Sodium in PDB 4dmi: Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences (Casp)

The structure of Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences (Casp), PDB code: 4dmi was solved by T.K.Craig, J.Abendroth, D.Lorimer, A.B.Burgin Jr, A.Segall, F.Rohwer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.41 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.570, 147.870, 57.850, 90.00, 112.05, 90.00
R / Rfree (%)	15.8 / 18.2

The binding sites of Sodium atom in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences (Casp) (pdb code 4dmi). 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 A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences (Casp), PDB code: 4dmi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences (Casp)


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 Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences (Casp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:30.0 occ:1.00 OE2 A:GLU72 2.2 34.6 1.0 O A:ALA155 2.4 15.2 1.0 O A:HOH478 2.6 45.2 1.0 OE1 C:GLU96 2.6 14.6 1.0 O A:HOH393 2.7 29.4 1.0 OE2 C:GLU96 2.9 25.6 1.0 CD C:GLU96 3.1 17.1 1.0 CD A:GLU72 3.3 27.8 1.0 C A:ALA155 3.5 13.6 1.0 OE1 A:GLU72 4.1 40.0 1.0 CG A:GLU72 4.2 14.7 1.0 CB C:ALA97 4.3 15.1 1.0 CA A:GLU156 4.4 11.2 1.0 N A:GLU156 4.4 11.2 1.0 CB A:ALA155 4.4 19.9 1.0 CA A:ALA155 4.4 14.0 1.0 O C:HOH417 4.5 29.4 1.0 O A:HOH447 4.6 36.8 1.0 CG C:GLU96 4.6 14.7 1.0 CA C:ALA97 4.7 12.4 1.0 O C:GLU96 4.8 17.9 1.0 NH2 A:ARG158 4.8 22.4 1.0 N C:ALA97 4.9 8.8 1.0 O C:HOH371 4.9 24.4 1.0 C C:GLU96 5.0 12.3 1.0 C A:GLU156 5.0 11.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences (Casp)


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 Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences (Casp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:30.0 occ:1.00 OE2 B:GLU72 2.0 33.5 1.0 O E:HOH386 2.2 29.2 1.0 O B:ALA155 2.3 18.2 1.0 O B:HOH482 2.3 34.4 1.0 OE2 E:GLU96 2.5 20.0 1.0 OE1 E:GLU96 2.8 17.6 1.0 CD E:GLU96 3.0 18.8 1.0 CD B:GLU72 3.2 36.0 1.0 C B:ALA155 3.4 18.6 1.0 OE1 B:GLU72 4.0 42.0 1.0 CG B:GLU72 4.1 24.1 1.0 CB B:ALA155 4.2 18.4 1.0 CA B:ALA155 4.2 16.9 1.0 NH2 B:ARG158 4.3 17.8 1.0 N B:GLU156 4.4 14.7 1.0 CA B:GLU156 4.5 14.1 1.0 CG E:GLU96 4.5 14.5 1.0 NE B:ARG158 4.6 14.7 1.0 CB E:ALA97 4.6 16.9 1.0 CA E:ALA97 4.7 13.0 1.0 O E:HOH426 4.9 30.5 1.0 O E:GLU96 4.9 18.2 1.0 CZ B:ARG158 4.9 14.5 1.0 N E:ALA97 4.9 12.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences (Casp)


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 Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences (Casp) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na203 b:30.0 occ:1.00 OE2 C:GLU72 2.3 20.9 1.0 O C:ALA155 2.3 11.7 1.0 O C:HOH516 2.4 29.0 1.0 O C:HOH405 2.4 29.6 1.0 O D:HOH252 2.5 22.0 1.0 OE2 D:GLU96 2.5 15.5 1.0 OE1 D:GLU96 2.5 13.0 1.0 CD D:GLU96 2.9 11.4 1.0 C C:ALA155 3.4 10.7 1.0 CD C:GLU72 3.5 22.1 1.0 CG C:GLU72 4.2 15.4 1.0 N C:GLU156 4.3 10.0 1.0 CA C:GLU156 4.3 8.8 1.0 NH2 C:ARG158 4.3 17.1 1.0 CA C:ALA155 4.3 8.7 1.0 O C:HOH485 4.3 46.3 1.0 CB C:ALA155 4.3 16.6 1.0 CG D:GLU96 4.4 10.2 1.0 OE1 C:GLU72 4.4 26.8 1.0 CB D:ALA97 4.5 14.0 1.0 NE C:ARG158 4.6 15.3 1.0 O D:HOH289 4.6 22.6 1.0 O D:HOH385 4.6 53.9 1.0 O D:HOH396 4.6 38.7 1.0 CA D:ALA97 4.7 10.9 1.0 O D:HOH249 4.8 16.0 1.0 C C:GLU156 4.8 8.5 1.0 N D:ALA97 4.9 9.5 1.0 CZ C:ARG158 4.9 13.3 1.0 O D:GLU96 4.9 13.8 1.0 C D:GLU96 5.0 10.8 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences (Casp)


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 Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences (Casp) within 5.0Å range: probe atom residue distance (Å) B Occ E:Na201 b:30.0 occ:1.00 OE2 E:GLU72 1.8 32.9 1.0 O E:HOH511 2.2 30.0 1.0 O E:HOH463 2.4 33.4 1.0 O E:HOH361 2.4 25.6 1.0 O E:ALA155 2.5 19.9 1.0 OE1 A:GLU96 2.8 17.4 1.0 CD E:GLU72 2.8 32.6 1.0 OE2 A:GLU96 3.1 29.4 1.0 CD A:GLU96 3.3 23.4 1.0 OE1 E:GLU72 3.4 32.2 1.0 C E:ALA155 3.7 19.7 1.0 O E:HOH473 3.7 45.2 1.0 CG E:GLU72 4.0 22.5 1.0 CB A:ALA97 4.1 17.1 1.0 O A:GLU96 4.4 20.9 1.0 CA E:ALA155 4.6 18.0 1.0 CA A:ALA97 4.6 13.6 1.0 CA E:GLU156 4.6 12.5 1.0 CB E:ALA155 4.6 22.5 1.0 N E:GLU156 4.6 15.5 1.0 O E:HOH480 4.7 51.6 1.0 O A:HOH400 4.7 36.8 1.0 O A:HOH503 4.7 42.6 1.0 NH2 E:ARG158 4.7 24.7 1.0 CG A:GLU96 4.8 15.6 1.0 C A:GLU96 4.9 14.1 1.0 N A:ALA97 4.9 12.1 1.0

T.K.Craig, J.Abendroth, D.Lorimer, A.B.Burgin Jr, A.Segall, F.Rohwer. Crystal Structure of A Pentameric Capsid Protein Isolated From Metagenomic Phage Sequences To Be Published.