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Magnesium in PDB 3g8s: Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme

Protein crystallography data

The structure of Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme, PDB code: 3g8s 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) 43.77 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.364, 228.480, 103.915, 90.00, 90.58, 90.00
R / Rfree (%) 24.6 / 30.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme (pdb code 3g8s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme, PDB code: 3g8s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3g8s

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Magnesium binding site 1 out of 10 in the Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg12

b:38.4
occ:1.00
 OP2 P:A31 2.4 72.1 1.0
OP1 E:C2 2.7 73.7 1.0
P P:A31 3.8 72.3 1.0
P E:C2 3.9 73.8 1.0
O6 P:G32 4.1 77.0 1.0
OP1 E:A2M0 4.3 78.7 1.0
OP2 E:C2 4.3 73.6 1.0
C3' P:G30 4.5 70.4 1.0
C5' E:A2M0 4.5 77.6 1.0
O3' P:G30 4.6 71.4 1.0
OP1 P:A31 4.6 72.5 1.0
C4' E:A-1 4.7 77.0 1.0
O5' P:A31 4.7 72.7 1.0
O5' E:C2 4.8 73.6 1.0
N7 P:A31 4.9 74.8 1.0
C5' P:G30 5.0 69.3 1.0

Magnesium binding site 2 out of 10 in 3g8s

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Magnesium binding site 2 out of 10 in the Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg2

b:27.4
occ:1.00
 OP2 P:C29 2.0 68.5 1.0
OP2 P:G30 2.1 67.7 1.0
OP2 E:C2 2.2 73.6 1.0
P P:G30 3.0 67.8 1.0
OP1 P:G30 3.2 67.7 1.0
P P:C29 3.4 68.4 1.0
P E:C2 3.5 73.8 1.0
O3' P:A28 3.8 68.3 1.0
O3' E:G1 3.9 74.2 1.0
O3' P:C29 4.0 67.6 1.0
C3' P:C29 4.1 67.2 1.0
O5' P:C29 4.3 67.8 1.0
O5' P:G30 4.4 68.3 1.0
OP1 P:C29 4.4 68.4 1.0
OP1 E:C2 4.5 73.7 1.0
O5' E:C2 4.5 73.6 1.0
C5' P:G30 4.6 69.3 1.0
C5' E:C2 4.7 73.5 1.0
C5' P:C29 4.8 67.3 1.0
C8 P:G30 4.9 69.8 1.0

Magnesium binding site 3 out of 10 in 3g8s

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Magnesium binding site 3 out of 10 in the Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme


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 Pre-Cleaved Bacillus Anthracis Glms Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg10

b:43.8
occ:1.00
 O2' P:A48 3.5 71.0 1.0
C5' P:U49 3.9 79.2 1.0
O P:HOH142 4.7 20.0 1.0
C4' P:U49 4.8 81.0 1.0
C2' P:A48 4.8 70.9 1.0
O5' P:U49 4.9 76.9 1.0

Magnesium binding site 4 out of 10 in 3g8s

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Magnesium binding site 4 out of 10 in the Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg3

b:39.8
occ:1.00
 OP2 Q:C29 2.1 45.2 1.0
OP2 F:C2 2.4 44.1 1.0
OP2 Q:G30 2.5 46.2 1.0
O3' Q:A28 2.8 44.8 1.0
P Q:C29 3.0 44.9 1.0
O2' Q:A28 3.5 45.0 1.0
O3' F:G1 3.5 45.5 1.0
P F:C2 3.6 43.8 1.0
P Q:G30 3.9 46.3 1.0
C3' Q:A28 4.0 44.8 1.0
O5' Q:C29 4.0 45.0 1.0
OP1 Q:C29 4.2 45.1 1.0
C3' Q:C29 4.2 45.0 1.0
C5' F:C2 4.3 41.4 1.0
C2' Q:A28 4.3 44.9 1.0
O3' Q:C29 4.3 45.5 1.0
O5' F:C2 4.4 42.7 1.0
O5' Q:G30 4.5 46.1 1.0
O2' F:G1 4.7 48.0 1.0
C5' Q:C29 4.7 45.2 1.0
OP1 F:C2 4.7 43.5 1.0
C3' F:G1 4.9 47.4 1.0

Magnesium binding site 5 out of 10 in 3g8s

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Magnesium binding site 5 out of 10 in the Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg4

b:42.1
occ:1.00
 OP1 R:U40 2.5 34.1 1.0
OP1 Q:U19 2.6 47.8 1.0
P R:U40 3.7 34.3 1.0
P Q:U19 4.0 47.6 1.0
O5' R:U40 4.1 34.8 1.0
C5' R:U40 4.1 35.2 1.0
OP2 R:U40 4.5 34.4 1.0
C5' Q:U19 4.5 47.3 1.0
O3' Q:G18 4.7 48.3 1.0
O5' Q:U19 4.7 47.5 1.0
O3' R:U39 5.0 34.2 1.0

Magnesium binding site 6 out of 10 in 3g8s

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Magnesium binding site 6 out of 10 in the Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg5

b:23.2
occ:1.00
 OP1 Q:U40 2.5 40.0 1.0
OP1 R:U19 2.9 54.6 1.0
P Q:U40 3.7 40.3 1.0
OP2 Q:U40 4.2 39.8 1.0
P R:U19 4.3 54.6 1.0
O5' Q:U40 4.4 40.7 1.0
C5' R:U19 4.8 56.2 1.0
O5' R:U19 4.8 55.4 1.0
C5' Q:U40 4.8 41.0 1.0
O3' R:G18 4.9 54.5 1.0
O3' Q:U39 5.0 40.5 1.0

Magnesium binding site 7 out of 10 in 3g8s

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Magnesium binding site 7 out of 10 in the Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme


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 Pre-Cleaved Bacillus Anthracis Glms Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg6

b:33.9
occ:1.00
 OP2 R:A46 2.2 31.0 1.0
P R:A46 3.5 31.0 1.0
N7 R:G47 3.7 46.6 1.0
O6 R:G47 3.7 47.1 1.0
O5' R:A46 3.8 32.2 1.0
N7 R:A46 4.2 36.1 1.0
O Q:HOH150 4.3 16.9 1.0
C8 R:A46 4.3 35.7 1.0
C3' R:G45 4.4 31.2 1.0
O3' R:G45 4.5 31.2 1.0
C5 R:G47 4.5 46.5 1.0
C6 R:G47 4.5 46.7 1.0
OP1 R:A46 4.5 31.2 1.0
N6 R:A48 4.6 56.5 1.0
C8 R:G47 4.8 46.3 1.0
OP2 R:G47 4.8 39.3 1.0

Magnesium binding site 8 out of 10 in 3g8s

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Magnesium binding site 8 out of 10 in the Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme


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 Pre-Cleaved Bacillus Anthracis Glms Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg7

b:32.9
occ:1.00
 OP2 R:C29 2.2 40.2 1.0
OP2 R:G30 2.3 37.6 1.0
OP2 G:C2 2.5 37.5 1.0
P R:C29 3.6 40.0 1.0
P R:G30 3.7 37.2 1.0
P G:C2 3.8 37.7 1.0
O3' R:A28 4.2 40.1 1.0
O5' G:C2 4.2 37.0 1.0
OP1 R:G30 4.3 37.1 1.0
C5' G:C2 4.3 36.1 1.0
OP1 R:C29 4.4 40.4 1.0
O3' G:G1 4.4 38.4 1.0
O3' R:C29 4.6 37.1 1.0
O5' R:C29 4.6 39.2 1.0
O5' R:G30 4.7 37.1 1.0
C3' R:C29 4.9 37.2 1.0

Magnesium binding site 9 out of 10 in 3g8s

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Magnesium binding site 9 out of 10 in the Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme


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 Pre-Cleaved Bacillus Anthracis Glms Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg12

b:29.1
occ:1.00
 OP2 S:A31 2.5 63.6 1.0
OP1 H:C2 2.6 56.2 1.0
P H:C2 3.9 56.1 1.0
P S:A31 4.0 63.4 1.0
OP2 H:C2 4.3 56.0 1.0
C3' S:G30 4.4 60.1 1.0
O6 S:G32 4.5 72.2 1.0
O3' S:G30 4.6 61.8 1.0
OP1 S:A31 4.8 63.7 1.0
C5' H:A2M0 4.8 64.4 1.0
O5' H:C2 4.8 55.3 1.0
O5' S:A31 4.9 64.2 1.0
O5' S:G30 4.9 56.7 1.0
OP1 H:A2M0 4.9 64.7 1.0
O3' H:G1 4.9 56.2 1.0

Magnesium binding site 10 out of 10 in 3g8s

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Magnesium binding site 10 out of 10 in the Crystal Structure of the Pre-Cleaved Bacillus Anthracis Glms Ribozyme


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 the Pre-Cleaved Bacillus Anthracis Glms Ribozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg9

b:29.1
occ:1.00
 OP2 H:C2 2.2 56.0 1.0
OP2 S:C29 2.3 53.4 1.0
OP2 S:G30 2.5 56.0 1.0
O3' S:A28 3.4 53.0 1.0
P S:C29 3.4 53.3 1.0
P H:C2 3.6 56.1 1.0
P S:G30 3.9 56.0 1.0
O2' S:A28 3.9 52.1 1.0
O3' H:G1 4.0 56.2 1.0
C5' H:C2 4.0 54.4 1.0
O5' H:C2 4.2 55.3 1.0
C3' S:A28 4.3 52.7 1.0
OP1 S:C29 4.4 53.5 1.0
OP1 S:G30 4.5 56.1 1.0
O5' S:C29 4.6 52.9 1.0
O3' S:C29 4.6 55.0 1.0
C2' S:A28 4.7 52.4 1.0
OP1 H:C2 4.8 56.2 1.0
C3' S:C29 4.8 54.0 1.0
O5' S:G30 4.9 56.7 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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