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Magnesium in PDB 3g96: Crystal Structure of the Bacillus Anthracis Glms Ribozyme Bound to MAN6P

Protein crystallography data

The structure of Crystal Structure of the Bacillus Anthracis Glms Ribozyme Bound to MAN6P, PDB code: 3g96 was solved by S.A.Strobel, J.C.Cochrane, S.V.Lipchock, K.D.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.75 / 3.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.401, 232.369, 104.657, 90.00, 90.65, 90.00
R / Rfree (%) 25.5 / 31.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Bacillus Anthracis Glms Ribozyme Bound to MAN6P (pdb code 3g96). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of the Bacillus Anthracis Glms Ribozyme Bound to MAN6P, PDB code: 3g96:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3g96

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Magnesium binding site 1 out of 9 in the Crystal Structure of the Bacillus Anthracis Glms Ribozyme Bound to MAN6P


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 the Bacillus Anthracis Glms Ribozyme Bound to MAN6P within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg1

b:64.6
occ:1.00
 O2P F:6MN12 3.5 65.2 1.0
OP2 Q:C52 3.8 61.4 1.0
O6 Q:G54 3.8 70.5 1.0
N7 Q:G53 4.3 70.1 1.0
N7 Q:G54 4.4 70.7 1.0
O6 Q:G53 4.5 70.3 1.0
N7 Q:A28 4.7 55.0 1.0
C6 Q:G54 4.7 70.4 1.0
C5 Q:G53 4.8 70.1 1.0
P F:6MN12 4.8 65.3 1.0
N4 Q:C55 4.9 69.1 1.0
C6 Q:G53 4.9 70.3 1.0
C5 Q:G54 4.9 70.6 1.0

Magnesium binding site 2 out of 9 in 3g96

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Magnesium binding site 2 out of 9 in the Crystal Structure of the Bacillus Anthracis Glms Ribozyme Bound to MAN6P


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 the Bacillus Anthracis Glms Ribozyme Bound to MAN6P within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg2

b:54.0
occ:1.00
 O F:HOH37 2.2 42.2 1.0
O6 Q:G57 3.7 64.1 1.0
N6 Q:A58 4.2 58.3 1.0
O3P F:6MN12 4.3 65.2 1.0
N7 Q:G57 4.3 63.7 1.0
C6 F:6MN12 4.4 65.8 1.0
O6 Q:G56 4.5 65.1 1.0
C6 Q:G57 4.6 63.9 1.0
N7 Q:G56 4.6 65.0 1.0
C5 Q:G57 4.9 63.9 1.0
C6 Q:A58 4.9 58.1 1.0
O6 F:6MN12 5.0 65.6 1.0

Magnesium binding site 3 out of 9 in 3g96

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Magnesium binding site 3 out of 9 in the Crystal Structure of the Bacillus Anthracis Glms Ribozyme Bound to MAN6P


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 the Bacillus Anthracis Glms Ribozyme Bound to MAN6P within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg4

b:77.4
occ:1.00
 O2A Q:GTP12 2.5 87.9 1.0
PA Q:GTP12 3.5 87.8 1.0
O1A Q:GTP12 3.7 87.8 1.0
O3A Q:GTP12 4.3 89.9 1.0
O1B Q:GTP12 4.7 91.9 1.0
O5' Q:GTP12 4.9 86.2 1.0

Magnesium binding site 4 out of 9 in 3g96

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Magnesium binding site 4 out of 9 in the Crystal Structure of the Bacillus Anthracis Glms Ribozyme Bound to MAN6P


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 the Bacillus Anthracis Glms Ribozyme Bound to MAN6P within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg12

b:75.2
occ:1.00
 OP1 G:C2 2.2 43.9 1.0
O5' G:A-1 3.1 62.5 1.0
P G:C2 3.4 43.4 1.0
OP2 G:C2 3.7 43.6 1.0
C5' G:A-1 3.7 64.4 1.0
OP2 R:A31 3.9 44.1 1.0
O5' G:C2 4.3 43.6 1.0
C5' G:A2M0 4.5 56.3 1.0
O3' G:G1 4.6 43.6 1.0
O5' R:G30 4.7 46.7 1.0
C5' R:G30 5.0 46.1 1.0

Magnesium binding site 5 out of 9 in 3g96

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Magnesium binding site 5 out of 9 in the Crystal Structure of the Bacillus Anthracis Glms Ribozyme Bound to MAN6P


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 the Bacillus Anthracis Glms Ribozyme Bound to MAN6P within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg13

b:47.0
occ:1.00
 N1 G:G1 3.8 47.4 1.0
N2 G:G1 4.0 47.3 1.0
C2 G:G1 4.4 47.2 1.0
N4 G:C2 4.7 45.2 1.0
O6 G:G1 4.7 48.4 1.0
C6 G:G1 4.7 47.3 1.0
N6 R:A28 4.8 52.6 1.0
MG R:MG5 4.8 55.7 1.0
MG R:MG8 5.0 49.4 1.0

Magnesium binding site 6 out of 9 in 3g96

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Magnesium binding site 6 out of 9 in the Crystal Structure of the Bacillus Anthracis Glms Ribozyme Bound to MAN6P


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 the Bacillus Anthracis Glms Ribozyme Bound to MAN6P within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg3

b:56.1
occ:1.00
 OP2 R:A46 2.1 37.2 1.0
P R:A46 3.5 37.3 1.0
O5' R:A46 3.9 36.3 1.0
N7 R:G47 4.0 38.7 1.0
C3' R:G45 4.2 37.5 1.0
O3' R:G45 4.3 37.6 1.0
N7 R:A46 4.3 29.6 1.0
O6 R:G47 4.4 39.7 1.0
OP2 Q:U49 4.4 62.0 1.0
C8 R:A46 4.4 30.1 1.0
N6 R:A48 4.6 44.0 1.0
OP1 R:A46 4.7 36.8 1.0
OP2 R:G47 4.7 39.3 1.0
C5' R:G45 4.8 38.3 1.0
C5 R:G47 5.0 38.1 1.0
C8 R:G47 5.0 39.5 1.0

Magnesium binding site 7 out of 9 in 3g96

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Magnesium binding site 7 out of 9 in the Crystal Structure of the Bacillus Anthracis Glms Ribozyme Bound to MAN6P


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 the Bacillus Anthracis Glms Ribozyme Bound to MAN6P within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg5

b:55.7
occ:1.00
 O6 R:G56 3.9 62.6 1.0
O6 R:G57 4.2 59.2 1.0
N7 R:G56 4.4 62.4 1.0
N7 R:G57 4.6 58.4 1.0
N6 R:A58 4.7 57.1 1.0
C6 R:G56 4.7 62.4 1.0
MG G:MG13 4.8 47.0 1.0
C5 R:G56 5.0 62.4 1.0

Magnesium binding site 8 out of 9 in 3g96

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Magnesium binding site 8 out of 9 in the Crystal Structure of the Bacillus Anthracis Glms Ribozyme Bound to MAN6P


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 the Bacillus Anthracis Glms Ribozyme Bound to MAN6P within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg6

b:72.5
occ:1.00
 O2A R:GTP12 3.2 97.4 1.0
O1A R:GTP12 3.3 97.5 1.0
PA R:GTP12 3.7 97.4 1.0
O3A R:GTP12 4.4 99.3 1.0

Magnesium binding site 9 out of 9 in 3g96

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Magnesium binding site 9 out of 9 in the Crystal Structure of the Bacillus Anthracis Glms Ribozyme Bound to MAN6P


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 the Bacillus Anthracis Glms Ribozyme Bound to MAN6P within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg8

b:49.4
occ:1.00
 OP2 R:C52 3.7 60.0 1.0
O6 R:G54 4.0 66.9 1.0
N7 R:G53 4.1 63.2 1.0
N7 R:G54 4.3 66.7 1.0
O6 R:G53 4.4 63.4 1.0
N4 R:C55 4.6 65.2 1.0
N7 R:A28 4.6 51.7 1.0
C5 R:G53 4.7 63.3 1.0
N6 R:A28 4.8 52.6 1.0
C6 R:G54 4.8 66.8 1.0
C6 R:G53 4.9 63.5 1.0
C8 R:G53 4.9 63.2 1.0
P R:C52 4.9 60.0 1.0
MG G:MG13 5.0 47.0 1.0
C5 R:G54 5.0 66.6 1.0

Reference:

J.C.Cochrane, S.V.Lipchock, K.D.Smith, S.A.Strobel. Structural and Chemical Basis For Glucosamine 6-Phosphate Binding and Activation of the Glms Ribozyme Biochemistry V. 48 3239 2009.
ISSN: ISSN 0006-2960
PubMed: 19228039
DOI: 10.1021/BI802069P
Page generated: Wed Aug 14 14:41:29 2024

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