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Magnesium in PDB 4r4d: Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex

Protein crystallography data

The structure of Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex, PDB code: 4r4d was solved by P.K.Mandal, G.W.Collie, B.Kauffmann, I.Huc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.54 / 1.29
Space group P -1
Cell size a, b, c (Å), α, β, γ (°) 31.610, 32.951, 46.250, 70.76, 80.77, 73.77
R / Rfree (%) 26.9 / 31.1

Other elements in 4r4d:

The structure of Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex (pdb code 4r4d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex, PDB code: 4r4d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4r4d

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Magnesium binding site 1 out of 8 in the Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:13.2
occ:0.50
 O B:HOH220 2.1 28.3 1.0
O B:HOH217 2.1 23.1 1.0
O A:HOH210 2.3 28.0 1.0
O2 B:DC7 4.1 14.9 1.0
O4' A:DA6 4.1 14.2 0.5
O4' B:DC8 4.5 17.9 1.0
O2 A:DT5 4.5 20.9 0.4
O B:HOH212 4.6 27.4 1.0
C4' A:DA6 4.6 16.6 0.5
O4' A:DA6 4.7 19.1 0.5
N2 A:DG4 4.7 14.6 1.0
C4' B:DC8 4.8 17.1 1.0
C5' B:DC8 4.9 20.7 1.0

Magnesium binding site 2 out of 8 in 4r4d

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Magnesium binding site 2 out of 8 in the Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:15.8
occ:0.60
 O A:HOH206 1.9 21.9 1.0
O A:HOH203 2.0 22.6 1.0
O A:HOH234 2.1 29.4 1.0
O A:HOH201 2.2 19.2 1.0
N7 A:DG3 4.1 12.9 1.0
O6 A:DG4 4.1 11.7 1.0
O A:HOH212 4.1 24.1 1.0
O6 A:DG3 4.3 12.1 1.0
N4 B:DC7 4.6 10.7 1.0
C5 A:DC2 4.8 14.4 1.0
C5 A:DG3 4.9 11.1 1.0
C6 A:DC2 4.9 15.3 1.0
C6 A:DG3 5.0 11.6 1.0

Magnesium binding site 3 out of 8 in 4r4d

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Magnesium binding site 3 out of 8 in the Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:19.2
occ:0.70
 O B:HOH213 1.9 32.4 1.0
O B:HOH225 1.9 34.0 1.0
O B:HOH216 2.1 23.9 1.0
OP1 B:DC8 2.1 31.1 1.0
O B:HOH218 2.4 32.5 1.0
P B:DC8 3.5 24.0 1.0
O3' B:DC7 3.9 24.1 1.0
O B:HOH226 4.3 29.6 1.0
OP2 B:DC8 4.5 31.0 1.0
O5' B:DC8 4.5 23.1 1.0
C5' B:DC8 4.6 20.7 1.0

Magnesium binding site 4 out of 8 in 4r4d

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Magnesium binding site 4 out of 8 in the Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:13.2
occ:0.60
 O B:HOH211 2.0 22.1 1.0
O B:HOH202 2.0 18.1 1.0
O B:HOH203 2.1 18.0 1.0
N7 B:DG9 4.1 14.7 1.0
O6 B:DG10 4.2 11.2 1.0
O B:HOH209 4.4 20.7 1.0
O6 B:DG9 4.5 12.2 1.0
N4 A:DC1 4.6 9.4 0.5
N4 A:DC1 4.7 14.0 0.5
C5 B:DC8 4.8 15.6 1.0
C6 B:DC8 4.9 17.7 1.0
C5 B:DG9 5.0 11.9 1.0
O B:HOH207 5.0 21.1 1.0

Magnesium binding site 5 out of 8 in 4r4d

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Magnesium binding site 5 out of 8 in the Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg103

b:26.2
occ:1.00
 O B:HOH210 2.0 23.9 1.0
O B:HOH224 3.4 31.0 1.0
O6 B:DG4 4.1 13.1 1.0
N7 B:DG3 4.1 16.5 1.0
C2' B:DC2 4.7 23.8 1.0
O B:HOH222 4.7 30.4 1.0
C8 B:DG3 4.9 16.0 1.0
O6 B:DG3 5.0 14.3 1.0

Magnesium binding site 6 out of 8 in 4r4d

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Magnesium binding site 6 out of 8 in the Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg104

b:23.6
occ:1.00
 O B:HOH234 1.7 24.7 1.0
O B:HOH229 2.1 24.7 1.0
OP1 B:DT5 2.8 18.4 0.5
OP1 B:DT5 3.7 13.1 0.5
OP1 B:DA6 4.0 24.7 0.5
C5' B:DT5 4.2 10.2 0.5
P B:DT5 4.2 14.8 0.5
O5' B:DT5 4.4 12.8 0.5
C5' B:DT5 4.5 19.9 0.5
OP2 B:DA6 4.6 17.6 0.5
OP2 B:DA6 4.7 24.1 0.5
P B:DA6 4.8 19.9 0.5
C4' B:DT5 4.8 18.7 0.5
OP2 B:DT5 4.8 26.0 0.5
P B:DT5 4.8 14.3 0.5
C4' B:DT5 4.9 12.8 0.5
O5' B:DT5 4.9 17.4 0.5
C3' B:DT5 5.0 17.5 0.5

Magnesium binding site 7 out of 8 in 4r4d

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Magnesium binding site 7 out of 8 in the Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:9.7
occ:0.50
 O C:HOH228 2.1 22.5 1.0
O C:HOH204 2.1 17.0 1.0
O C:HOH213 2.2 17.9 1.0
OP1 C:DC8 4.2 15.8 1.0
O C:HOH221 4.3 20.6 1.0
OP2 C:DG9 4.3 16.1 1.0
OP1 C:DG9 4.6 16.9 1.0
P C:DG9 4.9 14.2 1.0

Magnesium binding site 8 out of 8 in 4r4d

Go back to Magnesium Binding Sites List in 4r4d
Magnesium binding site 8 out of 8 in the Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Racemic Crystal Structure of A Magnesium-Bound B-Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:11.2
occ:1.00
 OP1 D:DC8 2.0 13.0 1.0
O D:HOH203 2.1 14.9 1.0
O D:HOH201 2.1 13.6 1.0
P D:DC8 3.3 12.1 1.0
O3' D:DC7 3.7 12.2 1.0
OP2 D:DC8 4.2 14.4 1.0
O A:HOH211 4.2 23.1 1.0
O A:HOH217 4.3 24.8 1.0
O A:HOH202 4.4 20.4 1.0
O5' D:DC8 4.5 11.7 1.0
C5' D:DC8 4.6 12.7 1.0
O D:HOH213 4.7 29.1 1.0
C3' D:DC7 5.0 12.8 1.0

Reference:

P.K.Mandal, G.W.Collie, B.Kauffmann, I.Huc. Racemic Dna Crystallography. Angew.Chem.Int.Ed.Engl. 2014.
ISSN: ESSN 1521-3773
PubMed: 25358289
DOI: 10.1002/ANIE.201409014
Page generated: Mon Aug 11 23:08:38 2025

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