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Magnesium in PDB 1egk: Crystal Structure of A Nucleic Acid Four-Way Junction

Protein crystallography data

The structure of Crystal Structure of A Nucleic Acid Four-Way Junction, PDB code: 1egk was solved by J.Nowakowski, P.J.Shim, C.D.Stout, G.F.Joyce, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 3.10
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 62.810, 114.260, 171.450, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 25.8

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of A Nucleic Acid Four-Way Junction (pdb code 1egk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Crystal Structure of A Nucleic Acid Four-Way Junction, PDB code: 1egk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 1egk

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Magnesium binding site 1 out of 14 in the Crystal Structure of A Nucleic Acid Four-Way Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Nucleic Acid Four-Way Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg21

b:74.5
occ:1.00
O A:HOH31 2.0 74.5 1.0
O A:HOH28 2.0 74.5 1.0
O A:HOH32 2.0 74.5 1.0
O A:HOH33 2.0 74.5 1.0
O A:HOH30 2.1 74.5 1.0
O A:HOH29 2.1 74.5 1.0
N7 A:G3 4.2 55.3 1.0
O6 A:G3 4.3 55.3 1.0
N7 A:G2 4.6 51.5 1.0
O6 A:G2 5.0 51.5 1.0

Magnesium binding site 2 out of 14 in 1egk

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Magnesium binding site 2 out of 14 in the Crystal Structure of A Nucleic Acid Four-Way Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Nucleic Acid Four-Way Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg22

b:0.7
occ:1.00
O B:HOH56 2.0 0.7 1.0
O B:HOH55 2.1 0.7 1.0
O B:HOH58 2.1 0.7 1.0
O B:HOH59 2.1 0.7 1.0
O B:HOH60 2.1 0.7 1.0
O B:HOH57 2.1 0.7 1.0
O6 B:DG31 4.3 54.7 1.0
O6 A:G9 4.9 54.4 1.0

Magnesium binding site 3 out of 14 in 1egk

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Magnesium binding site 3 out of 14 in the Crystal Structure of A Nucleic Acid Four-Way Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Nucleic Acid Four-Way Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg23

b:91.5
occ:1.00
O A:HOH36 2.0 91.5 1.0
O A:HOH34 2.0 91.5 1.0
O A:HOH35 2.0 91.5 1.0
O A:HOH37 2.1 91.5 1.0
O A:HOH39 2.1 91.5 1.0
O A:HOH38 2.1 91.5 1.0
O6 A:G18 4.1 67.4 1.0
N6 A:A19 4.4 57.9 1.0
N4 A:C17 4.6 56.5 1.0
N7 A:G18 4.7 67.4 1.0
C6 A:G18 5.0 67.4 1.0

Magnesium binding site 4 out of 14 in 1egk

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Magnesium binding site 4 out of 14 in the Crystal Structure of A Nucleic Acid Four-Way Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Nucleic Acid Four-Way Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg24

b:0.3
occ:1.00
O A:HOH43 2.1 0.3 1.0
O A:HOH44 2.1 0.3 1.0
O A:HOH42 2.1 0.3 1.0
O A:HOH40 2.1 0.3 1.0
O A:HOH41 2.1 0.3 1.0
O A:HOH45 2.1 0.3 1.0
OP2 A:A19 4.3 57.5 1.0

Magnesium binding site 5 out of 14 in 1egk

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Magnesium binding site 5 out of 14 in the Crystal Structure of A Nucleic Acid Four-Way Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Nucleic Acid Four-Way Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg25

b:0.4
occ:1.00
O B:HOH65 2.1 0.4 1.0
O A:HOH48 2.1 0.4 1.0
O D:HOH70 2.1 0.4 1.0
O B:HOH66 2.1 0.4 1.0
O A:HOH47 2.1 0.4 1.0
O A:HOH46 2.1 0.4 1.0
OP1 A:G3 2.9 61.5 1.0
O6 D:DG136 3.7 81.1 1.0
O6 B:DG32 3.7 62.0 1.0
P A:G3 4.3 61.5 1.0
N7 D:DG136 4.5 81.1 1.0
C6 D:DG136 4.7 81.1 1.0
N7 B:DG32 4.7 62.0 1.0
C6 B:DG32 4.7 62.0 1.0
O3' A:G2 4.8 53.7 1.0
N4 B:DC33 4.8 85.8 1.0
N7 D:DA135 4.9 98.3 1.0

Magnesium binding site 6 out of 14 in 1egk

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Magnesium binding site 6 out of 14 in the Crystal Structure of A Nucleic Acid Four-Way Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of A Nucleic Acid Four-Way Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg26

b:0.4
occ:1.00
O A:HOH54 2.0 0.4 1.0
O A:HOH49 2.1 0.4 1.0
O A:HOH50 2.1 0.4 1.0
O A:HOH51 2.1 0.4 1.0
O A:HOH53 2.1 0.4 1.0
O A:HOH52 2.1 0.4 1.0
O6 A:G16 3.6 70.0 1.0
O4 A:U15 3.9 60.3 1.0
C5 A:U15 4.5 60.3 1.0
C4 A:U15 4.5 60.3 1.0
N4 B:DC25 4.6 50.3 1.0
C6 A:G16 4.7 70.0 1.0

Magnesium binding site 7 out of 14 in 1egk

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Magnesium binding site 7 out of 14 in the Crystal Structure of A Nucleic Acid Four-Way Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of A Nucleic Acid Four-Way Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg27

b:0.6
occ:1.00
O A:HOH59 2.0 0.6 1.0
O A:HOH55 2.1 0.6 1.0
O A:HOH56 2.1 0.6 1.0
O A:HOH60 2.1 0.6 1.0
O A:HOH58 2.1 0.6 1.0
O A:HOH57 2.1 0.6 1.0
O6 A:G12 4.1 58.8 1.0
O6 A:G13 4.2 69.3 1.0
N7 A:G12 4.3 58.8 1.0
N7 A:G13 4.4 69.3 1.0
C6 A:G12 4.7 58.8 1.0
C5 A:G12 4.8 58.8 1.0
O6 A:G14 4.9 56.8 1.0

Magnesium binding site 8 out of 14 in 1egk

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Magnesium binding site 8 out of 14 in the Crystal Structure of A Nucleic Acid Four-Way Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of A Nucleic Acid Four-Way Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3

b:0.5
occ:1.00
O C:HOH28 2.0 0.5 1.0
O C:HOH29 2.1 0.5 1.0
O B:HOH61 2.1 0.5 1.0
O C:HOH32 2.1 0.5 1.0
O C:HOH31 2.1 0.5 1.0
O C:HOH30 2.1 0.5 1.0
O6 C:G105 4.1 95.0 1.0
N7 C:G105 4.2 95.0 1.0
N6 C:A104 4.7 87.3 1.0
N7 C:A104 4.8 87.3 1.0
C6 C:G105 4.9 95.0 1.0
C5 C:G105 4.9 95.0 1.0

Magnesium binding site 9 out of 14 in 1egk

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Magnesium binding site 9 out of 14 in the Crystal Structure of A Nucleic Acid Four-Way Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of A Nucleic Acid Four-Way Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg4

b:77.0
occ:1.00
O C:HOH37 2.0 77.0 1.0
O C:HOH34 2.0 77.0 1.0
O C:HOH36 2.0 77.0 1.0
O B:HOH63 2.0 77.0 1.0
O B:HOH62 2.1 77.0 1.0
O C:HOH35 2.1 77.0 1.0
O6 C:G102 4.3 79.2 1.0
N7 C:G102 4.3 79.2 1.0
N7 C:G103 4.4 89.0 1.0
O6 C:G103 4.6 89.0 1.0
OP2 B:DG44 4.7 87.1 1.0
O C:HOH31 4.7 0.5 1.0
C6 C:G102 4.9 79.2 1.0
C5 C:G102 4.9 79.2 1.0
OP1 B:DG44 5.0 87.1 1.0

Magnesium binding site 10 out of 14 in 1egk

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Magnesium binding site 10 out of 14 in the Crystal Structure of A Nucleic Acid Four-Way Junction


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of A Nucleic Acid Four-Way Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg6

b:1.0
occ:1.00
O C:HOH50 2.1 1.0 1.0
O C:HOH48 2.1 1.0 1.0
O C:HOH47 2.1 1.0 1.0
O C:HOH45 2.1 1.0 1.0
O C:HOH49 2.1 1.0 1.0
O C:HOH46 2.1 1.0 1.0
O6 C:G113 3.7 60.2 1.0
C6 C:G113 4.7 60.2 1.0
N7 C:G112 4.9 64.4 1.0
N7 C:G113 4.9 60.2 1.0

Reference:

J.Nowakowski, P.J.Shim, C.D.Stout, G.F.Joyce. Alternative Conformations of A Nucleic Acid Four-Way Junction. J.Mol.Biol. V. 300 93 2000.
ISSN: ISSN 0022-2836
PubMed: 10864501
DOI: 10.1006/JMBI.2000.3826
Page generated: Mon Dec 14 05:52:06 2020

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