Sodium in PDB 1q8c: A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins

The structure of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins, PDB code: 1q8c was solved by J.Liu, H.Yokota, R.Kim, S.-H.Kim, Berkeley Structural Genomics Center(Bsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	41.401, 41.401, 99.008, 90.00, 90.00, 90.00
R / Rfree (%)	25.4 / 27.2

The structure of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins also contains other interesting chemical elements:

Iodine	(I)	7 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins (pdb code 1q8c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins, PDB code: 1q8c:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins within 5.0Å range: probe atom residue distance (Å) B Occ A:Na161 b:55.1 occ:1.00 O A:HOH170 2.5 49.9 1.0 O A:LYS58 2.8 44.3 1.0 O A:HOH213 3.2 55.8 1.0 C A:LYS58 3.6 43.9 1.0 CG A:GLN40 3.7 43.4 1.0 CB A:GLN40 3.7 43.8 1.0 CA A:LYS58 3.8 44.0 1.0 N A:LYS62 3.9 43.7 1.0 CB A:LYS58 3.9 44.1 1.0 CB A:LYS62 4.0 44.2 1.0 CG1 A:VAL61 4.0 44.6 1.0 CA A:GLN40 4.0 43.8 1.0 CB A:VAL61 4.1 43.9 1.0 CA A:LYS62 4.2 44.1 1.0 C A:VAL61 4.3 43.6 1.0 CG A:LYS58 4.4 44.9 1.0 O A:GLN40 4.4 45.1 1.0 OE1 A:GLN40 4.4 45.3 1.0 CD A:GLN40 4.4 43.9 1.0 CD2 A:PHE43 4.6 43.5 1.0 C A:GLN40 4.7 44.1 1.0 CA A:VAL61 4.8 43.9 1.0 N A:LEU59 4.9 43.7 1.0 O A:VAL61 4.9 43.6 1.0 CB A:PHE43 5.0 44.0 1.0

Sodium binding site 2 out of 3 in the A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins within 5.0Å range: probe atom residue distance (Å) B Occ A:Na162 b:66.3 occ:1.00 O A:HOH187 2.5 55.7 1.0 I A:IOD158 2.7 63.2 0.3 O A:LEU12 3.7 44.1 1.0 CG A:ARG14 4.1 43.6 1.0 N A:ARG14 4.3 43.6 1.0 CD A:ARG17 4.3 46.0 1.0 NH1 A:ARG17 4.4 46.2 1.0 I A:IOD153 4.4 58.8 0.7 C A:THR13 4.5 43.8 1.0 NE A:ARG14 4.6 43.8 1.0 CA A:ARG14 4.7 43.5 1.0 C A:LEU12 4.7 44.4 1.0 CD A:ARG14 4.8 44.3 1.0 CA A:THR13 4.9 44.1 1.0 CB A:ARG14 5.0 43.6 1.0

Sodium binding site 3 out of 3 in the A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins within 5.0Å range: probe atom residue distance (Å) B Occ A:Na163 b:62.2 occ:1.00 ND2 A:ASN67 2.9 42.5 1.0 OE1 A:GLU66 3.1 48.3 1.0 I A:IOD156 3.9 59.9 0.4 CB A:GLU66 3.9 44.1 1.0 CG A:ASN67 4.0 43.4 1.0 CA A:ALA63 4.1 43.0 1.0 CE A:LYS114 4.2 47.1 1.0 CD A:GLU66 4.3 47.9 1.0 OD1 A:ASN67 4.3 42.9 1.0 O A:ALA63 4.3 42.5 1.0 CG A:LYS114 4.5 45.2 1.0 CB A:ALA63 4.5 43.4 1.0 CG A:GLU66 4.7 45.6 1.0 C A:ALA63 4.7 42.9 1.0 O A:LYS62 4.8 44.4 1.0 CD A:LYS114 4.9 45.6 1.0 N A:ALA63 5.0 43.5 1.0

J.Liu, H.Yokota, R.Kim, S.-H.Kim. A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins Proteins V. 55 1082 2004.
ISSN: ISSN 0887-3585
PubMed: 15146506
DOI: 10.1002/PROT.20119