Sodium in PDB 1m5q: Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum

The structure of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum, PDB code: 1m5q was solved by C.Mura, M.Phillips, A.Kozhukhovsky, D.Eisenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.322, 172.427, 148.108, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.6

The structure of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum also contains other interesting chemical elements:

Cadmium

(Cd)

28 atoms

The binding sites of Sodium atom in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum (pdb code 1m5q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum, PDB code: 1m5q:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3004 b:65.3 occ:1.23 CG2 A:VAL27 3.7 20.4 1.0 OE1 G:GLU32 3.8 30.1 1.0 OE1 A:GLN25 3.9 31.4 1.0 OE1 G:GLU58 4.0 41.9 1.0 CG2 A:VAL33 4.1 25.5 1.0 OH G:TYR34 4.3 27.9 1.0 CD G:GLU32 4.6 26.4 1.0 CD A:GLN25 4.6 32.9 1.0 CG1 A:VAL33 4.7 27.4 1.0 ND2 G:ASN54 4.7 27.8 1.0 CG1 A:VAL27 4.8 20.9 1.0 OE2 G:GLU32 4.9 26.7 1.0 NE2 A:HIS72 4.9 24.6 1.0 CD G:GLU58 4.9 39.6 1.0 CB A:VAL27 4.9 21.4 1.0 OE2 G:GLU58 5.0 40.4 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3001 b:76.2 occ:1.99 NZ C:LYS55 3.6 46.8 1.0 OE2 B:GLU58 3.6 42.9 1.0 OE1 C:GLN25 4.3 31.8 1.0 CG2 C:VAL33 4.3 27.8 1.0 OE1 B:GLU32 4.3 29.4 1.0 CE C:LYS55 4.5 47.5 1.0 CG2 C:VAL27 4.6 24.2 1.0 CD B:GLU58 4.6 43.4 1.0 OH B:TYR34 4.8 27.7 1.0 CG1 C:VAL33 4.8 26.5 1.0 ND2 B:ASN54 4.9 26.4 1.0 OE1 B:GLU58 4.9 44.2 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range: probe atom residue distance (Å) B Occ R:Na3005 b:83.0 occ:1.95 O Q:HOH2076 2.5 46.8 1.0 OE1 Q:GLU58 3.8 49.0 1.0 CG2 R:VAL33 4.1 27.5 1.0 OE1 R:GLN25 4.3 36.7 1.0 OE2 Q:GLU58 4.4 52.5 1.0 CG2 R:VAL27 4.5 28.0 1.0 CD Q:GLU58 4.6 48.7 1.0 CG1 R:VAL33 4.6 26.9 1.0 OE1 Q:GLU32 4.6 37.6 1.0 CD R:GLN25 4.9 36.3 1.0 CB R:VAL33 4.9 29.1 1.0 ND2 Q:ASN54 5.0 36.1 1.0 CE R:LYS55 5.0 47.2 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


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 A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range: probe atom residue distance (Å) B Occ S:Na3002 b:59.6 occ:1.61 O R:HOH4056 2.4 46.4 1.0 OE1 R:GLU58 3.8 46.9 1.0 NE2 S:GLN25 4.1 34.8 1.0 CG2 S:VAL33 4.2 30.5 1.0 NZ S:LYS55 4.2 42.9 1.0 OE2 R:GLU58 4.2 51.1 1.0 CD R:GLU58 4.4 47.3 1.0 CG1 S:VAL33 4.6 31.2 1.0 CD S:GLN25 4.7 34.6 1.0 OE1 R:GLU32 4.7 37.5 1.0 OE1 S:GLN25 4.8 36.2 1.0 CG2 S:VAL27 4.8 23.7 1.0 CB S:VAL33 5.0 30.7 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of A Novel Sm-Like Archaeal Protein From Pyrobaculum Aerophilum within 5.0Å range: probe atom residue distance (Å) B Occ V:Na3003 b:67.7 occ:1.67 O V:HOH5062 2.3 32.6 1.0 O V:HOH5089 2.5 37.1 1.0 OE2 V:GLU58 3.8 36.6 1.0 OE1 V:GLU32 3.8 23.2 1.0 O W:HOH5064 4.1 40.0 1.0 OE1 W:GLN25 4.3 26.7 1.0 CG2 W:VAL27 4.3 14.4 1.0 OH V:TYR34 4.4 19.7 1.0 CG2 W:VAL33 4.4 19.1 1.0 O V:HOH5053 4.5 29.1 1.0 CD V:GLU32 4.5 24.2 1.0 ND2 V:ASN54 4.7 21.3 1.0 OE2 V:GLU32 4.7 24.8 1.0 CD V:GLU58 4.8 38.1 1.0 NZ W:LYS55 4.9 40.8 1.0 CD W:GLN25 4.9 24.8 1.0 OE1 V:GLU58 5.0 41.8 1.0

C.Mura, M.Phillips, A.Kozhukhovsky, D.Eisenberg. Structure and Assembly of An Augmented Sm-Like Archaeal Protein 14-Mer Proc.Natl.Acad.Sci.Usa V. 100 4539 2003.
ISSN: ISSN 0027-8424
PubMed: 12668760
DOI: 10.1073/PNAS.0538042100