Magnesium in PDB 9bq0: Complex Structure of Protein Crystal of TRI17 with Atp

The structure of Complex Structure of Protein Crystal of TRI17 with Atp, PDB code: 9bq0 was solved by R.Zhai, W.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.44 / 2.90
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	87.095, 152.331, 229.642, 90, 90, 90
R / Rfree (%)	27.8 / 33

The binding sites of Magnesium atom in the Complex Structure of Protein Crystal of TRI17 with Atp (pdb code 9bq0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Complex Structure of Protein Crystal of TRI17 with Atp, PDB code: 9bq0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Complex Structure of Protein Crystal of TRI17 with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex Structure of Protein Crystal of TRI17 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:48.0 occ:1.00 O1G A:ATP601 2.6 71.3 1.0 O1B A:ATP601 2.7 47.7 1.0 HZ1 A:LYS194 3.2 68.0 1.0 HZ2 A:LYS194 3.4 68.0 1.0 O2G A:ATP601 3.4 64.3 1.0 PG A:ATP601 3.5 74.3 1.0 O2A A:ATP601 3.6 49.9 1.0 HO3' A:ATP601 3.6 109.7 1.0 NZ A:LYS194 3.6 56.6 1.0 PB A:ATP601 3.8 54.4 1.0 HE3 A:LYS194 3.8 72.5 1.0 O A:THR419 3.9 39.9 1.0 H5'1 A:ATP601 3.9 90.0 1.0 HH12 A:ARG436 4.0 64.6 1.0 O3A A:ATP601 4.0 47.8 1.0 O3B A:ATP601 4.0 67.0 1.0 HB2 A:SER186 4.0 55.5 1.0 OE1 A:GLU342 4.1 32.7 1.0 HB2 A:SER340 4.2 72.6 1.0 OE2 A:GLU342 4.3 45.6 1.0 CE A:LYS194 4.3 60.4 1.0 O3' A:ATP601 4.3 91.3 1.0 PA A:ATP601 4.4 72.4 1.0 HZ3 A:LYS194 4.4 68.0 1.0 HH22 A:ARG436 4.6 96.1 1.0 CD A:GLU342 4.6 42.3 1.0 HB3 A:SER340 4.6 72.6 1.0 C5' A:ATP601 4.8 75.0 1.0 NH1 A:ARG436 4.8 53.8 1.0 CB A:SER186 4.8 46.2 1.0 HB3 A:SER186 4.8 55.5 1.0 C A:THR419 4.8 30.3 1.0 O3G A:ATP601 4.8 57.5 1.0 HE2 A:LYS194 4.8 72.5 1.0 O5' A:ATP601 4.9 79.1 1.0 HA3 A:GLY420 4.9 41.6 1.0 CB A:SER340 4.9 60.4 1.0 HG A:SER186 4.9 70.0 1.0 HA A:THR419 4.9 34.4 1.0

Magnesium binding site 2 out of 6 in the Complex Structure of Protein Crystal of TRI17 with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex Structure of Protein Crystal of TRI17 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:50.2 occ:1.00 O1B B:ATP601 2.7 60.1 1.0 O1G B:ATP601 2.9 59.8 1.0 HZ1 B:LYS194 3.4 66.3 1.0 HH22 B:ARG436 3.5 81.7 1.0 HO3' B:ATP601 3.7 81.7 1.0 O B:THR419 3.7 48.4 1.0 HH21 B:ARG436 3.7 81.7 1.0 OE1 B:GLU342 3.8 46.2 1.0 HE3 B:LYS194 3.8 64.5 1.0 O5' B:ATP601 3.9 68.4 1.0 HZ2 B:LYS194 4.0 66.3 1.0 OE2 B:GLU342 4.0 61.4 1.0 NH2 B:ARG436 4.0 68.0 1.0 PB B:ATP601 4.0 51.9 1.0 NZ B:LYS194 4.0 55.2 1.0 PG B:ATP601 4.1 66.6 1.0 HB2 B:SER340 4.1 64.2 1.0 O1A B:ATP601 4.2 58.7 1.0 CD B:GLU342 4.3 41.0 1.0 O3B B:ATP601 4.3 55.5 1.0 CE B:LYS194 4.4 53.7 1.0 O2G B:ATP601 4.4 60.3 1.0 HB2 B:SER186 4.4 60.4 1.0 O3A B:ATP601 4.4 45.6 1.0 O3' B:ATP601 4.4 68.0 1.0 PA B:ATP601 4.5 65.8 1.0 HA3 B:GLY420 4.5 38.5 1.0 C B:THR419 4.7 36.0 1.0 HB3 B:SER340 4.7 64.2 1.0 HE2 B:LYS194 4.8 64.5 1.0 HZ3 B:LYS194 4.8 66.3 1.0 CB B:SER340 4.8 53.4 1.0 HA B:THR419 4.9 32.7 1.0 H5'1 B:ATP601 5.0 80.4 1.0 C5' B:ATP601 5.0 67.0 1.0

Magnesium binding site 3 out of 6 in the Complex Structure of Protein Crystal of TRI17 with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Complex Structure of Protein Crystal of TRI17 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:30.0 occ:1.00 HD1 B:HIS265 2.5 43.2 1.0 HZ1 B:LYS221 2.6 79.3 1.0 HZ3 B:LYS221 2.7 79.3 1.0 NZ B:LYS221 3.0 66.0 1.0 HD3 B:LYS221 3.1 43.4 1.0 HB3 B:HIS265 3.1 52.2 1.0 ND1 B:HIS265 3.3 36.0 1.0 HA B:HIS265 3.5 54.6 1.0 HE2 B:LYS221 3.7 70.0 1.0 CE B:LYS221 3.7 58.3 1.0 HZ2 B:LYS221 3.8 79.3 1.0 CB B:HIS265 3.8 43.4 1.0 CD B:LYS221 3.9 36.1 1.0 CD1 B:TRP39 3.9 45.1 1.0 HG21 B:VAL248 3.9 54.5 1.0 HD1 B:TRP39 3.9 54.2 1.0 CG B:HIS265 4.0 37.3 1.0 O B:HIS265 4.0 50.8 1.0 NE1 B:TRP39 4.0 65.6 1.0 CA B:HIS265 4.1 45.4 1.0 HE1 B:TRP39 4.2 78.8 1.0 HG22 B:VAL248 4.2 54.5 1.0 CG B:TRP39 4.3 33.6 1.0 HD2 B:LYS221 4.3 43.4 1.0 CE1 B:HIS265 4.4 40.9 1.0 CG2 B:VAL248 4.5 45.3 1.0 CE2 B:TRP39 4.5 59.7 1.0 HE1 B:HIS265 4.6 49.2 1.0 C B:HIS265 4.6 53.4 1.0 HE3 B:LYS221 4.6 70.0 1.0 HB3 B:TRP39 4.6 49.7 1.0 CD2 B:TRP39 4.7 53.9 1.0 HB2 B:HIS265 4.7 52.2 1.0 HG3 B:LYS221 4.8 51.0 1.0 HB2 B:TRP39 4.9 49.7 1.0 CB B:TRP39 4.9 41.4 1.0 HG23 B:VAL248 4.9 54.5 1.0

Magnesium binding site 4 out of 6 in the Complex Structure of Protein Crystal of TRI17 with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Complex Structure of Protein Crystal of TRI17 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:85.2 occ:1.00 O1B C:ATP601 2.7 93.4 1.0 O3G C:ATP601 2.7 69.0 1.0 O3B C:ATP601 2.8 85.4 1.0 O1G C:ATP601 3.0 93.7 1.0 PG C:ATP601 3.0 104.3 1.0 PB C:ATP601 3.4 106.6 1.0 HE3 C:LYS194 3.4 79.3 1.0 HH22 C:ARG436 3.4 123.3 1.0 HH12 C:ARG436 3.7 114.8 1.0 HB2 C:SER186 3.9 77.0 1.0 HO3' C:ATP601 4.0 70.7 1.0 NH2 C:ARG436 4.2 102.7 1.0 OE2 C:GLU342 4.3 66.2 1.0 OE1 C:GLU342 4.3 65.9 1.0 O C:THR419 4.3 33.7 1.0 O3' C:ATP601 4.3 58.8 1.0 CE C:LYS194 4.4 66.0 1.0 NH1 C:ARG436 4.4 95.6 1.0 O3A C:ATP601 4.4 84.5 1.0 O2G C:ATP601 4.5 92.1 1.0 HZ1 C:LYS194 4.5 64.0 1.0 O2B C:ATP601 4.5 98.2 1.0 HZ2 C:LYS194 4.6 64.0 1.0 HG21 C:THR190 4.6 115.0 1.0 HB3 C:SER186 4.6 77.0 1.0 HA3 C:GLY420 4.7 63.4 1.0 CB C:SER186 4.7 64.1 1.0 CD C:GLU342 4.7 67.5 1.0 HG22 C:THR190 4.7 115.0 1.0 NZ C:LYS194 4.7 53.3 1.0 CZ C:ARG436 4.8 106.7 1.0 HE2 C:LYS194 4.8 79.3 1.0 HH21 C:ARG436 4.8 123.3 1.0 H4' C:ATP601 4.9 98.4 1.0 HD2 C:LYS194 4.9 62.6 1.0 H C:SER187 5.0 70.5 1.0

Magnesium binding site 5 out of 6 in the Complex Structure of Protein Crystal of TRI17 with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Complex Structure of Protein Crystal of TRI17 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:50.8 occ:1.00 HH12 D:ARG436 2.6 141.7 1.0 O3G D:ATP601 3.0 85.4 1.0 HZ1 D:LYS194 3.1 65.6 1.0 NH1 D:ARG436 3.5 118.0 1.0 O2B D:ATP601 3.5 100.7 1.0 HH22 D:ARG436 3.5 113.1 1.0 HE2 D:LYS194 3.6 84.8 1.0 HA3 D:GLY420 3.7 61.0 1.0 NZ D:LYS194 3.9 54.6 1.0 O1G D:ATP601 3.9 93.8 1.0 PG D:ATP601 3.9 85.3 1.0 O D:THR419 3.9 40.2 1.0 HH11 D:ARG436 4.0 141.7 1.0 CE D:LYS194 4.1 70.6 1.0 HZ3 D:LYS194 4.2 65.6 1.0 NH2 D:ARG436 4.2 94.2 1.0 HE3 D:LYS194 4.3 84.8 1.0 HE21 D:GLN411 4.3 68.3 1.0 HO3' D:ATP601 4.3 72.7 1.0 CZ D:ARG436 4.3 113.7 1.0 O3B D:ATP601 4.4 79.9 1.0 HZ2 D:LYS194 4.5 65.6 1.0 PB D:ATP601 4.6 107.5 1.0 OE2 D:GLU342 4.6 61.8 1.0 CA D:GLY420 4.6 50.8 1.0 O3' D:ATP601 4.7 60.5 1.0 C D:THR419 4.8 40.0 1.0 HA2 D:GLY420 4.9 61.0 1.0 OE1 D:GLU342 4.9 71.4 1.0

Magnesium binding site 6 out of 6 in the Complex Structure of Protein Crystal of TRI17 with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Complex Structure of Protein Crystal of TRI17 with Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg603 b:30.0 occ:1.00 O1B D:ATP601 2.8 102.8 1.0 HH21 D:ARG436 3.3 113.1 1.0 OD2 D:ASP301 3.6 82.0 1.0 HB2 D:SER187 3.7 86.9 1.0 OD1 D:ASP301 3.9 86.1 1.0 CG D:ASP301 3.9 88.4 1.0 H1' D:ATP601 4.0 84.6 1.0 H4' D:ATP601 4.0 97.6 1.0 O4' D:ATP601 4.1 83.5 1.0 NH2 D:ARG436 4.1 94.2 1.0 PB D:ATP601 4.2 107.5 1.0 HE D:ARG436 4.4 107.7 1.0 HH22 D:ARG436 4.5 113.1 1.0 O D:SER187 4.5 95.4 1.0 C1' D:ATP601 4.6 70.4 1.0 O3A D:ATP601 4.6 74.7 1.0 C4' D:ATP601 4.6 81.3 1.0 CB D:SER187 4.7 72.3 1.0 O5' D:ATP601 4.8 61.3 1.0 O2' D:ATP601 4.8 62.0 1.0 HB3 D:SER187 5.0 86.9 1.0

A.Del Rio Flores, R.Zhai, D.W.Kastner, K.Seshadri, S.Yang, K.De Matias, Y.Shen, W.Cai, M.Narayanamoorthy, N.B.Do, Z.Xue, D.A.Marzooqi, H.J.Kulik, W.Zhang. Enzymatic Synthesis of Azide By A Promiscuous N-Nitrosylase. Nat.Chem. 2024.
ISSN: ESSN 1755-4349
PubMed: 39333393
DOI: 10.1038/S41557-024-01646-2