Sodium in PDB 4l37: SP2-SP3 - A Complex of Two Storage Proteins From Bombyx Mori Hemolymph

The structure of SP2-SP3 - A Complex of Two Storage Proteins From Bombyx Mori Hemolymph, PDB code: 4l37 was solved by A.J.Pietrzyk, A.Bujacz, J.Mueller-Dieckmann, M.Jaskolski, G.Bujacz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.90
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	192.750, 192.750, 180.820, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 22.3

The binding sites of Sodium atom in the SP2-SP3 - A Complex of Two Storage Proteins From Bombyx Mori Hemolymph (pdb code 4l37). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the SP2-SP3 - A Complex of Two Storage Proteins From Bombyx Mori Hemolymph, PDB code: 4l37:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the SP2-SP3 - A Complex of Two Storage Proteins From Bombyx Mori Hemolymph


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of SP2-SP3 - A Complex of Two Storage Proteins From Bombyx Mori Hemolymph within 5.0Å range: probe atom residue distance (Å) B Occ A:Na707 b:46.2 occ:1.00 OH A:TYR257 3.0 37.1 1.0 O A:PRO406 3.1 35.9 1.0 OE1 A:GLN410 3.4 37.5 1.0 CB A:PRO406 3.4 29.8 1.0 C A:PRO406 3.6 31.3 1.0 CA A:PRO406 3.7 30.5 1.0 CZ A:TYR257 4.1 32.0 1.0 O A:HOH879 4.1 41.3 1.0 NH1 A:ARG261 4.1 40.7 1.0 CG2 A:ILE269 4.1 45.2 1.0 OE1 A:GLU203 4.2 41.0 1.0 CB A:TYR409 4.3 25.7 1.0 CD A:GLN410 4.3 39.7 1.0 CD A:GLU203 4.3 39.1 1.0 CE2 A:TYR257 4.4 31.8 1.0 CG A:GLN410 4.4 40.3 1.0 OE2 A:GLU203 4.4 39.9 1.0 CD A:PRO270 4.6 47.1 1.0 N A:GLN410 4.6 28.5 1.0 CD2 A:TYR409 4.6 26.4 1.0 N A:ALA407 4.8 29.1 1.0 CG A:PRO406 4.8 29.7 1.0 CZ A:ARG261 4.8 39.4 1.0 CG A:TYR409 4.9 26.1 1.0 CB A:GLN410 5.0 34.6 1.0

Sodium binding site 2 out of 3 in the SP2-SP3 - A Complex of Two Storage Proteins From Bombyx Mori Hemolymph


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of SP2-SP3 - A Complex of Two Storage Proteins From Bombyx Mori Hemolymph within 5.0Å range: probe atom residue distance (Å) B Occ A:Na708 b:36.6 occ:1.00 N A:ILE392 2.7 39.0 1.0 O A:PRO383 2.8 35.9 1.0 N A:PRO385 3.3 33.4 1.0 CA A:PRO385 3.4 35.4 1.0 O A:ILE392 3.6 35.7 1.0 CA A:PHE391 3.6 37.4 1.0 CA A:ILE392 3.6 36.2 1.0 C A:PHE391 3.6 38.1 1.0 CB A:PHE391 3.6 35.1 1.0 CB A:ILE392 3.7 36.6 1.0 CD1 A:ILE392 3.7 43.4 1.0 C A:LYS384 3.7 36.9 1.0 CG A:PRO385 3.8 30.1 1.0 CD A:PRO385 3.8 30.7 1.0 C A:ILE392 4.0 34.1 1.0 C A:PRO383 4.0 36.0 1.0 CB A:PRO385 4.0 32.5 1.0 CB A:ALA382 4.2 30.4 1.0 O A:LYS384 4.2 42.2 1.0 CG1 A:ILE392 4.2 39.8 1.0 CA A:LYS384 4.3 38.2 1.0 CD2 A:PHE391 4.6 31.1 1.0 CG A:PHE391 4.6 33.1 1.0 N A:LYS384 4.6 35.2 1.0 O A:PHE391 4.8 37.1 1.0 C A:PRO385 4.8 37.3 1.0 OH A:TYR82 4.9 46.0 1.0 N A:PRO383 4.9 36.0 1.0

Sodium binding site 3 out of 3 in the SP2-SP3 - A Complex of Two Storage Proteins From Bombyx Mori Hemolymph


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of SP2-SP3 - A Complex of Two Storage Proteins From Bombyx Mori Hemolymph within 5.0Å range: probe atom residue distance (Å) B Occ B:Na707 b:38.8 occ:1.00 O B:GLN413 2.7 34.8 1.0 O B:PRO273 2.9 43.2 1.0 O B:HOH808 3.0 25.7 1.0 ND2 B:ASN416 3.3 40.5 1.0 C B:GLN413 3.6 33.8 1.0 CB B:ASN416 3.7 31.7 1.0 CA B:GLU274 3.7 38.3 1.0 OE2 B:GLU274 3.8 62.9 1.0 C B:PRO273 3.8 40.2 1.0 N B:ARG417 3.8 31.1 1.0 CA B:GLN413 3.8 32.5 1.0 CG B:ASN416 4.0 37.1 1.0 CD B:GLU274 4.1 58.0 1.0 N B:GLU274 4.1 39.1 1.0 CB B:GLN413 4.2 35.4 1.0 CB B:ARG417 4.2 28.5 1.0 CA B:ARG417 4.3 29.7 1.0 C B:ASN416 4.4 32.2 1.0 OE1 B:GLU274 4.5 65.2 1.0 CG B:GLN413 4.5 39.9 1.0 CB B:GLU274 4.5 43.0 1.0 CG B:GLU274 4.6 49.7 1.0 CA B:ASN416 4.6 31.4 1.0 CD1 B:PHE275 4.6 31.6 1.0 N B:PHE275 4.7 34.0 1.0 CG2 B:ILE272 4.7 32.6 1.0 O B:ILE272 4.7 42.2 1.0 C B:GLU274 4.7 37.4 1.0 CE1 B:PHE275 4.8 30.9 1.0 N B:LEU414 4.9 32.9 1.0 OE1 B:GLU420 4.9 80.8 1.0 O B:TYR412 5.0 29.1 1.0

A.J.Pietrzyk, A.Bujacz, J.Mueller-Dieckmann, M.Ochynska, M.Jaskolski, G.Bujacz. Crystallographic Identification of An Unexpected Protein Complex in Silkworm Haemolymph. Acta Crystallogr.,Sect.D V. 69 2353 2013.
ISSN: ISSN 0907-4449
PubMed: 24311577
DOI: 10.1107/S0907444913021823