1.0
C5 B:DG6 4.8 13.9 1.0
C3' E:DG6 4.9 15.7 1.0
C5' E:DG6 5.0 17.1 1.0

Magnesium binding site 7 out of 10 in 4kwx

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Magnesium binding site 7 out of 10 in the Linear Structure of the Holliday Junction Sequence (Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Linear Structure of the Holliday Junction Sequence (Tcggcgccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg102

b:15.7
occ:1.00
 OP2 E:DC5 2.0 15.0 1.0
O E:HOH209 2.1 17.2 1.0
O E:HOH210 2.1 17.2 1.0
O E:HOH206 2.1 19.6 1.0
O E:HOH207 2.2 14.5 1.0
O E:HOH208 2.2 15.8 1.0
P E:DC5 3.5 14.3 1.0
O E:HOH228 4.2 21.0 1.0
O E:HOH261 4.2 31.4 1.0
O5' E:DC5 4.2 13.7 1.0
C3' E:DG4 4.3 13.2 1.0
C2' E:DG4 4.3 12.5 1.0
OP1 E:DC5 4.3 15.2 1.0
O3' E:DG4 4.4 14.2 1.0
O E:HOH227 4.5 16.1 1.0

Magnesium binding site 8 out of 10 in 4kwx

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Magnesium binding site 8 out of 10 in the Linear Structure of the Holliday Junction Sequence (Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Linear Structure of the Holliday Junction Sequence (Tcggcgccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg103

b:19.0
occ:1.00
 O E:HOH221 2.1 22.1 1.0
O E:HOH222 2.1 20.5 1.0
O E:HOH219 2.1 18.6 1.0
O E:HOH217 2.2 19.2 1.0
O E:HOH218 2.2 22.9 1.0
O E:HOH220 2.2 22.5 1.0
OP1 E:DG4 4.3 18.4 1.0
OP1 E:DG3 4.3 20.9 1.0
O E:HOH235 4.3 24.2 1.0
OP2 E:DG4 4.7 19.0 1.0
O5' E:DG3 4.9 16.0 1.0
P E:DG4 4.9 15.4 1.0

Magnesium binding site 9 out of 10 in 4kwx

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Magnesium binding site 9 out of 10 in the Linear Structure of the Holliday Junction Sequence (Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Linear Structure of the Holliday Junction Sequence (Tcggcgccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg101

b:18.7
occ:1.00
 O F:HOH208 2.1 18.8 1.0
O E:HOH214 2.1 21.3 1.0
O E:HOH213 2.2 18.5 1.0
O E:HOH211 2.2 22.5 1.0
O F:HOH209 2.2 19.6 1.0
O E:HOH212 2.2 18.8 1.0
O E:HOH241 3.9 23.7 1.0
O4' E:DA10 4.0 14.2 1.0
O E:HOH237 4.1 21.6 1.0
O F:HOH232 4.1 27.0 1.0
O E:HOH252 4.2 31.0 1.0
N2 F:DG3 4.2 13.7 1.0
O4' F:DG4 4.2 21.3 1.0
O E:HOH248 4.3 19.4 1.0
O F:HOH224 4.4 21.0 1.0
N3 F:DG3 4.4 12.4 1.0
C4' E:DA10 4.4 15.2 1.0
N2 E:DG9 4.5 12.4 1.0
C4' F:DG4 4.5 22.4 1.0
C2 F:DG3 4.7 12.6 1.0
C5' F:DG4 4.8 23.3 1.0
C1' E:DA10 5.0 14.5 1.0

Magnesium binding site 10 out of 10 in 4kwx

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Magnesium binding site 10 out of 10 in the Linear Structure of the Holliday Junction Sequence (Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Linear Structure of the Holliday Junction Sequence (Tcggcgccga) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg102

b:26.9
occ:1.00
 O F:HOH211 2.2 23.3 1.0
O A:HOH208 2.2 27.5 1.0
O F:HOH210 2.2 28.5 1.0
O F:HOH213 2.2 30.0 1.0
O E:HOH216 2.2 27.3 1.0
O F:HOH212 2.2 26.1 1.0
N7 F:DG3 4.0 17.4 1.0
O A:HOH243 4.1 18.6 1.0
O6 F:DG3 4.3 13.8 1.0
O E:HOH254 4.4 28.0 1.0
N4 E:DC7 4.5 13.6 1.0
OP2 A:DG4 4.5 17.0 1.0
C5 F:DG3 4.7 14.8 1.0
O6 F:DG4 4.8 18.4 1.0
C6 F:DG3 4.8 13.4 1.0
C3' A:DG3 4.9 15.9 1.0
C8 F:DG3 4.9 17.4 1.0
O3' A:DG3 4.9 17.0 1.0

Reference:

G.Skamrova, I.Laponogov, N.Campbell, S.Neidle. Linear Structure of the Holliday Junction Sequence (Tcggcgccga) To Be Published.
Page generated: Sat Aug 17 04:23:15 2024

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