Sodium in PDB 5u4u: Pseudogtpase Domain (PG1) of P190RHOGAP-A

The structure of Pseudogtpase Domain (PG1) of P190RHOGAP-A, PDB code: 5u4u was solved by A.L.Stiegler, T.J.Boggon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.13 / 1.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	62.937, 62.937, 161.017, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 21.7

The binding sites of Sodium atom in the Pseudogtpase Domain (PG1) of P190RHOGAP-A (pdb code 5u4u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Pseudogtpase Domain (PG1) of P190RHOGAP-A, PDB code: 5u4u:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Pseudogtpase Domain (PG1) of P190RHOGAP-A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pseudogtpase Domain (PG1) of P190RHOGAP-A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na803 b:27.0 occ:1.00 O7 A:MLI801 2.2 36.5 1.0 NA A:NA804 2.3 38.1 1.0 O A:LEU632 2.3 23.1 1.0 O6 A:MLI802 2.4 40.0 1.0 O9 A:MLI801 2.5 32.8 1.0 O A:HOH957 2.6 40.8 1.0 C2 A:MLI802 3.2 43.4 1.0 C2 A:MLI801 3.3 37.8 1.0 C3 A:MLI801 3.4 37.7 1.0 C A:LEU632 3.5 22.6 1.0 C1 A:MLI801 3.6 32.2 1.0 O8 A:MLI802 3.8 61.2 1.0 C1 A:MLI802 3.9 46.2 1.0 N A:LEU632 4.0 18.8 1.0 O A:HOH911 4.0 37.6 1.0 O7 A:MLI802 4.0 43.6 1.0 CA A:LEU632 4.1 19.0 1.0 C3 A:MLI802 4.2 57.4 1.0 O6 A:MLI801 4.4 41.5 1.0 NH2 A:ARG612 4.4 27.5 1.0 CB A:LEU632 4.4 19.1 1.0 O8 A:MLI801 4.6 36.6 1.0 N A:ARG633 4.6 18.5 1.0 CD A:PRO634 4.8 24.1 1.0 CA A:ARG633 4.8 19.2 1.0 OG A:SER631 4.8 22.6 0.3

Sodium binding site 2 out of 3 in the Pseudogtpase Domain (PG1) of P190RHOGAP-A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pseudogtpase Domain (PG1) of P190RHOGAP-A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na804 b:38.1 occ:1.00 NA A:NA803 2.3 27.0 1.0 O8 A:MLI802 2.8 61.2 1.0 O A:HOH953 2.9 45.7 1.0 N A:LEU632 3.0 18.8 1.0 OG A:SER631 3.1 22.6 0.3 NH2 A:ARG612 3.2 27.5 1.0 O A:HOH957 3.2 40.8 1.0 O9 A:MLI801 3.2 32.8 1.0 O A:LEU632 3.3 23.1 1.0 CA A:SER631 3.5 20.3 0.7 CA A:SER631 3.5 20.3 0.3 O6 A:MLI802 3.6 40.0 1.0 C A:SER631 3.7 22.8 0.3 C A:SER631 3.7 22.9 0.7 C3 A:MLI802 3.8 57.4 1.0 CB A:SER631 3.9 23.0 0.7 CB A:SER631 3.9 22.8 0.3 CA A:LEU632 4.0 19.0 1.0 C A:LEU632 4.0 22.6 1.0 C1 A:MLI802 4.1 46.2 1.0 C2 A:MLI802 4.3 43.4 1.0 OG A:SER631 4.4 25.5 0.7 C3 A:MLI801 4.5 37.7 1.0 O7 A:MLI801 4.5 36.5 1.0 CZ A:ARG612 4.5 30.4 1.0 CB A:LEU632 4.5 19.1 1.0 O A:LEU630 4.6 26.2 1.0 N A:SER631 4.8 19.9 0.7 O A:SER631 4.8 23.9 0.3 N A:SER631 4.8 19.9 0.3 O A:SER631 4.8 23.8 0.7 O9 A:MLI802 4.9 64.0 1.0

Sodium binding site 3 out of 3 in the Pseudogtpase Domain (PG1) of P190RHOGAP-A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pseudogtpase Domain (PG1) of P190RHOGAP-A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na805 b:42.6 occ:1.00 O A:HOH958 2.3 34.9 1.0 O A:ASP587 2.3 27.3 1.0 OG A:SER586 2.4 40.0 1.0 O A:VAL590 2.4 29.5 1.0 O A:HOH964 2.8 50.0 1.0 O A:HOH955 2.9 40.4 1.0 C A:ASP587 3.4 31.0 1.0 C A:VAL590 3.5 24.4 1.0 CB A:SER586 3.6 35.2 1.0 N A:ARG592 4.0 24.6 1.0 CA A:PRO588 4.0 40.6 1.0 CA A:ASP591 4.0 22.0 1.0 N A:ASP587 4.0 29.7 1.0 C A:SER586 4.1 43.2 1.0 OE1 A:GLU629 4.1 51.3 1.0 N A:PRO588 4.2 35.0 1.0 O A:HOH968 4.2 51.0 1.0 N A:ASP591 4.2 22.9 1.0 C A:ASP591 4.2 26.4 1.0 CB A:ARG592 4.3 28.8 1.0 CA A:ASP587 4.3 31.7 1.0 N A:VAL590 4.4 23.3 1.0 C A:PRO588 4.4 40.3 1.0 O A:SER586 4.4 39.3 1.0 CA A:SER586 4.4 41.4 1.0 CA A:VAL590 4.5 27.3 1.0 O A:PRO588 4.6 37.8 1.0 CA A:ARG592 4.7 23.3 1.0 CD A:GLU629 4.9 54.0 1.0 CB A:ASP587 4.9 30.5 1.0 N A:ASN589 4.9 34.1 1.0

A.L.Stiegler, T.J.Boggon. P190RHOGAP Proteins Contain Pseudogtpase Domains. Nat Commun V. 8 506 2017.
ISSN: ESSN 2041-1723
PubMed: 28894085
DOI: 10.1038/S41467-017-00483-X