Sodium in PDB 5ch7: Crystal Structure of the Perchlorate Reductase Pcrab - PHE164 Gate Switch Intermediate - From Azospira Suillum Ps

The structure of Crystal Structure of the Perchlorate Reductase Pcrab - PHE164 Gate Switch Intermediate - From Azospira Suillum Ps, PDB code: 5ch7 was solved by C.-L.Tsai, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.38 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	132.884, 175.667, 193.278, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 23.3

The structure of Crystal Structure of the Perchlorate Reductase Pcrab - PHE164 Gate Switch Intermediate - From Azospira Suillum Ps also contains other interesting chemical elements:

Molybdenum	(Mo)	3 atoms
Zinc	(Zn)	3 atoms
Iron	(Fe)	57 atoms

The binding sites of Sodium atom in the Crystal Structure of the Perchlorate Reductase Pcrab - PHE164 Gate Switch Intermediate - From Azospira Suillum Ps (pdb code 5ch7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Perchlorate Reductase Pcrab - PHE164 Gate Switch Intermediate - From Azospira Suillum Ps, PDB code: 5ch7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Perchlorate Reductase Pcrab - PHE164 Gate Switch Intermediate - From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Perchlorate Reductase Pcrab - PHE164 Gate Switch Intermediate - From Azospira Suillum Ps within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1008 b:18.2 occ:1.00 O A:HOH1619 3.2 39.2 1.0 O A:HOH1343 3.3 21.0 1.0 N A:VAL777 3.3 18.8 1.0 CG2 A:VAL777 3.6 17.7 1.0 CE1 A:HIS88 3.7 22.9 1.0 CB A:VAL777 3.8 19.9 1.0 CD A:PRO87 4.0 26.7 1.0 CA A:ASN776 4.0 18.0 1.0 ND2 A:ASN776 4.0 17.8 1.0 C A:ASN776 4.2 21.2 1.0 CA A:VAL777 4.2 18.0 1.0 CG A:ASN776 4.3 17.6 1.0 ND1 A:HIS88 4.3 23.5 1.0 CB A:ASP82 4.5 19.5 1.0 OD2 A:ASP82 4.6 27.3 1.0 CG A:PRO87 4.6 24.5 1.0 CB A:ASN776 4.6 16.0 1.0 CG A:ASP82 4.7 25.9 1.0 O A:ASP775 4.7 18.0 1.0 NE2 A:HIS88 4.8 22.7 1.0 OD1 A:ASN776 4.8 20.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Perchlorate Reductase Pcrab - PHE164 Gate Switch Intermediate - From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Perchlorate Reductase Pcrab - PHE164 Gate Switch Intermediate - From Azospira Suillum Ps within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1007 b:26.4 occ:1.00 O C:HOH1333 3.1 35.1 1.0 N C:VAL777 3.4 27.0 1.0 CG2 C:VAL777 3.4 29.2 1.0 CE1 C:HIS88 3.8 32.0 1.0 CB C:VAL777 3.8 30.2 1.0 CD C:PRO87 3.9 36.7 1.0 CA C:ASN776 4.1 31.3 1.0 ND2 C:ASN776 4.2 30.6 1.0 CA C:VAL777 4.2 29.0 1.0 C C:ASN776 4.3 29.7 1.0 ND1 C:HIS88 4.3 35.2 1.0 CG C:ASN776 4.4 33.2 1.0 CG C:PRO87 4.5 28.9 1.0 CB C:ASP82 4.5 40.5 1.0 OD2 C:ASP82 4.7 39.5 1.0 CG C:ASP82 4.7 42.1 1.0 CB C:ASN776 4.8 31.5 1.0 O C:HOH1343 4.8 28.8 1.0 O C:ASP775 4.8 31.4 1.0 OD1 C:ASN776 4.9 32.3 1.0 NE2 C:HIS88 4.9 33.6 1.0 CA C:GLY86 4.9 40.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Perchlorate Reductase Pcrab - PHE164 Gate Switch Intermediate - From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Perchlorate Reductase Pcrab - PHE164 Gate Switch Intermediate - From Azospira Suillum Ps within 5.0Å range: probe atom residue distance (Å) B Occ E:Na1009 b:14.7 occ:1.00 O E:HOH1615 3.1 34.0 1.0 O E:HOH1375 3.1 20.6 1.0 N E:VAL777 3.2 18.6 1.0 CG2 E:VAL777 3.7 17.3 1.0 CE1 E:HIS88 3.8 25.4 1.0 CB E:VAL777 3.9 18.0 1.0 CA E:ASN776 3.9 17.8 1.0 ND2 E:ASN776 4.0 19.2 1.0 C E:ASN776 4.0 21.0 1.0 CD E:PRO87 4.1 23.8 1.0 CA E:VAL777 4.2 20.2 1.0 CG E:ASN776 4.2 23.8 1.0 ND1 E:HIS88 4.4 19.2 1.0 CB E:ASP82 4.5 23.7 1.0 OD2 E:ASP82 4.6 29.3 1.0 CB E:ASN776 4.6 15.6 1.0 OD1 E:ASN776 4.7 22.5 1.0 CG E:ASP82 4.7 28.6 1.0 O E:ASP775 4.7 20.1 1.0 CG E:PRO87 4.8 24.3 1.0 NE2 E:HIS88 5.0 26.4 1.0 O E:ASP82 5.0 18.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Perchlorate Reductase Pcrab - PHE164 Gate Switch Intermediate - From Azospira Suillum Ps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Perchlorate Reductase Pcrab - PHE164 Gate Switch Intermediate - From Azospira Suillum Ps within 5.0Å range: probe atom residue distance (Å) B Occ F:Na407 b:41.8 occ:1.00 O F:ASP91 3.8 20.4 1.0 OD2 F:ASP91 3.8 27.9 1.0 O F:GLY102 3.9 32.0 1.0 CB F:ASP91 4.0 21.9 1.0 CG F:ASP91 4.1 30.8 1.0 O F:ARG103 4.1 21.5 1.0 N F:ARG95 4.2 22.8 1.0 CE F:LYS100 4.2 50.7 1.0 CB F:ARG95 4.2 20.8 1.0 O C:HOH1449 4.3 38.1 1.0 CB F:LYS100 4.4 27.1 1.0 C F:GLY94 4.6 22.7 1.0 CA F:ARG95 4.6 25.1 1.0 C F:GLY102 4.7 26.9 1.0 CA F:GLY94 4.7 24.3 1.0 O F:HOH589 4.7 15.7 1.0 C F:ASP91 4.7 19.3 1.0 O F:PRO101 4.7 37.6 1.0 CD F:LYS100 4.8 45.2 1.0 C F:ARG103 4.9 23.2 1.0 CG2 F:VAL104 4.9 20.7 1.0 OD1 F:ASP91 5.0 23.2 1.0 CA F:ASP91 5.0 19.6 1.0

M.D.Youngblut, C.L.Tsai, I.C.Clark, H.K.Carlson, A.P.Maglaqui, P.S.Gau-Pan, S.A.Redford, A.Wong, J.A.Tainer, J.D.Coates. Perchlorate Reductase Is Distinguished By Active Site Aromatic Gate Residues. J.Biol.Chem. V. 291 9190 2016.
ISSN: ESSN 1083-351X
PubMed: 26940877
DOI: 10.1074/JBC.M116.714618