Magnesium in PDB 3wbz: Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp

All present enzymatic activity of Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp:
2.7.7.79;

The structure of Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp, PDB code: 3wbz was solved by A.Nakamura, T.Nemoto, T.Sonoda, K.Yamashita, I.Tanaka, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.26 / 2.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.830, 217.870, 87.240, 90.00, 113.68, 90.00
R / Rfree (%)	17.6 / 20.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp (pdb code 3wbz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp, PDB code: 3wbz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in the Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp


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 C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:33.4 occ:1.00 OD1 A:ASP76 2.1 24.7 1.0 O A:HOH554 2.1 32.4 1.0 OD2 A:ASP29 2.1 23.4 1.0 O2A A:ATP401 2.1 36.3 1.0 O A:HOH532 2.2 41.3 1.0 O A:HOH553 2.3 66.3 1.0 CG A:ASP76 3.1 24.1 1.0 PA A:ATP401 3.1 31.8 1.0 CG A:ASP29 3.1 22.9 1.0 OD2 A:ASP76 3.3 24.1 1.0 O1A A:ATP401 3.4 38.0 1.0 OD1 A:ASP29 3.4 24.7 1.0 MG A:MG404 3.6 24.7 1.0 O5' A:ATP401 3.7 28.5 1.0 C5' A:ATP401 4.0 27.3 1.0 O A:HOH510 4.1 21.1 1.0 OE1 A:GLU77 4.4 25.9 1.0 CB A:ASP76 4.4 23.7 1.0 OG A:SER75 4.5 26.9 1.0 CB A:ASP29 4.5 20.7 1.0 O A:HOH555 4.5 24.5 1.0 O3A A:ATP401 4.6 29.8 1.0 N A:ASP76 4.6 27.1 1.0 CB A:GLU77 4.6 22.0 1.0 C A:ASP76 4.7 22.8 1.0 O2G A:ATP401 4.7 28.4 1.0 O2B A:ATP401 4.8 26.0 1.0 CA A:ASP76 4.8 25.5 1.0 N A:GLU77 4.9 22.8 1.0 O A:ASP76 4.9 21.6 1.0

Magnesium binding site 2 out of 24 in the Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp


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 C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:24.7 occ:1.00 OD1 A:ASP29 1.9 24.7 1.0 O2G A:ATP401 1.9 28.4 1.0 O2B A:ATP401 2.1 26.0 1.0 O A:GLY30 2.1 23.2 1.0 OD2 A:ASP76 2.1 24.1 1.0 O2A A:ATP401 2.2 36.3 1.0 CG A:ASP29 3.0 22.9 1.0 PB A:ATP401 3.1 26.8 1.0 C A:GLY30 3.2 21.6 1.0 PG A:ATP401 3.2 32.2 1.0 CG A:ASP76 3.3 24.1 1.0 PA A:ATP401 3.4 31.8 1.0 OD2 A:ASP29 3.5 23.4 1.0 O3A A:ATP401 3.5 29.8 1.0 O3B A:ATP401 3.6 20.5 1.0 MG A:MG403 3.6 33.4 1.0 OD1 A:ASP76 3.7 24.7 1.0 O A:HOH520 3.7 20.3 1.0 N A:GLY30 3.8 21.7 1.0 CA A:GLY30 3.9 20.5 1.0 O A:HOH555 4.0 24.5 1.0 O3G A:ATP401 4.0 34.5 1.0 C A:ASP29 4.1 19.9 1.0 CB A:ASP29 4.3 20.7 1.0 N A:LYS31 4.3 24.0 1.0 C5' A:ATP401 4.3 27.3 1.0 O5' A:ATP401 4.3 28.5 1.0 O1G A:ATP401 4.4 30.3 1.0 O A:ASP29 4.5 20.2 1.0 O1B A:ATP401 4.5 33.0 1.0 O1A A:ATP401 4.5 38.0 1.0 N A:PHE33 4.5 25.1 1.0 N A:GLY32 4.5 24.4 1.0 CB A:ASP76 4.6 23.7 1.0 CA A:LYS31 4.6 25.2 1.0 O A:HOH554 4.6 32.4 1.0 CB A:PHE33 4.6 23.3 1.0 CA A:ASP29 4.7 21.4 1.0 C A:LYS31 4.9 26.9 1.0

Magnesium binding site 3 out of 24 in the Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp


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 C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:20.3 occ:1.00 O2G A:ATP402 1.9 21.4 1.0 O A:HOH555 2.0 24.5 1.0 O2A A:ATP402 2.1 32.8 1.0 O2B A:ATP402 2.2 27.8 1.0 O A:HOH544 2.2 23.5 1.0 O A:HOH556 2.3 23.4 1.0 PB A:ATP402 3.2 30.1 1.0 PG A:ATP402 3.3 27.0 1.0 PA A:ATP402 3.3 33.5 1.0 O3A A:ATP402 3.6 40.4 1.0 O3B A:ATP402 3.6 35.5 1.0 O A:HOH515 3.8 34.1 1.0 NZ B:LYS95 3.9 25.6 1.0 NH2 A:ARG132 3.9 22.2 1.0 O A:HOH557 4.0 36.5 1.0 O A:HOH520 4.2 20.3 1.0 O1G A:ATP401 4.2 30.3 1.0 O3G A:ATP402 4.2 27.9 1.0 O5' A:ATP402 4.3 51.5 1.0 O1G A:ATP402 4.3 26.6 1.0 O A:HOH516 4.4 26.9 1.0 O2G A:ATP401 4.4 28.4 1.0 O1A A:ATP402 4.5 31.2 1.0 OD2 A:ASP130 4.5 23.7 1.0 O1B A:ATP402 4.6 35.9 1.0 OD1 A:ASP29 4.8 24.7 1.0 PG A:ATP401 4.8 32.2 1.0 CG A:ASP29 4.9 22.9 1.0

Magnesium binding site 4 out of 24 in the Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp


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 C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:33.3 occ:1.00 O B:HOH563 2.0 43.4 1.0 O B:HOH562 2.1 38.4 1.0 O B:HOH536 2.1 29.4 1.0 OD1 B:ASP76 2.2 21.4 1.0 O2A B:ATP401 2.3 27.2 1.0 OD2 B:ASP29 2.3 23.2 1.0 CG B:ASP29 3.1 23.8 1.0 PA B:ATP401 3.2 25.8 1.0 CG B:ASP76 3.2 21.6 1.0 OD1 B:ASP29 3.3 21.6 1.0 O5' B:ATP401 3.5 25.4 1.0 OD2 B:ASP76 3.5 21.6 1.0 MG B:MG404 3.5 23.0 1.0 O1A B:ATP401 3.7 21.7 1.0 O B:HOH550 3.9 18.7 1.0 C5' B:ATP401 4.0 28.2 1.0 O B:HOH533 4.2 28.6 1.0 OG B:SER75 4.2 26.7 1.0 CB B:ASP29 4.6 23.4 1.0 CB B:ASP76 4.6 21.6 1.0 O2G B:ATP401 4.6 15.6 1.0 N B:ASP76 4.6 24.3 1.0 O3A B:ATP401 4.7 20.5 1.0 C B:ASP76 4.7 22.4 1.0 O1B B:ATP401 4.8 26.2 1.0 CB B:GLU77 4.8 23.5 1.0 OE1 B:GLU77 4.9 27.2 1.0 O B:ASP76 4.9 22.7 1.0 CA B:ASP76 4.9 24.5 1.0 N B:GLU77 4.9 20.1 1.0

Magnesium binding site 5 out of 24 in the Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp


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 C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:23.0 occ:1.00 OD1 B:ASP29 1.9 21.6 1.0 O B:GLY30 2.0 22.9 1.0 O1B B:ATP401 2.0 26.2 1.0 O2G B:ATP401 2.1 15.6 1.0 O2A B:ATP401 2.1 27.2 1.0 OD2 B:ASP76 2.1 21.6 1.0 CG B:ASP29 3.1 23.8 1.0 C B:GLY30 3.1 24.5 1.0 CG B:ASP76 3.2 21.6 1.0 PB B:ATP401 3.2 25.8 1.0 PG B:ATP401 3.3 22.9 1.0 PA B:ATP401 3.4 25.8 1.0 OD1 B:ASP76 3.5 21.4 1.0 O B:HOH550 3.5 18.7 1.0 MG B:MG403 3.5 33.3 1.0 O3B B:ATP401 3.6 24.1 1.0 N B:GLY30 3.6 21.2 1.0 OD2 B:ASP29 3.6 23.2 1.0 O3A B:ATP401 3.7 20.5 1.0 CA B:GLY30 3.7 21.7 1.0 O B:HOH515 3.8 19.7 1.0 O3G B:ATP401 3.9 19.0 1.0 C B:ASP29 4.1 22.4 1.0 C5' B:ATP401 4.1 28.2 1.0 N B:LYS31 4.2 25.2 1.0 O5' B:ATP401 4.2 25.4 1.0 CB B:ASP29 4.3 23.4 1.0 O B:HOH536 4.4 29.4 1.0 CB B:PHE33 4.5 24.7 1.0 O B:ASP29 4.5 22.0 1.0 CB B:ASP76 4.5 21.6 1.0 N B:PHE33 4.5 25.5 1.0 O1G B:ATP401 4.6 23.7 1.0 O2B B:ATP401 4.6 26.0 1.0 N B:GLY32 4.6 26.4 1.0 CA B:LYS31 4.6 26.1 1.0 O1A B:ATP401 4.6 21.7 1.0 CA B:ASP29 4.7 22.1 1.0 O B:HOH562 4.8 38.4 1.0 C B:LYS31 4.9 26.7 1.0

Magnesium binding site 6 out of 24 in the Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp


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 C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:27.3 occ:1.00 O2A B:ATP402 1.9 82.2 1.0 O2B B:ATP402 2.0 30.9 1.0 O B:HOH551 2.1 16.5 1.0 O B:HOH529 2.2 29.9 1.0 O2G B:ATP402 2.2 21.4 1.0 O B:HOH550 2.3 18.7 1.0 PB B:ATP402 3.2 30.1 1.0 PA B:ATP402 3.2 85.0 1.0 PG B:ATP402 3.4 25.9 1.0 O3A B:ATP402 3.6 0.1 1.0 O3B B:ATP402 3.6 32.6 1.0 O B:HOH531 3.8 21.7 1.0 NH2 B:ARG132 4.0 21.3 1.0 NZ A:LYS95 4.1 30.9 1.0 O1G B:ATP401 4.1 23.7 1.0 O5' B:ATP402 4.2 1.0 1.0 O2G B:ATP401 4.3 15.6 1.0 O3G B:ATP402 4.3 25.2 1.0 O1A B:ATP402 4.4 81.7 1.0 O B:HOH535 4.4 22.9 1.0 O B:HOH515 4.4 19.7 1.0 O1G B:ATP402 4.5 27.7 1.0 O1B B:ATP402 4.5 36.5 1.0 CG B:ASP29 4.6 23.8 1.0 O B:HOH536 4.6 29.4 1.0 OD1 B:ASP29 4.6 21.6 1.0 OD2 B:ASP130 4.7 23.7 1.0 OD2 B:ASP29 4.8 23.2 1.0 PG B:ATP401 4.8 22.9 1.0 CB B:ASP29 4.8 23.4 1.0 O B:HOH533 4.9 28.6 1.0

Magnesium binding site 7 out of 24 in the Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp


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 C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:33.9 occ:1.00 O C:HOH535 1.9 31.8 1.0 O1A C:ATP401 2.0 47.6 1.0 OD1 C:ASP76 2.1 28.8 1.0 OD2 C:ASP29 2.1 29.2 1.0 O C:HOH548 2.5 38.5 1.0 O C:HOH549 2.6 46.5 1.0 CG C:ASP29 2.9 26.9 1.0 CG C:ASP76 3.0 28.9 1.0 OD1 C:ASP29 3.1 27.5 1.0 PA C:ATP401 3.1 44.2 1.0 MG C:MG404 3.2 32.3 1.0 OD2 C:ASP76 3.3 28.4 1.0 O2A C:ATP401 3.6 46.6 1.0 O5' C:ATP401 3.8 46.5 1.0 C5' C:ATP401 4.1 45.4 1.0 CB C:ASP76 4.4 28.6 1.0 CB C:ASP29 4.4 28.8 1.0 O C:HOH533 4.4 24.0 1.0 O C:HOH543 4.4 31.6 1.0 C C:ASP76 4.5 29.8 1.0 O3A C:ATP401 4.5 24.4 1.0 O2G C:ATP401 4.5 33.7 1.0 CB C:GLU77 4.5 27.8 1.0 N C:ASP76 4.5 28.7 1.0 O1B C:ATP401 4.6 39.3 1.0 OG C:SER75 4.6 33.9 1.0 O C:ASP76 4.6 27.7 1.0 OE2 C:GLU77 4.7 30.9 1.0 CA C:ASP76 4.7 29.1 1.0 N C:GLU77 4.7 27.9 1.0

Magnesium binding site 8 out of 24 in the Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp


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 C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg404 b:32.3 occ:1.00 OD2 C:ASP76 2.0 28.4 1.0 OD1 C:ASP29 2.1 27.5 1.0 O1B C:ATP401 2.1 39.3 1.0 O1A C:ATP401 2.1 47.6 1.0 O C:GLY30 2.1 28.9 1.0 O2G C:ATP401 2.1 33.7 1.0 CG C:ASP76 3.1 28.9 1.0 CG C:ASP29 3.1 26.9 1.0 PB C:ATP401 3.2 34.2 1.0 MG C:MG403 3.2 33.9 1.0 C C:GLY30 3.3 28.7 1.0 PA C:ATP401 3.4 44.2 1.0 OD1 C:ASP76 3.4 28.8 1.0 PG C:ATP401 3.4 36.3 1.0 O3A C:ATP401 3.5 24.4 1.0 OD2 C:ASP29 3.6 29.2 1.0 O3B C:ATP401 3.6 22.5 1.0 N C:GLY30 3.7 25.1 1.0 CA C:GLY30 3.8 26.6 1.0 O C:HOH534 4.1 28.0 1.0 O C:HOH533 4.1 24.0 1.0 C C:ASP29 4.2 25.3 1.0 C5' C:ATP401 4.2 45.4 1.0 O5' C:ATP401 4.2 46.5 1.0 O1G C:ATP401 4.3 35.0 1.0 CB C:ASP76 4.4 28.6 1.0 CB C:ASP29 4.4 28.8 1.0 N C:LYS31 4.4 26.2 1.0 CB C:PHE33 4.5 31.1 1.0 O2B C:ATP401 4.5 34.9 1.0 O3G C:ATP401 4.6 42.2 1.0 N C:PHE33 4.6 29.3 1.0 O2A C:ATP401 4.6 46.6 1.0 O C:ASP29 4.6 25.4 1.0 N C:GLY32 4.7 31.7 1.0 CA C:LYS31 4.7 29.0 1.0 CA C:ASP29 4.8 26.3 1.0 O C:HOH549 4.9 46.5 1.0 O C:ASP76 4.9 27.7 1.0 O C:HOH548 4.9 38.5 1.0 C C:LYS31 5.0 31.2 1.0

Magnesium binding site 9 out of 24 in the Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp


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 C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg405 b:24.2 occ:1.00 O1A C:ATP402 1.9 29.8 1.0 O1G C:ATP402 2.0 28.5 1.0 O C:HOH532 2.0 22.2 1.0 O C:HOH533 2.1 24.0 1.0 O C:HOH540 2.3 22.5 1.0 O1B C:ATP402 2.3 28.3 1.0 PA C:ATP402 3.3 31.5 1.0 PB C:ATP402 3.3 31.4 1.0 PG C:ATP402 3.3 29.5 1.0 O3A C:ATP402 3.6 48.3 1.0 O3B C:ATP402 3.6 28.5 1.0 O C:HOH546 3.8 38.7 1.0 NZ D:LYS95 3.9 30.2 1.0 O C:HOH524 3.9 33.8 1.0 O3G C:ATP401 4.0 42.2 1.0 NH2 C:ARG132 4.0 23.8 1.0 O3G C:ATP402 4.1 24.2 1.0 O5' C:ATP402 4.2 40.9 1.0 O C:HOH534 4.3 28.0 1.0 O2A C:ATP402 4.4 31.1 1.0 OD2 C:ASP130 4.4 26.1 1.0 O C:HOH512 4.4 25.3 1.0 O2G C:ATP401 4.4 33.7 1.0 O2G C:ATP402 4.5 31.0 1.0 O2B C:ATP402 4.7 36.4 1.0 OD1 C:ASP29 4.8 27.5 1.0 PG C:ATP401 4.8 36.3 1.0 O D:HOH513 4.9 35.8 1.0 CG C:ASP29 4.9 26.9 1.0

Magnesium binding site 10 out of 24 in the Crystal Structure of C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp


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 C. Albicans Trna(His) Guanylyltransferase (THG1) with Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg403 b:39.3 occ:1.00 O D:HOH542 2.0 42.4 1.0 O D:HOH524 2.0 49.2 1.0 OD1 D:ASP76 2.1 28.1 1.0 OD2 D:ASP29 2.2 29.7 1.0 O D:HOH541 2.4 44.0 1.0 O1A D:ATP401 2.5 43.0 1.0 CG D:ASP29 3.2 31.0 1.0 CG D:ASP76 3.2 28.8 1.0 PA D:ATP401 3.3 40.3 1.0 OD1 D:ASP29 3.4 33.6 1.0 OD2 D:ASP76 3.6 27.1 1.0 O2A D:ATP401 3.6 42.2 1.0 O5' D:ATP401 3.7 30.7 1.0 MG D:MG404 3.9 28.7 1.0 C5' D:ATP401 4.1 30.5 1.0 O D:HOH539 4.2 29.9 1.0 OG D:SER75 4.3 36.3 1.0 OE1 D:GLU77 4.3 33.3 1.0 CB D:GLU77 4.4 34.0 1.0 N D:ASP76 4.4 29.7 1.0 CB D:ASP76 4.5 28.3 1.0 C D:ASP76 4.5 30.4 1.0 CB D:ASP29 4.6 29.2 1.0 N D:GLU77 4.6 33.4 1.0 CA D:ASP76 4.7 33.2 1.0 O D:HOH533 4.8 25.5 1.0 CB D:SER75 4.8 32.3 1.0 O3A D:ATP401 4.8 30.9 1.0 O D:ASP76 4.9 28.8 1.0 O1G D:ATP401 5.0 30.8 1.0

A.Nakamura, T.Nemoto, I.U.Heinemann, K.Yamashita, T.Sonoda, K.Komoda, I.Tanaka, D.Soll, M.Yao. Structural Basis of Reverse Nucleotide Polymerization Proc.Natl.Acad.Sci.Usa V. 110 20970 2013.
ISSN: ISSN 0027-8424
PubMed: 24324136
DOI: 10.1073/PNAS.1321312111