Atomistry » Sodium » PDB 4kxy-4lgn » 4l37
Atomistry »
  Sodium »
    PDB 4kxy-4lgn »
      4l37 »

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

Protein crystallography data

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

Sodium Binding Sites:

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 4l37

Go back to Sodium Binding Sites List in 4l37
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 4l37

Go back to Sodium Binding Sites List in 4l37
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 4l37

Go back to Sodium Binding Sites List in 4l37
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

Reference:

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
Page generated: Tue Dec 15 06:51:11 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy