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Magnesium in PDB 1enn: Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution

Protein crystallography data

The structure of Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution, PDB code: 1enn was solved by M.Soler-Lopez, L.Malinina, J.A.Subirana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 0.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 21.938, 36.540, 52.728, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 16.1

Other elements in 1enn:

The structure of Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution (pdb code 1enn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution, PDB code: 1enn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 1enn

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Magnesium binding site 1 out of 7 in the Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg19

b:6.5
occ:1.00
 O B:HOH21 2.0 7.6 1.0
O A:HOH24 2.0 10.4 1.0
O A:HOH20 2.1 6.9 1.0
O B:HOH23 2.1 8.1 1.0
O A:HOH25 2.1 7.6 1.0
O A:HOH22 2.1 8.8 1.0
O6 A:DG3 4.1 6.5 1.0
O A:HOH114 4.2 10.1 1.0
O B:HOH113 4.2 25.9 1.0
O A:HOH112 4.3 7.2 1.0
N7 A:DG3 4.3 6.2 1.0
O B:HOH71 4.3 16.7 1.0
O A:HOH63 4.4 11.9 1.0
OP2 A:DC2 4.4 9.4 0.4
CL A:CL51 4.4 14.5 1.0
O B:HOH155 4.4 13.4 0.7
O4 B:DT16 4.5 6.6 1.0
O A:HOH64 4.5 16.6 1.0
C7 B:DT16 4.8 6.9 1.0
C5 A:DC2 4.8 6.7 1.0
C6 A:DG3 4.9 5.9 1.0
C7 B:DT15 5.0 7.6 1.0
C5 A:DG3 5.0 5.9 1.0

Magnesium binding site 2 out of 7 in 1enn

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Magnesium binding site 2 out of 7 in the Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg26

b:7.6
occ:1.00
 O A:HOH30 2.0 9.0 1.0
O A:HOH28 2.1 8.7 1.0
O A:HOH29 2.1 10.9 1.0
O A:HOH27 2.1 10.4 1.0
N7 A:DG1 2.3 7.5 1.0
C8 A:DG1 3.1 7.7 1.0
C5 A:DG1 3.5 7.1 1.0
O6 A:DG1 4.1 7.7 1.0
C6 A:DG1 4.2 7.3 1.0
N9 A:DG1 4.4 7.5 1.0
O A:HOH114 4.5 10.1 1.0
O A:HOH60 4.6 15.7 1.0
C4 A:DG1 4.6 6.6 1.0
CL A:CL51 4.6 14.5 1.0
O A:HOH115 4.7 9.1 1.0

Magnesium binding site 3 out of 7 in 1enn

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Magnesium binding site 3 out of 7 in the Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg31

b:9.5
occ:1.00
 O B:HOH36 1.9 18.1 0.2
O B:HOH37 2.0 8.4 0.6
O B:HOH32 2.0 18.1 1.0
O B:HOH35 2.0 14.4 1.0
O A:HOH34 2.1 13.9 1.0
O B:HOH33 2.1 13.2 1.0
O B:HOH36 2.1 16.2 0.8
O B:HOH37 2.4 9.3 0.5
O A:HOH85 4.0 10.0 1.0
O4' A:DG9 4.1 9.4 1.0
O B:HOH59 4.2 10.8 1.0
O B:HOH135 4.3 23.0 1.0
N3 A:DG9 4.3 8.5 1.0
C5' B:DA14 4.4 9.4 1.0
N2 B:DG12 4.5 7.0 1.0
N3 B:DA13 4.5 8.2 1.0
O4' B:DA13 4.7 8.7 1.0
C1' A:DG9 4.8 8.6 1.0
C4' B:DA14 4.9 9.2 1.0
C2 A:DG9 4.9 8.2 1.0
O4' B:DA14 4.9 11.5 1.0
N2 A:DG9 4.9 10.2 1.0
C1' B:DA13 4.9 9.0 1.0
C4 A:DG9 5.0 8.3 1.0
C4' A:DG9 5.0 9.5 1.0

Magnesium binding site 4 out of 7 in 1enn

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Magnesium binding site 4 out of 7 in the Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg38

b:10.5
occ:1.00
 O A:HOH43 2.0 24.8 0.5
O A:HOH39 2.0 17.2 1.0
OP2 A:DA4 2.0 10.2 1.0
O A:HOH42 2.0 13.3 1.0
O A:HOH40 2.1 12.1 1.0
O A:HOH41 2.1 16.0 1.0
O A:HOH43 2.1 9.7 0.5
P A:DA4 3.3 7.7 1.0
O A:HOH116 3.8 17.0 1.0
O5' A:DA4 3.8 7.6 1.0
OP1 A:DA4 4.1 9.9 1.0
O A:HOH77 4.2 18.3 1.0
O A:HOH69 4.3 8.3 1.0
O A:HOH162 4.3 33.3 0.4
C8 A:DA4 4.4 7.3 1.0
O3' A:DG3 4.5 7.2 1.0
N7 A:DA4 5.0 7.8 1.0

Magnesium binding site 5 out of 7 in 1enn

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Magnesium binding site 5 out of 7 in the Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg50

b:21.1
occ:0.75
 O A:HOH177 1.8 39.1 0.5
O B:HOH160 1.8 14.0 0.3
O A:HOH158 1.9 11.1 0.4
O A:HOH158 2.0 12.5 0.6
O B:HOH160 2.0 14.0 0.3
O A:HOH90 2.1 17.7 1.0
O A:HOH176 3.4 16.7 0.5
O B:HOH160 3.6 13.6 0.3
N2 B:DG18 4.1 9.0 1.0
O2 A:DC2 4.2 7.9 1.0
O A:HOH130 4.5 15.1 1.0
O4' A:DG3 4.6 6.6 1.0
C5' A:DG3 4.8 6.7 1.0
C4' A:DG3 4.8 6.5 1.0

Magnesium binding site 6 out of 7 in 1enn

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Magnesium binding site 6 out of 7 in the Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg44

b:29.5
occ:1.00
 O B:HOH46 1.9 24.5 1.0
O A:HOH176 2.1 16.7 0.5
O A:HOH45 2.2 22.9 0.6
O B:HOH47 2.2 21.6 1.0
O A:HOH48 2.2 17.6 1.0
O B:HOH160 3.5 13.6 0.3
O B:HOH160 3.9 14.0 0.3
O A:HOH70 3.9 19.1 1.0
O A:HOH130 3.9 15.1 1.0
O A:HOH141 4.6 18.8 0.5
O B:HOH109 4.8 16.0 1.0
N2 B:DG18 4.8 9.0 1.0
N3 B:DG18 4.8 8.3 1.0
N2 A:DG3 4.9 7.4 1.0

Magnesium binding site 7 out of 7 in 1enn

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Magnesium binding site 7 out of 7 in the Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Solvent Organization in An Oligonucleotide Crystal: the Structure of D(Gcgaattcg)2 at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg49

b:22.3
occ:1.00
 O A:HOH52 1.9 21.1 1.0
O B:HOH56 1.9 37.5 0.7
O A:HOH58 2.1 9.8 0.3
O B:HOH53 2.2 21.7 1.0
O B:HOH54 2.3 16.4 0.6
O B:HOH57 2.7 43.5 1.0
O B:HOH159 3.5 13.5 0.5
O6 B:DG12 4.2 7.4 1.0
N7 B:DG12 4.3 8.0 1.0
O A:HOH163 4.4 32.4 0.7
O A:HOH120 4.4 26.5 1.0
O A:HOH172 4.4 38.1 0.5
O B:HOH159 4.5 14.3 0.5
O4 A:DT7 4.5 9.9 1.0
C7 A:DT6 4.8 11.8 1.0
C6 B:DG12 4.9 6.8 1.0
C7 A:DT7 4.9 9.9 1.0
C5 B:DG12 5.0 7.4 1.0

Reference:

M.Soler-Lopez, L.Malinina, J.A.Subirana. Solvent Organization in An Oligonucleotide Crystal. the Structure of D(Gcgaattcg)2 at Atomic Resolution. J.Biol.Chem. V. 275 23034 2000.
ISSN: ISSN 0021-9258
PubMed: 10749874
DOI: 10.1074/JBC.M002119200
Page generated: Tue Aug 13 03:00:03 2024

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