Atomistry » Magnesium » PDB 8rau-8rjf » 8rer
Atomistry »
  Magnesium »
    PDB 8rau-8rjf »
      8rer »

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

Go back to Magnesium Binding Sites List in 8rer
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

Go back to Magnesium Binding Sites List in 8rer
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

Go back to Magnesium Binding Sites List in 8rer
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

Go back to Magnesium Binding Sites List in 8rer
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

Go back to Magnesium Binding Sites List in 8rer
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

Go back to Magnesium Binding Sites List in 8rer
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

Go back to Magnesium Binding Sites List in 8rer
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

Go back to Magnesium Binding Sites List in 8rer
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: Fri Aug 15 13:58:06 2025

Last articles

Zn in 9QI3
Zn in 9QAN
Zn in 9QAO
Zn in 9QAQ
Zn in 9QUL
Zn in 9QAM
Zn in 9QME
Zn in 9OTI
Zn in 9Q1J
Zn in 9PRR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy