Magnesium in PDB 7xb6: Crystal Structure of the O-Carbamoyltransferase Vtdb in Complex with Carbamoyl Adenylate Intermediate

The structure of Crystal Structure of the O-Carbamoyltransferase Vtdb in Complex with Carbamoyl Adenylate Intermediate, PDB code: 7xb6 was solved by H.Zhang, Y.Teng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.19 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.391, 245.567, 96.946, 90, 92.04, 90
R / Rfree (%)	18.7 / 26.9

The binding sites of Magnesium atom in the Crystal Structure of the O-Carbamoyltransferase Vtdb in Complex with Carbamoyl Adenylate Intermediate (pdb code 7xb6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the O-Carbamoyltransferase Vtdb in Complex with Carbamoyl Adenylate Intermediate, PDB code: 7xb6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the O-Carbamoyltransferase Vtdb in Complex with Carbamoyl Adenylate Intermediate


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 O-Carbamoyltransferase Vtdb in Complex with Carbamoyl Adenylate Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:22.8 occ:1.00 N2B A:CA0602 1.8 63.5 1.0 OD1 A:ASP363 1.9 50.9 1.0 OD2 A:ASP180 2.1 64.3 1.0 NE2 A:HIS157 2.1 55.0 1.0 NE2 A:HIS161 2.2 52.7 1.0 O2A A:CA0602 2.4 80.2 1.0 CG A:ASP363 2.9 53.6 1.0 CB A:CA0602 3.0 63.0 1.0 CG A:ASP180 3.0 70.7 1.0 CE1 A:HIS161 3.1 51.0 1.0 CD2 A:HIS157 3.1 55.4 1.0 CE1 A:HIS157 3.1 56.8 1.0 CD2 A:HIS161 3.3 50.5 1.0 O3A A:CA0602 3.3 75.6 1.0 OD2 A:ASP363 3.4 55.9 1.0 CB A:ASP180 3.4 67.6 1.0 PA A:CA0602 3.4 84.5 1.0 O1B A:CA0602 4.1 55.3 1.0 OD1 A:ASP180 4.2 91.3 1.0 ND1 A:HIS161 4.2 48.0 1.0 ND1 A:HIS157 4.2 53.1 1.0 CG A:HIS157 4.2 51.9 1.0 CB A:ASP363 4.2 52.6 1.0 CG A:HIS161 4.4 50.3 1.0 O1A A:CA0602 4.4 76.3 1.0 CA A:ASP363 4.5 51.1 1.0 O5' A:CA0602 4.5 83.5 1.0 CG1 A:VAL366 4.6 52.1 1.0 N A:ASP363 4.7 51.3 1.0 CA A:ASP180 4.8 64.8 1.0 O A:GLN182 4.9 75.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the O-Carbamoyltransferase Vtdb in Complex with Carbamoyl Adenylate Intermediate


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 O-Carbamoyltransferase Vtdb in Complex with Carbamoyl Adenylate Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:27.5 occ:1.00 O1A B:CA0602 1.8 108.1 1.0 NE2 B:HIS157 2.0 50.6 1.0 OD2 B:ASP180 2.1 93.9 1.0 OD1 B:ASP363 2.2 67.0 1.0 N2B B:CA0602 2.2 88.4 1.0 NE2 B:HIS161 2.2 46.3 1.0 CG B:ASP180 2.9 74.0 1.0 OD1 B:ASP180 2.9 67.0 1.0 CE1 B:HIS157 3.0 48.8 1.0 CD2 B:HIS157 3.1 49.9 1.0 PA B:CA0602 3.1 118.3 1.0 CE1 B:HIS161 3.1 48.2 1.0 CB B:CA0602 3.2 100.2 1.0 CD2 B:HIS161 3.3 45.7 1.0 CG B:ASP363 3.4 73.0 1.0 O3A B:CA0602 3.4 123.0 1.0 OD2 B:ASP363 4.0 81.0 1.0 ND1 B:HIS157 4.1 47.3 1.0 O2A B:CA0602 4.1 102.9 1.0 O5' B:CA0602 4.1 122.9 1.0 CG B:HIS157 4.2 51.3 1.0 O1B B:CA0602 4.3 84.5 1.0 ND1 B:HIS161 4.3 48.8 1.0 CB B:ASP180 4.3 64.5 1.0 CG B:HIS161 4.4 47.2 1.0 O B:GLN182 4.4 79.9 1.0 CB B:ASP363 4.5 67.4 1.0 CA B:ASP363 4.6 66.0 1.0 CG1 B:VAL366 4.6 46.1 1.0 N B:ASP363 4.8 62.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the O-Carbamoyltransferase Vtdb in Complex with Carbamoyl Adenylate Intermediate


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 O-Carbamoyltransferase Vtdb in Complex with Carbamoyl Adenylate Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:29.9 occ:1.00 N2B C:CA0602 2.0 107.4 1.0 NE2 C:HIS157 2.1 53.5 1.0 OD1 C:ASP180 2.1 64.9 1.0 NE2 C:HIS161 2.1 39.6 1.0 OD1 C:ASP363 2.1 55.6 1.0 CE1 C:HIS157 2.9 51.2 1.0 CG C:ASP180 3.0 55.9 1.0 CD2 C:HIS161 3.1 39.3 1.0 O1A C:CA0602 3.1 128.9 1.0 CE1 C:HIS161 3.1 40.3 1.0 CD2 C:HIS157 3.2 55.2 1.0 CB C:CA0602 3.3 111.7 1.0 CG C:ASP363 3.4 56.7 1.0 OD2 C:ASP180 3.5 57.3 1.0 O3A C:CA0602 3.8 127.6 1.0 PA C:CA0602 4.0 138.5 1.0 ND1 C:HIS157 4.1 53.1 1.0 O1B C:CA0602 4.2 103.7 1.0 CB C:ASP180 4.2 54.7 1.0 CG C:HIS157 4.2 54.9 1.0 OD2 C:ASP363 4.2 59.0 1.0 CG1 C:VAL366 4.2 55.8 1.0 ND1 C:HIS161 4.2 41.9 1.0 CG C:HIS161 4.2 42.2 1.0 O C:GLN182 4.2 94.7 1.0 CA C:ASP363 4.2 54.0 1.0 CB C:ASP363 4.3 55.6 1.0 N C:ASP363 4.5 51.8 1.0 O5' C:CA0602 4.8 129.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the O-Carbamoyltransferase Vtdb in Complex with Carbamoyl Adenylate Intermediate


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 O-Carbamoyltransferase Vtdb in Complex with Carbamoyl Adenylate Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:22.8 occ:1.00 N2B D:CA0602 2.0 71.8 1.0 OD2 D:ASP180 2.0 61.2 1.0 NE2 D:HIS161 2.1 51.9 1.0 OD1 D:ASP363 2.1 54.9 1.0 NE2 D:HIS157 2.1 50.8 1.0 O2A D:CA0602 2.4 103.8 1.0 OD1 D:ASP180 2.5 77.4 1.0 CG D:ASP180 2.6 65.7 1.0 CD2 D:HIS161 3.0 55.2 1.0 CG D:ASP363 3.0 54.0 1.0 CE1 D:HIS157 3.1 49.2 1.0 CE1 D:HIS161 3.1 55.8 1.0 CD2 D:HIS157 3.1 51.9 1.0 CB D:CA0602 3.2 77.4 1.0 OD2 D:ASP363 3.3 53.4 1.0 PA D:CA0602 3.5 108.5 1.0 O3A D:CA0602 3.6 93.0 1.0 CB D:ASP180 4.0 62.6 1.0 CG D:HIS161 4.2 55.6 1.0 ND1 D:HIS157 4.2 47.7 1.0 ND1 D:HIS161 4.2 55.9 1.0 O1B D:CA0602 4.2 75.6 1.0 CG D:HIS157 4.2 51.4 1.0 CB D:ASP363 4.4 52.3 1.0 O5' D:CA0602 4.5 109.3 1.0 CA D:ASP363 4.6 49.0 1.0 O1A D:CA0602 4.7 111.7 1.0 O D:GLN182 4.7 82.3 1.0 CG1 D:VAL366 4.8 59.0 1.0 N D:ASP363 4.9 44.6 1.0 CA D:ASP180 5.0 62.5 1.0 CA D:GLY334 5.0 44.9 1.0

H.Zhang, Y.Teng. Crystal Structure of O-Carbamoyltransferase Vtdb From Streptomyces Sp. NO1W98 in Complex with Carbamoyladenylate To Be Published.