Magnesium in PDB 2nz4: Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor

The structure of Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor, PDB code: 2nz4 was solved by J.C.Cochrane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.94 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.127, 234.157, 105.003, 90.00, 90.65, 90.00
R / Rfree (%)	22.2 / 26.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor (pdb code 2nz4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor, PDB code: 2nz4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg9005 b:50.2 occ:1.00 O P:HOH9014 1.9 41.6 1.0 O P:HOH9015 2.0 39.0 1.0 O P:HOH9016 2.0 55.6 1.0 O P:HOH9011 2.1 51.4 1.0 O P:HOH9013 2.2 37.0 1.0 O P:HOH9012 2.3 55.4 1.0 OP2 P:C52 3.4 49.1 1.0 N7 P:G53 4.1 57.9 1.0 O3P P:GLP5001 4.1 53.0 1.0 N6 P:A28 4.2 35.5 1.0 O2P P:GLP5001 4.2 56.0 1.0 O6 P:G53 4.3 57.1 1.0 OP2 P:G53 4.4 54.5 1.0 O6 P:G54 4.4 60.4 1.0 P P:C52 4.5 49.1 1.0 N7 P:G54 4.6 59.7 1.0 N7 P:A28 4.6 37.0 1.0 C5 P:G53 4.7 57.0 1.0 P P:GLP5001 4.8 56.0 1.0 OP1 P:C52 4.8 50.0 1.0 C6 P:G53 4.8 58.0 1.0 C8 P:G53 4.9 57.3 1.0

Magnesium binding site 2 out of 16 in the Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg9006 b:59.3 occ:1.00 O P:HOH9021 2.0 62.8 1.0 O P:HOH9017 2.0 49.6 1.0 O P:HOH9018 2.0 38.0 1.0 O P:HOH9022 2.3 50.4 1.0 O P:HOH9020 2.9 49.4 1.0 O P:HOH9019 3.3 50.2 1.0 O1P P:GLP5001 3.3 54.7 1.0 O3P P:GLP5001 4.0 53.0 1.0 P P:GLP5001 4.2 56.0 1.0 C6 P:GLP5001 4.6 53.1 1.0 N4 P:C55 4.7 54.0 1.0 O6 P:G56 4.8 58.6 1.0 O6 P:GLP5001 4.9 52.7 1.0 C5 P:C55 5.0 54.9 1.0

Magnesium binding site 3 out of 16 in the Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg9009 b:70.6 occ:1.00 O E:HOH131 2.0 53.1 1.0 OP2 P:A31 2.1 42.2 1.0 O P:HOH9028 2.4 53.0 1.0 P P:A31 3.6 42.1 1.0 OP1 E:C2 3.7 33.0 1.0 OP1 E:A2M0 3.8 44.8 1.0 O5' P:A31 4.2 43.5 1.0 C3' P:G30 4.4 43.4 1.0 O3' P:G30 4.5 43.0 1.0 N7 P:G32 4.5 43.7 1.0 OP1 P:A31 4.5 42.4 1.0 N7 P:A31 4.7 48.3 1.0 C8 P:A31 4.7 47.9 1.0 C5' P:G30 4.8 42.9 1.0 O6 P:G32 4.8 43.5 1.0 C5' E:A2M0 4.9 40.4 1.0

Magnesium binding site 4 out of 16 in the Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg9010 b:49.6 occ:1.00 O E:HOH80 2.1 35.4 1.0 OP2 E:C2 2.1 31.9 1.0 OP2 P:C29 2.2 39.8 1.0 OP2 P:G30 2.3 41.6 1.0 O3' P:A28 3.1 38.4 1.0 O3' E:G1 3.2 34.6 1.0 P E:C2 3.2 31.5 1.0 P P:C29 3.2 37.4 1.0 O2' P:A28 3.5 39.5 1.0 P P:G30 3.6 42.0 1.0 O5' P:C29 4.1 39.6 1.0 O5' E:C2 4.1 33.8 1.0 O2' E:G1 4.1 35.8 1.0 OP1 P:G30 4.2 41.7 1.0 C3' P:A28 4.2 36.6 1.0 C5' E:C2 4.2 32.8 1.0 C3' P:C29 4.3 41.2 1.0 OP1 E:C2 4.4 33.0 1.0 OP1 P:C29 4.4 40.0 1.0 C2' P:A28 4.4 37.4 1.0 O3' P:C29 4.5 41.2 1.0 C3' E:G1 4.5 36.3 1.0 C5' P:C29 4.7 39.8 1.0 O5' P:G30 4.8 42.1 1.0 C8 P:G30 4.8 42.0 1.0 C2' E:G1 4.9 36.5 1.0 N7 P:G30 5.0 41.5 1.0

Magnesium binding site 5 out of 16 in the Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg9011 b:73.7 occ:1.00 OP2 F:A2M0 2.3 37.8 1.0 OP1 F:C2 2.3 24.6 1.0 OP2 Q:A31 3.5 33.1 1.0 P F:C2 3.5 25.6 1.0 P F:A2M0 3.8 39.0 1.0 OP2 F:C2 3.9 24.6 1.0 C5' Q:G30 4.0 31.4 1.0 O5' F:A2M0 4.4 36.0 1.0 O5' F:C2 4.5 26.1 1.0 O3' F:G1 4.6 25.1 1.0 C5' F:A2M0 4.6 31.4 1.0 OP2 Q:G30 4.6 31.5 1.0 OP1 F:A2M0 4.7 37.8 1.0 C3' Q:G30 4.8 32.1 1.0 O3' F:A-1 4.8 37.3 1.0 O6 Q:G32 4.8 34.3 1.0 P Q:A31 4.8 31.1 1.0 O5' Q:G30 4.9 31.0 1.0 C3' F:G1 4.9 26.7 1.0 C4' Q:G30 4.9 31.2 1.0

Magnesium binding site 6 out of 16 in the Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg9007 b:42.3 occ:1.00 O Q:HOH9015 2.1 38.7 1.0 O F:HOH35 2.1 50.4 1.0 O Q:HOH9013 2.1 58.8 1.0 O Q:HOH9014 2.2 38.9 1.0 O Q:HOH9016 2.3 43.5 1.0 O F:HOH33 2.5 47.2 1.0 O1P F:GLP5002 3.4 51.3 1.0 OP2 Q:C52 3.7 40.7 1.0 O2P F:GLP5002 3.8 51.0 1.0 P F:GLP5002 4.1 50.1 1.0 OP2 Q:G53 4.4 42.1 1.0 N6 Q:A28 4.4 26.2 1.0 N7 Q:G53 4.6 40.5 1.0 N7 Q:G54 4.7 41.0 1.0 N7 Q:A28 4.8 25.4 1.0 N2 F:G1 4.8 29.7 1.0 P Q:C52 4.8 43.6 1.0 O3P F:GLP5002 4.9 48.5 1.0 OP1 Q:C52 4.9 42.5 1.0 O6 Q:G54 4.9 40.9 1.0

Magnesium binding site 7 out of 16 in the Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg9008 b:46.0 occ:1.00 O Q:HOH9019 1.8 56.9 1.0 O F:HOH37 1.8 52.9 1.0 O Q:HOH9018 2.0 68.0 1.0 O F:HOH40 2.1 40.6 1.0 O Q:HOH9017 2.1 42.0 1.0 O F:HOH42 2.5 41.6 1.0 O F:HOH82 3.8 42.7 1.0 N7 Q:G56 4.3 32.8 1.0 O6 Q:G56 4.5 32.8 1.0 O6 Q:G57 4.6 37.2 1.0 N7 Q:G57 4.7 37.4 1.0 O3P F:GLP5002 4.7 48.5 1.0 O2P F:GLP5002 4.9 51.0 1.0

Magnesium binding site 8 out of 16 in the Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg9012 b:56.2 occ:1.00 O Q:HOH9027 2.2 33.6 1.0 OP2 F:C2 2.3 24.6 1.0 OP2 Q:C29 2.3 30.4 1.0 OP2 Q:G30 2.5 31.5 1.0 O3' Q:A28 3.0 30.8 1.0 O2' Q:A28 3.1 29.1 1.0 P Q:C29 3.2 30.8 1.0 O3' F:G1 3.4 25.1 1.0 P F:C2 3.4 25.6 1.0 P Q:G30 3.7 31.9 1.0 O2' F:G1 4.0 25.8 1.0 C3' Q:A28 4.0 29.9 1.0 O5' Q:C29 4.1 31.7 1.0 C2' Q:A28 4.1 29.4 1.0 OP1 Q:G30 4.2 29.6 1.0 C3' Q:C29 4.2 31.5 1.0 O5' F:C2 4.3 26.1 1.0 C5' F:C2 4.3 25.9 1.0 O3' Q:C29 4.4 31.9 1.0 OP1 Q:C29 4.4 33.5 1.0 OP1 F:C2 4.6 24.6 1.0 C3' F:G1 4.6 26.7 1.0 C5' Q:C29 4.7 31.2 1.0 C2' F:G1 4.8 27.0 1.0 C1' Q:A28 4.9 26.9 1.0 C8 Q:G30 5.0 28.2 1.0

Magnesium binding site 9 out of 16 in the Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg9013 b:68.4 occ:1.00 O G:HOH9020 2.3 42.9 1.0 OP1 G:C2 2.5 24.9 1.0 O5' G:A-1 3.3 33.9 1.0 OP2 R:A31 3.4 32.4 1.0 P G:C2 3.8 25.5 1.0 OP1 G:A2M0 4.0 36.4 1.0 OP2 G:C2 4.4 25.4 1.0 C5' G:A2M0 4.4 31.7 1.0 O6 R:G32 4.5 35.1 1.0 C5' G:A-1 4.7 35.2 1.0 O5' G:C2 4.7 25.7 1.0 O5' R:G30 4.8 31.6 1.0 P R:A31 4.8 28.0 1.0 O3' G:G1 4.9 24.2 1.0

Magnesium binding site 10 out of 16 in the Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg9001 b:51.8 occ:1.00 O R:HOH9018 1.9 58.7 1.0 O G:HOH9014 2.0 62.7 1.0 O R:HOH9017 2.0 59.1 1.0 O G:HOH9015 2.0 50.3 1.0 O R:HOH9015 2.2 54.4 1.0 O R:HOH9016 2.3 45.5 1.0 N7 R:G56 3.9 33.6 1.0 O G:HOH9018 4.1 40.9 1.0 O6 R:G56 4.2 33.2 1.0 O6 R:G57 4.3 36.0 1.0 N7 R:G57 4.3 37.8 1.0 O2P G:GLP5003 4.5 47.9 1.0 O3P G:GLP5003 4.5 49.0 1.0 C5 R:G56 4.7 34.8 1.0 C6 R:G56 4.8 34.2 1.0 N4 R:C55 4.9 39.4 1.0 C6 G:GLP5003 4.9 47.5 1.0 C8 R:G56 4.9 34.6 1.0 C6 R:G57 5.0 37.5 1.0

J.C.Cochrane, S.V.Lipchock, S.A.Strobel. Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor Chem.Biol. V. 14 97 2007.
ISSN: ISSN 1074-5521
PubMed: 17196404
DOI: 10.1016/J.CHEMBIOL.2006.12.005