Magnesium in PDB 4ncj: Crystal Structure of Pyrococcus Furiosis RAD50 R805E Mutation with Adp Beryllium Flouride

The structure of Crystal Structure of Pyrococcus Furiosis RAD50 R805E Mutation with Adp Beryllium Flouride, PDB code: 4ncj was solved by S.Classen, G.J.Williams, A.S.Arvai, R.S.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.41 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.020, 108.482, 148.744, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25.8

The structure of Crystal Structure of Pyrococcus Furiosis RAD50 R805E Mutation with Adp Beryllium Flouride also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Magnesium atom in the Crystal Structure of Pyrococcus Furiosis RAD50 R805E Mutation with Adp Beryllium Flouride (pdb code 4ncj). 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 Pyrococcus Furiosis RAD50 R805E Mutation with Adp Beryllium Flouride, PDB code: 4ncj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Pyrococcus Furiosis RAD50 R805E Mutation with Adp Beryllium Flouride


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 Pyrococcus Furiosis RAD50 R805E Mutation with Adp Beryllium Flouride within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:19.4 occ:1.00 OG A:SER37 2.0 19.8 1.0 O A:HOH1053 2.0 23.5 1.0 F1 A:BEF902 2.0 14.4 1.0 OE1 A:GLN140 2.1 21.9 1.0 O1B A:ADP901 2.2 16.0 1.0 O A:HOH1045 2.2 17.3 1.0 HE22 A:GLN140 3.1 31.9 1.0 CD A:GLN140 3.1 25.1 1.0 PB A:ADP901 3.2 16.8 1.0 CB A:SER37 3.2 20.2 1.0 BE A:BEF902 3.2 12.1 1.0 HB2 A:SER37 3.2 24.3 1.0 H A:SER37 3.3 21.4 1.0 O3B A:ADP901 3.4 15.6 1.0 H C:GLY794 3.5 27.3 1.0 NE2 A:GLN140 3.5 26.6 1.0 HB3 A:SER37 3.8 24.3 1.0 HB2 C:SER793 3.9 23.4 1.0 O A:HOH1003 4.0 28.6 1.0 N A:SER37 4.0 17.8 1.0 HE2 A:LYS36 4.0 28.6 1.0 OD1 A:ASP822 4.0 20.5 1.0 F2 A:BEF902 4.0 20.8 1.0 HB2 A:LYS36 4.1 25.7 1.0 CA A:SER37 4.2 18.7 1.0 O2A A:ADP901 4.2 17.9 1.0 OD2 A:ASP822 4.2 24.9 1.0 O3A A:ADP901 4.2 17.8 1.0 O A:HOH1014 4.2 21.6 1.0 HB2 A:GLN140 4.2 31.6 1.0 O2B A:ADP901 4.3 16.1 1.0 N C:GLY794 4.3 22.7 1.0 HE21 A:GLN140 4.4 31.9 1.0 HZ1 A:LYS36 4.4 31.0 1.0 HA3 C:GLY794 4.4 27.6 1.0 F3 A:BEF902 4.5 18.4 1.0 CG A:GLN140 4.5 27.1 1.0 CG A:ASP822 4.5 21.8 1.0 HA A:SER37 4.6 22.4 1.0 PA A:ADP901 4.6 17.2 1.0 HZ3 A:LYS36 4.7 31.0 1.0 CB A:GLN140 4.7 26.4 1.0 HB3 A:GLN140 4.8 31.6 1.0 NZ A:LYS36 4.8 25.8 1.0 CE A:LYS36 4.8 23.9 1.0 H C:GLY795 4.8 29.0 1.0 CB C:SER793 4.9 19.5 1.0 HG11 A:VAL853 4.9 39.8 1.0 HB2 A:GLU823 4.9 27.5 1.0 HA C:SER793 5.0 26.2 1.0 CA C:GLY794 5.0 23.0 1.0 HG3 A:GLN140 5.0 32.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Pyrococcus Furiosis RAD50 R805E Mutation with Adp Beryllium Flouride


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 Pyrococcus Furiosis RAD50 R805E Mutation with Adp Beryllium Flouride within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:21.0 occ:1.00 F3 B:BEF902 2.0 18.3 1.0 OE1 B:GLN140 2.1 24.8 1.0 O B:HOH1065 2.1 18.6 1.0 OG B:SER37 2.1 21.7 1.0 O B:HOH1003 2.1 17.1 1.0 O3B B:ADP901 2.1 20.9 1.0 CD B:GLN140 3.1 24.5 1.0 HE22 B:GLN140 3.1 28.5 1.0 HB2 B:SER37 3.1 25.3 1.0 CB B:SER37 3.2 21.1 1.0 BE B:BEF902 3.2 18.2 1.0 PB B:ADP901 3.2 20.8 1.0 H B:SER37 3.4 25.6 1.0 H D:GLY794 3.4 28.0 1.0 NE2 B:GLN140 3.4 23.8 1.0 O2B B:ADP901 3.5 18.1 1.0 HB3 B:SER37 3.8 25.3 1.0 HB2 D:SER793 3.9 30.0 1.0 HE2 B:LYS36 3.9 33.1 1.0 O B:HOH1012 4.0 26.8 1.0 F1 B:BEF902 4.0 19.4 1.0 O2A B:ADP901 4.0 17.9 1.0 O B:HOH1066 4.1 26.8 1.0 HB2 B:LYS36 4.1 30.1 1.0 N B:SER37 4.1 21.3 1.0 OD1 B:ASP822 4.1 26.0 1.0 HB2 B:GLN140 4.2 29.8 1.0 CA B:SER37 4.2 20.7 1.0 OD2 B:ASP822 4.2 26.6 1.0 O3A B:ADP901 4.2 16.0 1.0 N D:GLY794 4.3 23.3 1.0 HE21 B:GLN140 4.3 28.5 1.0 F2 B:BEF902 4.3 17.8 1.0 HA3 D:GLY794 4.3 29.2 1.0 O1B B:ADP901 4.4 22.2 1.0 CG B:GLN140 4.4 24.7 1.0 HA B:SER37 4.5 24.8 1.0 HZ1 B:LYS36 4.6 35.3 1.0 PA B:ADP901 4.6 19.1 1.0 CG B:ASP822 4.6 26.5 1.0 CB B:GLN140 4.7 24.8 1.0 HB3 B:GLN140 4.7 29.8 1.0 CE B:LYS36 4.8 27.6 1.0 H D:GLY795 4.8 28.8 1.0 HG3 B:GLN140 4.8 29.7 1.0 HZ3 B:LYS36 4.8 35.3 1.0 CB D:SER793 4.8 25.0 1.0 CA D:GLY794 4.9 24.4 1.0 HB2 B:GLU823 4.9 28.3 1.0 HA D:SER793 4.9 28.1 1.0 NZ B:LYS36 4.9 29.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Pyrococcus Furiosis RAD50 R805E Mutation with Adp Beryllium Flouride


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 Pyrococcus Furiosis RAD50 R805E Mutation with Adp Beryllium Flouride within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg903 b:22.5 occ:1.00 O C:HOH1002 1.9 21.3 1.0 F1 C:BEF902 2.0 20.3 1.0 OG C:SER37 2.0 23.4 1.0 O2B C:ADP901 2.0 22.6 1.0 OE1 C:GLN140 2.1 28.7 1.0 O C:HOH1001 2.3 20.1 1.0 BE C:BEF902 3.1 19.1 1.0 PB C:ADP901 3.2 22.6 1.0 CD C:GLN140 3.2 29.2 1.0 CB C:SER37 3.2 22.2 1.0 H C:SER37 3.3 28.1 1.0 HB2 C:SER37 3.3 26.6 1.0 HE22 C:GLN140 3.3 36.6 1.0 HZ2 C:LYS36 3.5 37.2 1.0 H A:GLY794 3.5 32.4 1.0 O1B C:ADP901 3.5 19.8 1.0 NE2 C:GLN140 3.6 30.5 1.0 HB3 C:SER37 3.8 26.6 1.0 HB2 A:SER793 3.8 31.0 1.0 HB2 C:LYS36 4.0 32.0 1.0 N C:SER37 4.0 23.4 1.0 F2 C:BEF902 4.0 19.1 1.0 O C:HOH1023 4.0 28.0 1.0 O2A C:ADP901 4.0 20.6 1.0 O C:HOH1010 4.1 18.0 1.0 OD1 C:ASP822 4.1 27.4 1.0 O3A C:ADP901 4.2 20.6 1.0 HB2 C:GLN140 4.2 32.7 1.0 OD2 C:ASP822 4.2 25.1 1.0 CA C:SER37 4.2 23.3 1.0 NZ C:LYS36 4.3 31.0 1.0 O3B C:ADP901 4.3 24.7 1.0 F3 C:BEF902 4.3 20.7 1.0 N A:GLY794 4.4 27.0 1.0 HZ1 C:LYS36 4.4 37.2 1.0 CG C:GLN140 4.5 28.2 1.0 HE21 C:GLN140 4.5 36.6 1.0 HA3 A:GLY794 4.6 30.2 1.0 PA C:ADP901 4.6 20.9 1.0 CG C:ASP822 4.6 27.0 1.0 HA C:SER37 4.6 27.9 1.0 CB C:GLN140 4.7 27.2 1.0 O A:HOH1083 4.7 40.1 1.0 HB3 C:GLN140 4.7 32.7 1.0 HG11 C:VAL853 4.7 42.3 1.0 HZ3 C:LYS36 4.8 37.2 1.0 CB A:SER793 4.8 25.8 1.0 CB C:LYS36 4.8 26.7 1.0 HB3 C:LYS36 4.8 32.0 1.0 H A:GLY795 4.9 26.9 1.0 HB2 C:GLU823 4.9 29.6 1.0 HA A:SER793 4.9 31.7 1.0 HE3 C:LYS36 5.0 38.4 1.0 O1A C:ADP901 5.0 19.4 1.0 HG3 C:GLN140 5.0 33.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Pyrococcus Furiosis RAD50 R805E Mutation with Adp Beryllium Flouride


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 Pyrococcus Furiosis RAD50 R805E Mutation with Adp Beryllium Flouride within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg903 b:21.4 occ:1.00 F1 D:BEF902 1.9 16.5 1.0 O D:HOH1005 2.0 18.6 1.0 OG D:SER37 2.0 21.5 1.0 O D:HOH1004 2.1 24.4 1.0 O1B D:ADP901 2.1 20.8 1.0 OE1 D:GLN140 2.1 25.5 1.0 HB2 D:SER37 3.1 27.0 1.0 HE22 D:GLN140 3.1 29.7 1.0 CD D:GLN140 3.1 25.5 1.0 CB D:SER37 3.1 22.5 1.0 BE D:BEF902 3.2 14.8 1.0 PB D:ADP901 3.2 21.1 1.0 H B:GLY794 3.3 33.0 1.0 H D:SER37 3.4 29.5 1.0 NE2 D:GLN140 3.5 24.7 1.0 O3B D:ADP901 3.5 18.6 1.0 HB3 D:SER37 3.7 27.0 1.0 HB2 B:SER793 3.8 28.8 1.0 O2A D:ADP901 4.0 23.0 1.0 F2 D:BEF902 4.0 21.6 1.0 N D:SER37 4.0 24.6 1.0 N B:GLY794 4.1 27.5 1.0 O3A D:ADP901 4.1 20.6 1.0 HA3 B:GLY794 4.1 33.1 1.0 O D:HOH1024 4.2 30.2 1.0 CA D:SER37 4.2 23.7 1.0 HB2 D:LYS36 4.2 27.7 1.0 OD1 D:ASP822 4.2 21.6 1.0 O D:HOH1018 4.2 22.5 1.0 HB2 D:GLN140 4.2 31.6 1.0 HE2 D:LYS36 4.2 34.5 1.0 OD2 D:ASP822 4.3 24.4 1.0 HE21 D:GLN140 4.3 29.7 1.0 O2B D:ADP901 4.4 22.5 1.0 F3 D:BEF902 4.4 26.6 1.0 HZ1 D:LYS36 4.5 36.0 1.0 PA D:ADP901 4.5 22.0 1.0 CG D:GLN140 4.5 26.4 1.0 O D:HOH1086 4.5 38.1 1.0 HA D:SER37 4.6 28.4 1.0 CG D:ASP822 4.6 23.5 1.0 CA B:GLY794 4.7 27.6 1.0 HG11 D:VAL853 4.7 45.9 1.0 HZ3 D:LYS36 4.7 36.0 1.0 CB D:GLN140 4.8 26.4 1.0 CB B:SER793 4.8 24.0 1.0 HB3 D:GLN140 4.8 31.6 1.0 HA B:SER793 4.9 28.5 1.0 H B:GLY795 4.9 28.1 1.0 NZ D:LYS36 4.9 30.0 1.0 O1A D:ADP901 5.0 22.1 1.0

R.A.Deshpande, G.J.Williams, O.Limbo, R.S.Williams, J.Kuhnlein, J.H.Lee, S.Classen, G.Guenther, P.Russell, J.A.Tainer, T.T.Paull. Atp-Driven RAD50 Conformations Regulate Dna Tethering, End Resection, and Atm Checkpoint Signaling. Embo J. V. 33 482 2014.
ISSN: ISSN 0261-4189
PubMed: 24493214
DOI: 10.1002/EMBJ.201386100