Sodium in PDB 4znm: Crystal Structure of SGCC5 Protein From Streptomyces Globisporus (Apo Form)

The structure of Crystal Structure of SGCC5 Protein From Streptomyces Globisporus (Apo Form), PDB code: 4znm was solved by K.Michalska, L.Bigelow, R.Jedrzejczak, G.Babnigg, J.Lohman, M.Ma, J.Rudolf, C.-Y.Chang, B.Shen, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), Enzyme Discovery For Natural Product Biosynthesis(Natpro), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.74 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.596, 104.542, 108.465, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.2

The structure of Crystal Structure of SGCC5 Protein From Streptomyces Globisporus (Apo Form) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of SGCC5 Protein From Streptomyces Globisporus (Apo Form) (pdb code 4znm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of SGCC5 Protein From Streptomyces Globisporus (Apo Form), PDB code: 4znm:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of SGCC5 Protein From Streptomyces Globisporus (Apo Form)


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 SGCC5 Protein From Streptomyces Globisporus (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:23.6 occ:1.00 O A:SER127 2.2 22.3 0.5 O A:HOH739 2.3 30.1 1.0 O A:GLU130 2.3 22.9 1.0 O A:PRO132 2.3 20.9 1.0 OG A:SER127 2.5 26.0 0.6 O A:SER127 2.5 23.8 0.6 C A:SER127 3.2 20.8 0.5 C A:SER127 3.3 21.7 0.6 C A:PRO132 3.4 19.6 1.0 C A:GLU130 3.5 26.1 1.0 N A:SER127 3.6 20.6 0.6 N A:SER127 3.6 20.7 0.5 CB A:SER127 3.6 19.7 0.6 N A:PRO132 3.6 24.9 1.0 C A:LEU131 3.6 24.9 1.0 CA A:SER127 3.6 21.7 0.6 CA A:SER127 3.7 21.6 0.5 CD1 A:LEU126 3.8 49.6 1.0 O A:LEU131 4.0 25.4 1.0 CB A:SER127 4.0 24.0 0.5 CD A:PRO132 4.1 27.1 1.0 CA A:LEU131 4.1 27.0 1.0 CA A:PRO132 4.1 20.2 1.0 N A:LEU131 4.2 22.0 1.0 CD2 A:LEU133 4.3 24.9 1.0 C A:LEU126 4.3 24.4 1.0 N A:VAL128 4.4 22.4 1.0 N A:LEU133 4.4 18.0 1.0 N A:GLU130 4.4 22.9 1.0 CA A:GLU130 4.5 23.9 1.0 CG A:LEU126 4.6 37.5 1.0 CG A:GLU130 4.6 49.5 1.0 CA A:LEU133 4.7 20.1 1.0 CG A:PRO132 4.7 24.5 1.0 CA A:VAL128 4.8 22.5 1.0 O A:HOH791 4.8 38.0 1.0 OG A:SER127 4.9 25.5 0.5 O A:HOH648 4.9 34.0 1.0 CA A:LEU126 4.9 26.2 1.0 O A:LEU126 5.0 28.7 1.0 CD A:GLU130 5.0 87.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of SGCC5 Protein From Streptomyces Globisporus (Apo Form)


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 SGCC5 Protein From Streptomyces Globisporus (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:42.8 occ:1.00 OD1 A:ASN179 2.4 29.1 1.0 O A:HOH772 2.4 42.4 1.0 O A:HOH683 2.4 36.0 1.0 CG A:ASN179 3.5 27.9 1.0 O A:HOH630 4.0 37.3 1.0 ND2 A:ASN179 4.0 30.2 1.0 O A:ARG177 4.4 27.9 1.0 O A:GLY178 4.7 32.1 1.0 CB A:ASN179 4.7 28.4 1.0 CA A:ASN179 4.9 31.0 1.0 C A:GLY178 5.0 28.1 1.0 OD2 A:ASP384 5.0 35.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of SGCC5 Protein From Streptomyces Globisporus (Apo Form)


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 SGCC5 Protein From Streptomyces Globisporus (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:23.6 occ:1.00 O B:PRO132 2.2 22.9 1.0 O B:GLU130 2.3 21.4 1.0 O B:SER127 2.3 25.5 1.0 O B:HOH811 2.4 29.4 1.0 C B:SER127 3.3 25.3 1.0 C B:PRO132 3.3 21.9 1.0 C B:GLU130 3.5 27.8 1.0 N B:SER127 3.6 20.9 1.0 N B:PRO132 3.6 23.6 1.0 C B:LEU131 3.6 24.8 1.0 CA B:SER127 3.7 24.1 1.0 CB B:SER127 3.8 24.9 1.0 CD1 B:LEU126 3.9 39.0 1.0 CA B:PRO132 4.0 19.7 1.0 CA B:LEU131 4.0 24.8 1.0 O B:LEU131 4.0 21.3 1.0 CD B:PRO132 4.1 29.5 1.0 N B:LEU131 4.2 22.3 1.0 C B:LEU126 4.3 24.0 1.0 N B:LEU133 4.3 20.7 1.0 CD2 B:LEU133 4.4 26.3 1.0 N B:VAL128 4.4 20.5 1.0 CG B:LEU126 4.4 25.9 1.0 CG B:GLU130 4.5 64.1 1.0 N B:GLU130 4.5 22.6 1.0 CG B:PRO132 4.5 20.7 1.0 O B:HOH779 4.6 40.7 1.0 CA B:GLU130 4.6 32.5 1.0 O B:HOH788 4.6 42.5 1.0 CA B:LEU133 4.7 25.4 1.0 OG B:SER127 4.8 33.2 1.0 CA B:VAL128 4.9 21.6 1.0 CA B:LEU126 4.9 24.4 1.0 O B:LEU126 5.0 23.1 1.0 CB B:PRO132 5.0 23.3 1.0

K.Michalska, L.Bigelow, R.Jedrzejczak, G.Babnigg, J.Lohman, M.Ma, J.Rudolf, C.-Y.Chang, B.Shen, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), Enzyme Discovery For Natural Product Biosynthesis (Natpro). Crystal Structure of SGCC5 Protein From Streptomyces Globisporus (Apo Form) To Be Published.