Sodium in PDB 7rcg: I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui

The structure of I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui, PDB code: 7rcg was solved by A.T.Smiley, R.A.Werther, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.95 / 2.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.195, 64.903, 165.063, 90, 90, 90
R / Rfree (%)	20.1 / 25.1

The structure of I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui (pdb code 7rcg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui, PDB code: 7rcg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:38.3 occ:1.00 OG A:SER243 2.6 32.7 1.0 OD1 A:ASP244 2.7 31.4 1.0 CG A:ASP244 3.5 31.1 1.0 N A:ASP244 3.5 35.5 1.0 C A:SER243 3.6 32.5 1.0 CB A:SER243 3.6 27.3 1.0 CE A:LYS241 3.8 37.4 1.0 O A:SER243 3.9 31.1 1.0 CA A:ASP244 3.9 34.2 1.0 OD2 A:ASP244 4.1 29.9 1.0 NZ A:LYS248 4.1 31.5 1.0 CA A:SER243 4.2 32.4 1.0 CB A:ASP244 4.2 28.9 1.0 CE A:LYS248 4.3 32.1 1.0 NZ A:LYS241 4.7 41.0 1.0 OD2 A:ASP247 4.7 37.1 1.0 CD A:LYS241 4.9 36.6 1.0

Sodium binding site 2 out of 5 in the I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:29.2 occ:1.00 O A:HOH511 2.6 17.2 1.0 OE1 A:GLU201 2.7 24.1 1.0 N7 B:DA16 3.0 28.4 1.0 C6 B:DC15 3.4 22.4 1.0 CD A:GLU201 3.4 21.5 1.0 CG A:GLU201 3.4 21.3 1.0 CB A:GLU201 3.7 20.4 1.0 C5 B:DC15 3.7 22.8 1.0 N6 B:DA16 3.8 26.6 1.0 C8 B:DA16 3.9 24.7 1.0 C5 B:DA16 3.9 26.4 1.0 CB A:SER180 4.0 22.5 1.0 O A:GLU201 4.1 22.6 1.0 C2' B:DC15 4.1 21.8 1.0 OG A:SER203 4.2 20.1 1.0 C A:GLU201 4.2 22.8 1.0 N A:SER203 4.2 19.6 1.0 CB A:SER203 4.3 20.6 1.0 N1 B:DC15 4.3 24.3 1.0 C6 B:DA16 4.3 25.0 1.0 OE2 A:GLU201 4.6 21.3 1.0 N A:ILE202 4.6 20.8 1.0 CA A:GLU201 4.6 21.9 1.0 C A:ILE202 4.6 23.2 1.0 CA A:ILE202 4.7 20.9 1.0 C1' B:DC15 4.7 21.2 1.0 OG A:SER180 4.8 21.9 1.0 CA A:SER203 4.8 16.4 1.0 C4 B:DC15 4.9 24.2 1.0 O A:ASP178 4.9 21.8 1.0

Sodium binding site 3 out of 5 in the I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:38.9 occ:1.00 OP1 B:DA16 2.6 25.7 1.0 OD2 A:ASP265 2.9 33.2 1.0 O A:HOH536 3.0 30.3 1.0 NZ A:LYS262 3.1 26.0 1.0 CG A:LYS262 3.5 27.7 1.0 P B:DA16 3.6 24.5 1.0 O B:HOH202 3.8 26.2 1.0 OP2 B:DA16 3.8 25.8 1.0 CE A:LYS262 4.0 26.0 1.0 CG A:ASP265 4.2 31.2 1.0 CD A:LYS262 4.4 26.4 1.0 CA A:LYS262 4.5 29.7 1.0 O A:HOH504 4.6 22.3 1.0 CB A:LYS262 4.6 28.4 1.0 O3' B:DC15 4.6 22.9 1.0 N A:LYS262 4.6 30.3 1.0 O A:HOH535 4.7 19.9 1.0 O5' B:DA16 4.8 24.4 1.0 OD1 A:ASP265 4.9 33.4 1.0 C A:MET261 4.9 30.6 1.0 CB A:MET261 4.9 26.3 1.0

Sodium binding site 4 out of 5 in the I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:41.5 occ:1.00 OG A:SER78 2.9 29.2 1.0 CL A:CL405 3.0 51.5 1.0 CG2 A:VAL80 3.1 32.5 1.0 O C:HOH103 3.3 24.6 1.0 N4 B:DC8 3.8 28.1 1.0 CB A:SER78 3.8 30.3 1.0 ND2 A:ASN72 4.0 30.2 1.0 OD1 A:ASN72 4.2 29.2 1.0 CG2 A:THR46 4.5 22.4 1.0 CB A:VAL80 4.5 32.2 1.0 CG A:ASN72 4.5 34.5 1.0 CD1 A:LEU70 4.6 29.8 1.0 N7 B:DG7 4.7 32.2 1.0 CE A:MET48 4.7 22.5 1.0 O6 B:DG7 4.8 23.9 1.0 CG1 A:VAL80 4.9 28.5 1.0 O6 C:DG18 4.9 27.1 1.0

Sodium binding site 5 out of 5 in the I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of I-ONUI_E-HPD1-F Final Stage Reengineered Variant of I-Onui within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:40.7 occ:1.00 OP1 B:DC13 2.5 28.8 1.0 O C:HOH110 2.8 23.7 1.0 CL A:CL403 3.0 45.1 1.0 C5' B:DC13 3.1 21.2 1.0 NE1 A:TRP140 3.5 26.6 1.0 O B:HOH208 3.5 35.6 1.0 O5' B:DC13 3.5 24.8 1.0 P B:DC13 3.6 21.5 1.0 O C:HOH113 4.0 25.7 1.0 CE2 A:TRP140 4.2 20.5 1.0 CZ2 A:TRP140 4.2 18.0 1.0 O C:HOH108 4.3 28.0 1.0 O3' B:DT12 4.5 26.7 1.0 CD1 A:TRP140 4.5 27.0 1.0 C4' B:DC13 4.5 22.5 1.0 C4' B:DT12 4.6 22.7 1.0 OP2 B:DC13 4.7 30.2 1.0

R.A.Werther, N.C.Ubilla-Rodriguez, A.T.Smiley, K.Havens, A.R.Lambert, B.L.Stoddard. Characterization of the Stepwise Engineering and Optimization of A Retargeted Dna Binding Protein and Gene-Editing Meganuclease To Be Published.