Magnesium in PDB 6huf: Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A

The structure of Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A, PDB code: 6huf was solved by M.Jamshidiha, I.Perez-Dorado, J.W.Murray, E.W.Tate, E.Cota, R.J.Read, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.15 / 2.82
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.420, 132.410, 230.590, 90.00, 103.57, 90.00
R / Rfree (%)	31.2 / 34.2

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A (pdb code 6huf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A, PDB code: 6huf:
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 Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:30.0 occ:1.00 OG1 A:THR23 1.9 56.8 1.0 O3G A:GNP202 1.9 48.0 1.0 OG1 A:THR41 2.2 68.8 1.0 O2B A:GNP202 2.3 47.3 1.0 O A:HOH301 3.0 47.8 1.0 PG A:GNP202 3.2 58.2 1.0 CB A:THR41 3.2 66.7 1.0 CB A:THR23 3.3 59.7 1.0 PB A:GNP202 3.3 45.2 1.0 N3B A:GNP202 3.4 53.9 1.0 OD1 A:ASP64 3.8 56.2 1.0 OD2 A:ASP64 3.9 54.6 1.0 CG2 A:THR23 4.0 64.7 1.0 N A:THR41 4.0 67.9 1.0 O2G A:GNP202 4.1 46.9 1.0 O1A A:GNP202 4.1 41.3 1.0 N A:THR23 4.2 60.0 1.0 O A:THR65 4.2 48.3 1.0 CG2 A:THR41 4.2 68.3 1.0 CA A:THR41 4.2 73.9 1.0 CA A:THR23 4.3 62.1 1.0 CG A:ASP64 4.3 51.2 1.0 O1G A:GNP202 4.3 45.1 1.0 O3A A:GNP202 4.4 39.9 1.0 O1B A:GNP202 4.4 60.5 1.0 O A:HOH303 4.5 23.6 1.0 PA A:GNP202 4.6 56.0 1.0 O A:ILE39 4.7 53.4 1.0 CG A:LYS22 4.8 72.9 1.0 O2A A:GNP202 4.8 49.5 1.0

Magnesium binding site 2 out of 16 in the Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A within 5.0Å range: probe atom residue distance (Å) B Occ O:Mg201 b:28.9 occ:1.00 OG1 O:THR23 1.7 44.5 1.0 O1G O:GNP202 1.9 45.7 1.0 O1B O:GNP202 2.2 55.4 1.0 OG1 O:THR41 2.2 49.5 1.0 CB O:THR23 3.1 43.7 1.0 PG O:GNP202 3.2 50.9 1.0 CB O:THR41 3.3 50.5 1.0 PB O:GNP202 3.3 49.0 1.0 N3B O:GNP202 3.4 47.8 1.0 OD1 O:ASP64 3.7 50.8 1.0 OD2 O:ASP64 3.8 41.2 1.0 CG2 O:THR23 3.8 45.9 1.0 O2A O:GNP202 4.1 38.5 1.0 O3G O:GNP202 4.1 45.6 1.0 N O:THR23 4.1 50.5 1.0 CA O:THR23 4.1 46.4 1.0 N O:THR41 4.1 57.3 1.0 CG O:ASP64 4.1 46.7 1.0 CG2 O:THR41 4.2 49.1 1.0 O3A O:GNP202 4.3 45.1 1.0 O2G O:GNP202 4.3 45.4 1.0 O O:THR65 4.3 43.1 1.0 CA O:THR41 4.3 57.1 1.0 O2B O:GNP202 4.5 61.9 1.0 PA O:GNP202 4.5 48.2 1.0 O1A O:GNP202 4.6 51.8 1.0 O O:ILE39 4.7 57.7 1.0 CG O:LYS22 4.8 61.5 1.0

Magnesium binding site 3 out of 16 in the Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg201 b:34.3 occ:1.00 OG1 N:THR23 1.8 69.8 1.0 O3G N:GNP202 2.1 47.9 1.0 O2B N:GNP202 2.1 48.1 1.0 OG1 N:THR41 2.2 64.7 1.0 CB N:THR23 3.1 64.8 1.0 CB N:THR41 3.2 69.5 1.0 PB N:GNP202 3.4 56.4 1.0 PG N:GNP202 3.4 51.3 1.0 N3B N:GNP202 3.6 52.7 1.0 OD1 N:ASP64 3.7 60.0 1.0 OD2 N:ASP64 3.7 42.8 1.0 CG2 N:THR23 3.8 70.0 1.0 N N:THR23 4.1 60.7 1.0 CG N:ASP64 4.1 51.1 1.0 CA N:THR23 4.1 61.4 1.0 N N:THR41 4.1 59.5 1.0 CG2 N:THR41 4.2 71.6 1.0 O2A N:GNP202 4.2 53.7 1.0 O N:THR65 4.2 54.6 1.0 CA N:THR41 4.3 62.4 1.0 O1G N:GNP202 4.3 50.0 1.0 O2G N:GNP202 4.4 61.9 1.0 O3A N:GNP202 4.4 46.9 1.0 O1B N:GNP202 4.5 58.0 1.0 PA N:GNP202 4.6 52.0 1.0 O1A N:GNP202 4.7 48.7 1.0 CG N:LYS22 4.8 63.5 1.0 O N:ILE39 4.8 65.7 1.0

Magnesium binding site 4 out of 16 in the Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:35.9 occ:1.00 OG1 B:THR23 1.8 79.1 1.0 O1B B:GNP202 2.1 44.6 1.0 OG1 B:THR41 2.2 61.3 1.0 O3G B:GNP202 2.3 57.1 1.0 CB B:THR23 3.1 71.5 1.0 CB B:THR41 3.2 66.6 1.0 PB B:GNP202 3.3 50.0 1.0 N3B B:GNP202 3.3 59.2 1.0 PG B:GNP202 3.3 57.2 1.0 CG2 B:THR23 3.8 73.1 1.0 O1A B:GNP202 3.8 49.9 1.0 N B:THR41 3.9 58.4 1.0 OD2 B:ASP64 4.0 43.0 1.0 OD1 B:ASP64 4.1 47.0 1.0 CA B:THR41 4.1 62.4 1.0 O3A B:GNP202 4.2 49.9 1.0 CA B:THR23 4.2 72.2 1.0 O1G B:GNP202 4.2 64.5 1.0 N B:THR23 4.2 75.3 1.0 CG2 B:THR41 4.3 62.6 1.0 O2G B:GNP202 4.4 59.5 1.0 CG B:ASP64 4.4 55.4 1.0 O B:ILE39 4.4 62.1 1.0 PA B:GNP202 4.4 53.9 1.0 O2B B:GNP202 4.5 55.7 1.0 O B:THR65 4.6 71.5 1.0 O2A B:GNP202 4.8 65.2 1.0 C B:THR40 4.9 69.1 1.0

Magnesium binding site 5 out of 16 in the Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:38.5 occ:1.00 OG1 E:THR23 1.8 59.2 1.0 O1B E:GNP202 2.0 45.5 1.0 O1G E:GNP202 2.1 67.5 1.0 OG1 E:THR41 2.3 57.3 1.0 PB E:GNP202 3.2 50.9 1.0 CB E:THR23 3.2 55.2 1.0 PG E:GNP202 3.3 59.7 1.0 CB E:THR41 3.3 60.7 1.0 N3B E:GNP202 3.3 55.0 1.0 OD1 E:ASP64 3.8 56.4 1.0 OD2 E:ASP64 3.9 48.8 1.0 CG2 E:THR23 4.0 51.7 1.0 O3G E:GNP202 4.0 61.8 1.0 O1A E:GNP202 4.0 54.9 1.0 N E:THR23 4.1 52.6 1.0 N E:THR41 4.1 59.2 1.0 CA E:THR23 4.2 55.4 1.0 O3A E:GNP202 4.2 43.6 1.0 CG E:ASP64 4.2 53.4 1.0 O E:THR65 4.2 70.8 1.0 CG2 E:THR41 4.2 65.9 1.0 O2B E:GNP202 4.2 57.5 1.0 CA E:THR41 4.3 57.6 1.0 O2G E:GNP202 4.4 66.6 1.0 PA E:GNP202 4.5 58.4 1.0 CG E:LYS22 4.7 61.8 1.0 O2A E:GNP202 4.8 56.2 1.0 O E:ILE39 4.8 48.0 1.0 CE E:LYS22 5.0 60.9 1.0

Magnesium binding site 6 out of 16 in the Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:43.5 occ:1.00 O1G C:GNP202 1.7 62.2 1.0 OG1 C:THR23 1.8 70.9 1.0 O1B C:GNP202 2.3 49.3 1.0 OG1 C:THR41 2.4 65.7 1.0 PG C:GNP202 3.0 58.5 1.0 CB C:THR23 3.2 69.6 1.0 N3B C:GNP202 3.3 59.7 1.0 PB C:GNP202 3.3 60.0 1.0 OD1 C:ASP64 3.4 52.9 1.0 CB C:THR41 3.4 59.9 1.0 OD2 C:ASP64 3.6 42.0 1.0 O3G C:GNP202 3.8 62.0 1.0 CG C:ASP64 3.9 51.9 1.0 N C:THR23 3.9 72.5 1.0 CG2 C:THR23 4.0 64.6 1.0 O C:THR65 4.0 63.7 1.0 CA C:THR23 4.0 72.1 1.0 O2G C:GNP202 4.1 48.9 1.0 CG2 C:THR41 4.2 60.3 1.0 O2B C:GNP202 4.3 59.7 1.0 O2A C:GNP202 4.4 51.8 1.0 CG C:LYS22 4.5 85.3 1.0 O3A C:GNP202 4.5 55.3 1.0 N C:THR41 4.5 53.3 1.0 CA C:THR41 4.6 53.9 1.0 CE C:LYS22 4.8 80.6 1.0 PA C:GNP202 4.8 56.2 1.0 O1A C:GNP202 4.8 57.3 1.0 C C:LYS22 4.8 80.7 1.0

Magnesium binding site 7 out of 16 in the Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg201 b:34.2 occ:1.00 O3G K:GNP202 1.9 46.9 1.0 O2B K:GNP202 2.0 48.0 1.0 OG1 K:THR23 2.1 50.0 1.0 OG1 K:THR41 2.3 73.3 1.0 PG K:GNP202 3.0 51.8 1.0 PB K:GNP202 3.1 57.5 1.0 CB K:THR41 3.2 73.0 1.0 N3B K:GNP202 3.3 51.3 1.0 CB K:THR23 3.5 49.6 1.0 OD1 K:ASP64 3.6 58.6 1.0 O1G K:GNP202 3.7 50.3 1.0 O K:THR65 3.9 88.2 1.0 OD2 K:ASP64 3.9 48.1 1.0 O2A K:GNP202 4.0 58.9 1.0 O1B K:GNP202 4.1 46.7 1.0 CG2 K:THR41 4.1 72.2 1.0 CG K:ASP64 4.1 54.6 1.0 O3A K:GNP202 4.2 49.6 1.0 N K:THR41 4.2 70.6 1.0 N K:THR23 4.3 67.5 1.0 O2G K:GNP202 4.3 49.5 1.0 CG2 K:THR23 4.3 39.4 1.0 CA K:THR41 4.3 69.5 1.0 CA K:THR23 4.4 56.9 1.0 PA K:GNP202 4.5 54.3 1.0 CG K:LYS22 4.5 82.2 1.0 CE K:LYS22 4.7 80.2 1.0 O1A K:GNP202 4.7 54.3 1.0

Magnesium binding site 8 out of 16 in the Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg201 b:34.7 occ:1.00 OG1 M:THR23 1.8 89.3 1.0 O3G M:GNP202 2.0 56.2 1.0 O2B M:GNP202 2.0 42.9 1.0 OG1 M:THR41 2.2 67.0 1.0 CB M:THR23 3.2 78.3 1.0 PB M:GNP202 3.2 50.5 1.0 CB M:THR41 3.3 64.8 1.0 PG M:GNP202 3.3 51.8 1.0 N3B M:GNP202 3.4 53.4 1.0 OD1 M:ASP64 3.6 72.5 1.0 OD2 M:ASP64 3.8 52.1 1.0 CG2 M:THR23 3.9 75.4 1.0 O2G M:GNP202 4.0 50.5 1.0 N M:THR23 4.1 73.5 1.0 CG M:ASP64 4.1 61.0 1.0 CA M:THR23 4.2 76.0 1.0 O M:THR65 4.2 51.6 1.0 O1A M:GNP202 4.2 56.6 1.0 CG2 M:THR41 4.2 65.4 1.0 N M:THR41 4.2 73.6 1.0 O1B M:GNP202 4.2 52.1 1.0 O3A M:GNP202 4.3 49.5 1.0 CA M:THR41 4.3 69.1 1.0 O1G M:GNP202 4.5 46.7 1.0 PA M:GNP202 4.7 58.5 1.0 CG M:LYS22 4.7 83.6 1.0 O M:ILE39 4.9 70.7 1.0 O2A M:GNP202 5.0 56.8 1.0

Magnesium binding site 9 out of 16 in the Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:39.9 occ:1.00 OG1 D:THR23 1.7 76.0 1.0 O2B D:GNP202 2.0 44.8 1.0 OG1 D:THR41 2.2 69.1 1.0 O3G D:GNP202 2.5 73.6 1.0 CB D:THR23 3.1 85.8 1.0 PB D:GNP202 3.1 50.8 1.0 N3B D:GNP202 3.3 62.3 1.0 CB D:THR41 3.4 66.5 1.0 PG D:GNP202 3.4 69.2 1.0 OD1 D:ASP64 3.7 64.4 1.0 OD2 D:ASP64 3.8 56.2 1.0 CG2 D:THR23 3.9 88.3 1.0 N D:THR23 4.0 95.8 1.0 CA D:THR23 4.1 86.7 1.0 CG D:ASP64 4.2 64.5 1.0 N D:THR41 4.2 58.6 1.0 O2G D:GNP202 4.2 67.0 1.0 O3A D:GNP202 4.2 44.4 1.0 O1A D:GNP202 4.3 47.5 1.0 O1B D:GNP202 4.3 62.0 1.0 O D:THR65 4.3 88.4 1.0 CG2 D:THR41 4.3 63.1 1.0 CA D:THR41 4.4 63.0 1.0 O1G D:GNP202 4.6 69.5 1.0 CG D:LYS22 4.7 81.1 1.0 PA D:GNP202 4.7 51.4 1.0 O D:ILE39 4.8 65.5 1.0

Magnesium binding site 10 out of 16 in the Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Coping with Strong Translational Non-Crystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg201 b:41.7 occ:1.00 OG1 P:THR23 1.9 70.9 1.0 O1G P:GNP202 2.2 83.6 1.0 O1B P:GNP202 2.2 45.3 1.0 OG1 P:THR41 2.3 51.6 1.0 CB P:THR41 3.2 53.6 1.0 PB P:GNP202 3.2 53.2 1.0 CB P:THR23 3.3 67.5 1.0 N3B P:GNP202 3.3 65.7 1.0 PG P:GNP202 3.3 67.5 1.0 OD1 P:ASP64 3.7 53.6 1.0 OD2 P:ASP64 3.9 52.4 1.0 N P:THR41 4.0 58.4 1.0 CG2 P:THR23 4.0 70.7 1.0 O P:THR65 4.1 96.1 1.0 CG P:ASP64 4.1 61.9 1.0 CG2 P:THR41 4.2 51.1 1.0 N P:THR23 4.2 73.0 1.0 CA P:THR41 4.2 57.0 1.0 O1A P:GNP202 4.2 40.8 1.0 CA P:THR23 4.3 71.0 1.0 O2G P:GNP202 4.3 62.7 1.0 O3G P:GNP202 4.3 69.1 1.0 O2B P:GNP202 4.4 64.8 1.0 O3A P:GNP202 4.4 45.7 1.0 CG P:LYS22 4.7 78.5 1.0 O P:ILE39 4.7 63.8 1.0 PA P:GNP202 4.8 50.1 1.0 CE P:LYS22 4.9 77.7 1.0

M.Jamshidiha, I.Perez-Dorado, J.W.Murray, E.W.Tate, E.Cota, R.J.Read. Coping with Strong Translational Noncrystallographic Symmetry and Extreme Anisotropy in Molecular Replacement with Phaser: Human RAB27A. Acta Crystallogr D Struct V. 75 342 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 30950405
DOI: 10.1107/S2059798318017825