Magnesium in PDB 3o6x: Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis

The structure of Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis, PDB code: 3o6x was solved by J.M.Van Rooyen, H.Belrhali, V.R.Abratt, B.T.Sewell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.87 / 3.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	198.250, 203.960, 234.590, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 26.9

The structure of Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis (pdb code 3o6x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis, PDB code: 3o6x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis


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 Type III Glutamine Synthetase From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:3.2 occ:1.00 OE2 A:GLU472 1.8 44.6 1.0 O1B A:ADP4001 2.1 80.6 1.0 ND1 A:HIS342 2.1 31.3 1.0 OE2 A:GLU215 2.4 28.9 1.0 O3A A:P3S3001 2.9 0.5 1.0 PB A:ADP4001 2.9 80.3 1.0 CE1 A:HIS342 2.9 31.3 1.0 CD A:GLU472 2.9 44.6 1.0 OE1 A:GLU215 3.0 28.9 1.0 CD A:GLU215 3.0 28.9 1.0 O3A A:ADP4001 3.1 81.8 1.0 CG A:HIS342 3.2 31.3 1.0 NH1 A:ARG474 3.2 72.6 1.0 O2B A:ADP4001 3.2 81.1 1.0 OE1 A:GLU472 3.5 44.6 1.0 CB A:HIS342 3.6 31.3 1.0 PA A:P3S3001 3.9 0.6 1.0 O2A A:P3S3001 4.0 0.1 1.0 NE2 A:HIS342 4.0 31.3 1.0 CG A:GLU472 4.1 44.6 1.0 CD2 A:HIS342 4.2 31.3 1.0 CZ A:ARG474 4.2 72.6 1.0 CG A:GLU215 4.5 28.9 1.0 O3B A:ADP4001 4.5 84.2 1.0 PA A:ADP4001 4.6 84.2 1.0 O1A A:P3S3001 4.8 0.5 1.0 CD A:ARG474 4.8 72.6 1.0 O5' A:ADP4001 4.9 89.4 1.0 NE A:ARG474 4.9 72.6 1.0 ND2 A:ASN344 4.9 40.8 1.0 NH2 A:ARG474 5.0 72.6 1.0

Magnesium binding site 2 out of 12 in the Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis


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 Type III Glutamine Synthetase From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:37.5 occ:1.00 OE2 A:GLU286 2.3 28.6 1.0 NE A:P3S3001 2.5 0.2 1.0 CG A:GLU293 2.7 69.3 1.0 PA A:P3S3001 3.1 0.6 1.0 OE1 A:GLU217 3.1 37.3 1.0 O1A A:P3S3001 3.1 0.5 1.0 CD A:GLU293 3.2 69.3 1.0 CB A:GLU293 3.2 69.3 1.0 OE1 A:GLU293 3.2 69.3 1.0 O3A A:P3S3001 3.2 0.5 1.0 CD A:GLU286 3.3 28.6 1.0 CD A:GLU217 3.6 37.3 1.0 CG A:GLU217 3.6 37.3 1.0 OE1 A:GLU286 3.7 28.6 1.0 SD A:P3S3001 4.1 0.3 1.0 OE2 A:GLU293 4.1 69.3 1.0 NE2 A:HIS284 4.2 32.2 1.0 CE1 A:HIS284 4.3 32.2 1.0 CA A:GLU293 4.3 7.9 1.0 OE1 A:GLU215 4.4 28.9 1.0 CG A:P3S3001 4.5 0.4 1.0 OE2 A:GLU217 4.6 37.3 1.0 CG A:GLU286 4.6 28.6 1.0 O2A A:P3S3001 4.6 0.1 1.0 CE A:P3S3001 4.8 0.4 1.0 CB A:GLU217 4.9 37.3 1.0 N A:GLU293 5.0 7.9 1.0

Magnesium binding site 3 out of 12 in the Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis


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 Type III Glutamine Synthetase From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:15.6 occ:1.00 OE2 B:GLU472 2.1 54.9 1.0 O1B B:ADP4001 2.2 0.8 1.0 ND1 B:HIS342 2.2 44.0 1.0 OE2 B:GLU215 2.4 47.7 1.0 OE1 B:GLU215 2.6 47.7 1.0 CD B:GLU215 2.8 47.7 1.0 CD B:GLU472 2.8 54.9 1.0 CE1 B:HIS342 3.0 44.0 1.0 PB B:ADP4001 3.0 0.4 1.0 OE1 B:GLU472 3.1 54.9 1.0 O3A B:ADP4001 3.1 0.0 1.0 CG B:HIS342 3.3 44.0 1.0 O2B B:ADP4001 3.4 0.2 1.0 O2A B:P3S3001 3.5 0.1 1.0 O3A B:P3S3001 3.6 0.5 1.0 CB B:HIS342 3.8 44.0 1.0 CG B:GLU472 4.1 54.9 1.0 PA B:P3S3001 4.1 0.6 1.0 NE2 B:HIS342 4.2 44.0 1.0 CG B:GLU215 4.3 47.7 1.0 CD2 B:HIS342 4.4 44.0 1.0 PA B:ADP4001 4.5 0.4 1.0 NH2 B:ARG474 4.6 86.2 1.0 O3B B:ADP4001 4.6 0.4 1.0 NE B:ARG474 4.6 86.2 1.0 O5' B:ADP4001 4.7 0.6 1.0 CZ B:ARG474 4.8 86.2 1.0 ND2 B:ASN344 4.9 38.0 1.0 CB B:GLU215 4.9 47.7 1.0 OD1 B:ASN344 5.0 38.0 1.0

Magnesium binding site 4 out of 12 in the Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis


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 Type III Glutamine Synthetase From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:52.7 occ:1.00 OE1 B:GLU286 2.6 35.6 1.0 O3A B:P3S3001 2.6 0.5 1.0 OE1 B:GLU217 2.9 47.3 1.0 NE B:P3S3001 3.0 0.2 1.0 CD B:GLU293 3.0 61.8 1.0 PA B:P3S3001 3.0 0.6 1.0 CG B:GLU293 3.0 61.8 1.0 OE2 B:GLU293 3.0 61.8 1.0 CB B:GLU293 3.1 61.8 1.0 O1A B:P3S3001 3.2 0.5 1.0 CD B:GLU286 3.3 35.6 1.0 OE2 B:GLU286 3.5 35.6 1.0 CG B:GLU217 3.5 47.3 1.0 CD B:GLU217 3.6 47.3 1.0 OE1 B:GLU293 3.7 61.8 1.0 CE1 B:HIS284 3.8 48.3 1.0 NE2 B:HIS284 3.9 48.3 1.0 CA B:GLU293 4.5 13.2 1.0 OE1 B:GLU215 4.5 47.7 1.0 CG B:GLU286 4.5 35.6 1.0 SD B:P3S3001 4.6 0.3 1.0 O2A B:P3S3001 4.6 0.1 1.0 OE2 B:GLU217 4.9 47.3 1.0 ND1 B:HIS284 5.0 48.3 1.0 O2A B:ADP4001 5.0 0.8 1.0 CB B:GLU217 5.0 47.3 1.0

Magnesium binding site 5 out of 12 in the Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis


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 Type III Glutamine Synthetase From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1001 b:8.7 occ:1.00 OE2 C:GLU472 2.1 57.8 1.0 O1B C:ADP4001 2.2 0.0 1.0 ND1 C:HIS342 2.2 38.1 1.0 OE2 C:GLU215 2.3 41.9 1.0 OE1 C:GLU215 2.7 41.9 1.0 CD C:GLU472 2.8 57.8 1.0 CD C:GLU215 2.8 41.9 1.0 CE1 C:HIS342 3.0 38.1 1.0 OE1 C:GLU472 3.0 57.8 1.0 PB C:ADP4001 3.0 99.6 1.0 O3A C:ADP4001 3.1 0.2 1.0 CG C:HIS342 3.4 38.1 1.0 O2B C:ADP4001 3.4 0.5 1.0 O2A C:P3S3001 3.5 0.1 1.0 O3A C:P3S3001 3.6 0.5 1.0 CB C:HIS342 3.8 38.1 1.0 CG C:GLU472 4.1 57.8 1.0 PA C:P3S3001 4.2 0.6 1.0 NE2 C:HIS342 4.2 38.1 1.0 CG C:GLU215 4.3 41.9 1.0 CD2 C:HIS342 4.4 38.1 1.0 NH2 C:ARG474 4.5 78.0 1.0 PA C:ADP4001 4.5 0.6 1.0 O3B C:ADP4001 4.6 0.6 1.0 NE C:ARG474 4.6 78.0 1.0 O5' C:ADP4001 4.7 0.8 1.0 CZ C:ARG474 4.8 78.0 1.0 ND2 C:ASN344 4.9 35.0 1.0 OD1 C:ASN344 4.9 35.0 1.0 CB C:GLU215 4.9 41.9 1.0

Magnesium binding site 6 out of 12 in the Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis


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 Type III Glutamine Synthetase From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2001 b:33.0 occ:1.00 OE1 C:GLU286 2.6 34.7 1.0 O3A C:P3S3001 2.6 0.5 1.0 OE1 C:GLU217 2.8 36.8 1.0 NE C:P3S3001 2.9 0.2 1.0 PA C:P3S3001 3.0 0.6 1.0 CD C:GLU293 3.0 77.4 1.0 OE2 C:GLU293 3.1 77.4 1.0 CG C:GLU293 3.1 77.4 1.0 CB C:GLU293 3.2 77.4 1.0 O1A C:P3S3001 3.2 0.5 1.0 CD C:GLU286 3.3 34.7 1.0 OE2 C:GLU286 3.4 34.7 1.0 CG C:GLU217 3.6 36.8 1.0 CD C:GLU217 3.6 36.8 1.0 OE1 C:GLU293 3.7 77.4 1.0 CE1 C:HIS284 3.8 45.7 1.0 NE2 C:HIS284 3.9 45.7 1.0 SD C:P3S3001 4.5 0.3 1.0 CG C:GLU286 4.5 34.7 1.0 OE1 C:GLU215 4.5 41.9 1.0 CA C:GLU293 4.5 15.4 1.0 O2A C:P3S3001 4.6 0.1 1.0 OE2 C:GLU217 4.8 36.8 1.0 ND1 C:HIS284 5.0 45.7 1.0

Magnesium binding site 7 out of 12 in the Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis


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 Type III Glutamine Synthetase From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1001 b:10.4 occ:1.00 OE2 D:GLU472 2.1 44.6 1.0 O1B D:ADP4001 2.2 93.5 1.0 ND1 D:HIS342 2.2 31.9 1.0 OE2 D:GLU215 2.3 31.0 1.0 OE1 D:GLU215 2.7 31.0 1.0 CD D:GLU215 2.8 31.0 1.0 CD D:GLU472 2.8 44.6 1.0 CE1 D:HIS342 3.0 31.9 1.0 PB D:ADP4001 3.0 93.1 1.0 OE1 D:GLU472 3.1 44.6 1.0 O3A D:ADP4001 3.1 94.7 1.0 CG D:HIS342 3.3 31.9 1.0 O2B D:ADP4001 3.4 93.9 1.0 O2A D:P3S3001 3.5 0.1 1.0 O3A D:P3S3001 3.6 0.5 1.0 CB D:HIS342 3.8 31.9 1.0 CG D:GLU472 4.1 44.6 1.0 PA D:P3S3001 4.2 0.6 1.0 NE2 D:HIS342 4.2 31.9 1.0 CG D:GLU215 4.3 31.0 1.0 CD2 D:HIS342 4.4 31.9 1.0 PA D:ADP4001 4.5 97.0 1.0 NH2 D:ARG474 4.6 94.5 1.0 O3B D:ADP4001 4.6 97.1 1.0 NE D:ARG474 4.7 94.5 1.0 O5' D:ADP4001 4.7 0.2 1.0 CZ D:ARG474 4.8 94.5 1.0 ND2 D:ASN344 4.9 32.2 1.0 CB D:GLU215 4.9 31.0 1.0 OD1 D:ASN344 4.9 32.2 1.0

Magnesium binding site 8 out of 12 in the Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis


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 Type III Glutamine Synthetase From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2001 b:32.4 occ:1.00 OE1 D:GLU286 2.6 36.6 1.0 O3A D:P3S3001 2.6 0.5 1.0 OE1 D:GLU217 2.9 38.8 1.0 NE D:P3S3001 2.9 0.2 1.0 PA D:P3S3001 3.0 0.6 1.0 CD D:GLU293 3.0 66.8 1.0 CG D:GLU293 3.1 66.8 1.0 OE2 D:GLU293 3.1 66.8 1.0 CB D:GLU293 3.1 66.8 1.0 O1A D:P3S3001 3.2 0.5 1.0 CD D:GLU286 3.3 36.6 1.0 OE2 D:GLU286 3.5 36.6 1.0 CG D:GLU217 3.5 38.8 1.0 CD D:GLU217 3.6 38.8 1.0 OE1 D:GLU293 3.7 66.8 1.0 CE1 D:HIS284 3.8 35.3 1.0 NE2 D:HIS284 3.9 35.3 1.0 CA D:GLU293 4.5 14.5 1.0 OE1 D:GLU215 4.5 31.0 1.0 CG D:GLU286 4.5 36.6 1.0 SD D:P3S3001 4.5 0.3 1.0 O2A D:P3S3001 4.6 0.1 1.0 OE2 D:GLU217 4.8 38.8 1.0 ND1 D:HIS284 5.0 35.3 1.0 CB D:GLU217 5.0 38.8 1.0

Magnesium binding site 9 out of 12 in the Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis


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 Type III Glutamine Synthetase From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1001 b:10.2 occ:1.00 O1B E:ADP4001 2.1 99.6 1.0 OE2 E:GLU472 2.2 53.9 1.0 ND1 E:HIS342 2.2 54.5 1.0 OE2 E:GLU215 2.4 41.7 1.0 OE1 E:GLU215 2.6 41.7 1.0 CD E:GLU215 2.8 41.7 1.0 CD E:GLU472 2.9 53.9 1.0 CE1 E:HIS342 3.0 54.5 1.0 PB E:ADP4001 3.0 99.2 1.0 O3A E:ADP4001 3.1 0.8 1.0 OE1 E:GLU472 3.1 53.9 1.0 CG E:HIS342 3.4 54.5 1.0 O2A E:P3S3001 3.4 0.1 1.0 O2B E:ADP4001 3.4 0.0 1.0 O3A E:P3S3001 3.5 0.5 1.0 CB E:HIS342 3.8 54.5 1.0 PA E:P3S3001 4.1 0.6 1.0 CG E:GLU472 4.2 53.9 1.0 NE2 E:HIS342 4.2 54.5 1.0 CG E:GLU215 4.3 41.7 1.0 CD2 E:HIS342 4.4 54.5 1.0 PA E:ADP4001 4.5 0.1 1.0 O3B E:ADP4001 4.5 0.2 1.0 NH2 E:ARG474 4.6 76.2 1.0 NE E:ARG474 4.7 76.2 1.0 O5' E:ADP4001 4.7 0.4 1.0 CZ E:ARG474 4.8 76.2 1.0 CB E:GLU215 4.9 41.7 1.0 ND2 E:ASN344 5.0 49.4 1.0

Magnesium binding site 10 out of 12 in the Crystal Structure of the Type III Glutamine Synthetase From Bacteroides Fragilis


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 Type III Glutamine Synthetase From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg2001 b:41.7 occ:1.00 OE1 E:GLU286 2.6 44.5 1.0 O3A E:P3S3001 2.6 0.5 1.0 OE1 E:GLU217 2.9 57.7 1.0 NE E:P3S3001 2.9 0.2 1.0 PA E:P3S3001 3.0 0.6 1.0 CD E:GLU293 3.0 58.9 1.0 OE2 E:GLU293 3.1 58.9 1.0 CG E:GLU293 3.1 58.9 1.0 CB E:GLU293 3.1 58.9 1.0 O1A E:P3S3001 3.2 0.5 1.0 CD E:GLU286 3.3 44.5 1.0 OE2 E:GLU286 3.5 44.5 1.0 CG E:GLU217 3.6 57.7 1.0 CD E:GLU217 3.6 57.7 1.0 OE1 E:GLU293 3.7 58.9 1.0 CE1 E:HIS284 3.8 43.1 1.0 NE2 E:HIS284 3.9 43.1 1.0 CA E:GLU293 4.5 13.1 1.0 CG E:GLU286 4.5 44.5 1.0 OE1 E:GLU215 4.5 41.7 1.0 SD E:P3S3001 4.5 0.3 1.0 O2A E:P3S3001 4.6 0.1 1.0 OE2 E:GLU217 4.9 57.7 1.0 ND1 E:HIS284 4.9 43.1 1.0 O2A E:ADP4001 5.0 0.6 1.0

J.M.Van Rooyen, V.R.Abratt, H.Belrhali, T.Sewell. Crystal Structure of Type III Glutamine Synthetase: Surprising Reversal of the Inter-Ring Interface. Structure V. 19 471 2011.
ISSN: ISSN 0969-2126
PubMed: 21481771
DOI: 10.1016/J.STR.2011.02.001