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Magnesium in PDB 8rer: Major Groove Intercalation with Polypyridyl Ruthenium Complex

Protein crystallography data

The structure of Major Groove Intercalation with Polypyridyl Ruthenium Complex, PDB code: 8rer was solved by A.Abdullrahman, C.J.Cardin, J.P.Hall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.68 / 1.20
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 32.676, 32.676, 103.988, 90, 90, 90
R / Rfree (%) 17.2 / 20.3

Other elements in 8rer:

The structure of Major Groove Intercalation with Polypyridyl Ruthenium Complex also contains other interesting chemical elements:

Ruthenium (Ru) 5 atoms
Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Major Groove Intercalation with Polypyridyl Ruthenium Complex (pdb code 8rer). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Major Groove Intercalation with Polypyridyl Ruthenium Complex, PDB code: 8rer:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8rer

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Magnesium binding site 1 out of 8 in the Major Groove Intercalation with Polypyridyl Ruthenium Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Major Groove Intercalation with Polypyridyl Ruthenium Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:39.9
occ:1.00
 OP2 A:DT4 2.1 27.6 1.0
O A:HOH222 2.2 45.2 1.0
O A:HOH226 2.4 56.0 1.0
O A:HOH213 2.4 47.1 1.0
H3' A:DA3 3.2 24.6 1.0
P A:DT4 3.5 24.0 1.0
C3' A:DA3 4.0 20.5 1.0
O3' A:DA3 4.1 21.7 1.0
O A:HOH219 4.2 43.4 1.0
OP1 A:DT4 4.3 23.5 1.0
OP1 A:DA3 4.4 24.3 1.0
H5'' A:DA3 4.4 23.2 1.0
O5' A:DT4 4.6 23.6 1.0

Magnesium binding site 2 out of 8 in 8rer

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Magnesium binding site 2 out of 8 in the Major Groove Intercalation with Polypyridyl Ruthenium Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Major Groove Intercalation with Polypyridyl Ruthenium Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:46.6
occ:1.00
 O A:HOH204 2.0 33.8 1.0
O A:HOH237 2.1 35.1 1.0
O A:HOH205 2.3 31.3 1.0
O A:HOH241 2.3 40.0 1.0
H1 A:DG7 3.5 28.5 1.0
H22 A:DG7 3.9 27.4 1.0
O B:HOH242 4.1 47.4 1.0
H2'' A:DA5 4.2 29.5 1.0
N7 A:DG6 4.2 21.5 1.0
N1 A:DG7 4.3 23.7 1.0
O6 A:DG6 4.3 23.1 1.0
O A:HOH212 4.4 32.8 1.0
H2' A:DA5 4.5 29.5 1.0
N2 A:DG7 4.6 22.9 1.0
H8 A:DA5 4.7 26.8 1.0
C2' A:DA5 4.8 24.6 1.0
C2 A:DG7 4.9 22.4 1.0
O6 A:DG7 5.0 25.0 1.0

Magnesium binding site 3 out of 8 in 8rer

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Magnesium binding site 3 out of 8 in the Major Groove Intercalation with Polypyridyl Ruthenium Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Major Groove Intercalation with Polypyridyl Ruthenium Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:69.2
occ:1.00
 O B:HOH240 2.0 36.7 1.0
O B:HOH253 2.4 41.2 1.0
O B:HOH215 2.4 32.1 1.0
O B:HOH256 2.5 52.5 1.0
O B:HOH202 2.8 36.0 1.0
H3' B:DT3 4.2 27.6 1.0
OP2 B:DA4 4.2 27.3 1.0
H8 B:DA4 4.2 27.2 1.0
N7 B:DA4 4.4 22.8 1.0
H73 B:DT5 4.5 28.7 1.0
O B:HOH209 4.5 34.5 1.0
H2' B:DT3 4.5 24.7 1.0
C8 B:DA4 4.6 22.6 1.0
CL B:CL104 4.7 28.4 1.0
H71 B:DT5 4.7 28.7 1.0
O B:HOH226 4.8 25.3 1.0
H1 B:KSB101 4.9 20.9 1.0
O B:HOH225 5.0 56.4 1.0

Magnesium binding site 4 out of 8 in 8rer

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Magnesium binding site 4 out of 8 in the Major Groove Intercalation with Polypyridyl Ruthenium Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Major Groove Intercalation with Polypyridyl Ruthenium Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg103

b:50.4
occ:1.00
 O B:HOH224 2.0 39.7 1.0
OP1 B:DC2 2.1 26.4 1.0
O B:HOH207 2.2 42.3 1.0
O B:HOH233 2.2 33.4 1.0
O B:HOH248 2.3 36.0 1.0
O B:HOH201 2.6 36.6 1.0
P B:DC2 3.1 25.9 1.0
OP2 B:DC2 3.5 30.0 1.0
O B:HOH216 3.9 38.2 1.0
O3' B:DC1 3.9 25.5 1.0
O5' B:DC2 4.4 24.5 1.0
H5'' B:DC2 4.5 26.9 1.0
O B:HOH258 4.9 40.4 1.0
H4' B:DC1 5.0 31.7 1.0
C5' B:DC2 5.0 22.4 1.0

Magnesium binding site 5 out of 8 in 8rer

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Magnesium binding site 5 out of 8 in the Major Groove Intercalation with Polypyridyl Ruthenium Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Major Groove Intercalation with Polypyridyl Ruthenium Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:27.6
occ:1.00
 O D:HOH249 4.1 37.4 1.0
O B:HOH222 4.2 40.5 1.0
H22 C:DG1 4.3 24.3 1.0
H8 C:KSB101 4.3 25.1 1.0
O C:HOH220 4.3 24.4 1.0
O B:HOH237 4.5 25.4 1.0
N6 C:KSB101 4.5 19.7 1.0
H21 C:DG1 4.5 24.3 1.0
O2 D:DC7 4.5 19.9 1.0
H1' D:DC7 4.7 25.5 1.0
N2 C:DG1 4.7 20.3 1.0
H2'' D:DC7 4.8 27.2 1.0
C21 C:KSB101 4.8 20.9 1.0

Magnesium binding site 6 out of 8 in 8rer

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Magnesium binding site 6 out of 8 in the Major Groove Intercalation with Polypyridyl Ruthenium Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Major Groove Intercalation with Polypyridyl Ruthenium Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg103

b:38.5
occ:1.00
 O B:HOH218 2.0 26.4 1.0
O C:HOH212 2.0 48.4 1.0
OP2 C:DT4 2.1 27.3 1.0
O C:HOH227 2.3 50.0 1.0
O C:HOH205 2.3 40.0 1.0
O B:HOH210 2.4 48.5 1.0
H3' C:DA3 3.0 24.1 1.0
P C:DT4 3.5 24.1 1.0
C3' C:DA3 3.9 20.1 1.0
O3' C:DA3 4.0 21.4 1.0
O2 B:DC2 4.2 32.4 1.0
O C:HOH217 4.2 44.4 1.0
O C:HOH206 4.2 44.2 1.0
O C:HOH228 4.2 48.7 1.0
H11 B:KSB101 4.2 24.6 1.0
OP1 C:DA3 4.3 24.3 1.0
OP1 C:DT4 4.3 22.9 1.0
H5'' C:DA3 4.3 23.8 1.0
N3 B:DC2 4.4 26.3 1.0
N7 B:KSB101 4.5 20.6 1.0
O5' C:DT4 4.5 23.4 1.0
C2 B:DC2 4.7 28.2 1.0
C27 B:KSB101 4.8 20.5 1.0
C2' C:DA3 4.8 21.0 1.0
C4' C:DA3 4.9 20.0 1.0
H2' C:DA3 4.9 25.2 1.0
H2'' C:DA3 4.9 25.2 1.0
C5' C:DA3 5.0 19.8 1.0
O C:HOH243 5.0 40.1 1.0

Magnesium binding site 7 out of 8 in 8rer

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Magnesium binding site 7 out of 8 in the Major Groove Intercalation with Polypyridyl Ruthenium Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Major Groove Intercalation with Polypyridyl Ruthenium Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg104

b:48.4
occ:1.00
 O A:HOH210 2.4 33.9 1.0
O C:HOH203 2.4 46.0 1.0
O C:HOH239 2.6 50.2 1.0
N10 B:KSB101 2.9 25.2 1.0
O C:HOH233 3.0 48.2 1.0
H16 B:KSB101 3.1 30.8 1.0
O A:HOH224 3.1 35.8 1.0
C32 B:KSB101 3.7 24.0 1.0
C33 B:KSB101 3.7 25.7 1.0
H15 B:KSB101 3.8 29.5 1.0
O A:HOH227 3.8 52.3 1.0
C31 B:KSB101 3.8 24.6 1.0
OP1 C:DA5 4.0 32.4 1.0
O C:HOH218 4.2 29.8 1.0
O C:HOH222 4.4 48.9 1.0
O A:HOH211 4.7 36.5 1.0
O B:HOH239 4.7 50.5 1.0
C29 B:KSB101 5.0 22.8 1.0

Magnesium binding site 8 out of 8 in 8rer

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Magnesium binding site 8 out of 8 in the Major Groove Intercalation with Polypyridyl Ruthenium Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Major Groove Intercalation with Polypyridyl Ruthenium Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg102

b:60.0
occ:1.00
 O D:HOH238 2.2 35.4 1.0
O D:HOH214 2.3 30.7 1.0
O D:HOH250 2.6 50.2 1.0
O D:HOH204 3.1 43.8 1.0
H71 D:DT5 4.2 29.5 1.0
O D:HOH230 4.3 48.4 1.0
H8 D:DA4 4.3 27.1 1.0
N7 D:DA4 4.4 22.1 1.0
H3' D:DT3 4.4 26.4 1.0
OP2 D:DA4 4.4 27.4 1.0
O D:HOH208 4.5 36.6 1.0
O D:HOH223 4.6 24.8 1.0
O C:HOH240 4.6 49.9 1.0
H2' D:DT3 4.6 24.4 1.0
CL D:CL103 4.7 27.9 1.0
C8 D:DA4 4.7 22.6 1.0
O D:HOH209 4.7 48.9 1.0
H1 D:KSB101 4.8 22.0 1.0
O D:HOH244 5.0 44.5 1.0
H73 D:DT5 5.0 29.5 1.0

Reference:

A.Abdullrahman, K.Mcquaid, C.J.Cardin, J.P.Hall. Ruthenium Polypyridyl Complex Intercalating in Major and Minor Groove Dna To Be Published.
Page generated: Sat Feb 8 20:42:29 2025

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