Sodium in PDB 5dow: Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration

The structure of Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration, PDB code: 5dow was solved by J.P.Keller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.81 / 1.70
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	98.874, 98.874, 128.583, 90.00, 90.00, 120.00
R / Rfree (%)	9.7 / 14.1

The structure of Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration also contains other interesting chemical elements:

Chlorine	(Cl)	11 atoms
Calcium	(Ca)	16 atoms

The binding sites of Sodium atom in the Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration (pdb code 5dow). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration, PDB code: 5dow:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:43.9 occ:1.00 O A:HOH501 2.3 28.4 1.0 O A:HOH515 2.5 39.6 1.0 OE1 A:GLU7 2.5 20.9 1.0 CD A:GLU7 3.6 18.9 1.0 CB A:GLU7 3.7 15.2 1.0 CG A:GLU7 4.1 17.5 1.0 CL A:CL206 4.4 26.1 1.0 OE2 A:GLU7 4.6 19.8 1.0

Sodium binding site 2 out of 5 in the Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration within 5.0Å range: probe atom residue distance (Å) B Occ C:Na208 b:48.6 occ:1.00 OD2 C:ASP123 2.2 32.1 1.0 CG C:ASP123 3.3 25.6 1.0 OE1 C:GLU120 3.4 25.8 0.4 OD2 C:ASP119 3.4 22.7 0.4 CG C:GLU120 3.7 22.8 0.6 CB C:ASP123 4.0 22.5 1.0 CA C:GLU120 4.0 18.6 0.6 CG C:ASP119 4.0 18.3 0.4 CA C:GLU120 4.1 17.6 0.4 O C:ASP119 4.2 16.0 0.6 N C:GLU120 4.2 15.7 0.4 N C:GLU120 4.2 15.8 0.6 C C:ASP119 4.3 16.3 0.6 OD1 C:ASP123 4.3 24.0 1.0 C C:ASP119 4.3 15.9 0.4 O C:ASP119 4.4 15.4 0.4 O C:HOH397 4.4 33.6 1.0 CD C:GLU120 4.5 22.3 0.4 CB C:GLU120 4.5 19.4 0.6 CB C:ASP119 4.5 16.7 0.4 CB C:GLU120 4.7 18.4 0.4 OD1 C:ASP119 4.8 20.8 0.4 CB C:ASP119 4.8 17.9 0.6 CD C:GLU120 4.9 24.7 0.6

Sodium binding site 3 out of 5 in the Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration within 5.0Å range: probe atom residue distance (Å) B Occ C:Na209 b:77.7 occ:1.00 O E:HOH350 2.6 28.5 1.0 OE2 C:GLU83 2.7 43.8 1.0 CD C:GLU83 3.7 40.6 1.0 OG G:SER82 3.9 34.9 0.8 O C:HOH347 3.9 35.4 1.0 O G:HOH358 4.0 31.9 1.0 OE1 C:GLU83 4.1 45.5 1.0 CG2 G:ILE86 4.3 25.8 1.0 CG G:GLU83 4.4 25.5 1.0 CG1 G:VAL143 4.5 21.6 1.0 NH2 C:ARG87 4.6 49.1 1.0 O G:SER82 4.6 23.5 0.8 CB G:SER82 4.7 28.7 0.8 CB G:SER82 4.7 24.1 0.2 O G:SER82 4.7 23.6 0.2 C G:SER82 4.7 22.7 0.8 C G:SER82 4.7 22.9 0.2 CG2 G:THR147 4.8 52.4 1.0 N G:GLU83 4.8 21.6 1.0 CA G:GLU83 4.8 20.5 1.0 OE2 E:GLU140 4.8 21.2 1.0 CB G:ILE86 4.9 22.6 1.0

Sodium binding site 4 out of 5 in the Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration within 5.0Å range: probe atom residue distance (Å) B Occ C:Na210 b:42.6 occ:1.00 OE1 C:GLU140 2.4 18.6 0.6 OE2 G:GLU83 2.6 29.8 1.0 O C:HOH340 2.8 23.2 1.0 CD G:GLU83 3.3 27.8 1.0 CD C:GLU140 3.3 17.9 0.6 OE1 G:GLU83 3.6 30.2 1.0 CG1 C:VAL143 3.7 26.0 1.0 OE2 C:GLU140 3.7 21.1 0.6 O E:HOH460 3.8 24.7 1.0 CB C:VAL143 3.8 23.7 1.0 O C:HOH388 4.0 28.9 1.0 O G:HOH438 4.0 32.9 1.0 CG2 C:VAL143 4.1 23.7 1.0 O E:HOH401 4.1 33.1 1.0 CA C:GLU140 4.3 17.0 0.4 CA C:GLU140 4.3 17.3 0.6 CG C:GLU140 4.3 17.9 0.4 O G:HOH358 4.3 31.9 1.0 O C:GLU140 4.4 16.2 0.4 O C:GLU140 4.4 15.6 0.6 CG G:GLU83 4.4 25.5 1.0 O C:HOH347 4.4 35.4 1.0 CB C:GLU140 4.4 17.2 0.4 CG C:GLU140 4.5 18.6 0.6 CB C:GLU140 4.5 17.6 0.6 CE2 C:TYR139 4.8 24.8 1.0 C C:GLU140 4.8 16.0 0.4 C C:GLU140 4.8 16.0 0.6 O G:HOH492 4.9 44.5 1.0

Sodium binding site 5 out of 5 in the Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Solution of the Variably-Twinned Structure of A Novel Calmodulin- Peptide Complex in A Novel Configuration within 5.0Å range: probe atom residue distance (Å) B Occ G:Na207 b:59.0 occ:1.00 OD2 G:ASP79 2.8 54.5 1.0 O G:HOH431 3.4 37.6 1.0 CG G:ASP79 3.8 50.0 1.0 CG G:ARG75 3.9 25.6 1.0 CD G:LYS78 4.0 49.7 1.0 OD1 G:ASP79 4.1 51.1 1.0 CB G:LYS78 4.2 41.7 1.0 CG G:LYS78 4.3 45.8 1.0 CA G:ARG75 4.3 22.6 1.0 O G:ARG75 4.4 26.9 1.0 NZ G:LYS78 4.6 48.5 1.0 CB G:ARG75 4.6 23.0 1.0 CE G:LYS78 4.7 52.0 1.0 CD G:ARG75 4.8 26.9 1.0 C G:ARG75 4.8 24.1 1.0

J.P.Keller, J.P.Keller. N/A N/A.
ISSN: ISSN 2059-7983
PubMed: 28045382
DOI: 10.1107/S2059798316019318