Atomistry » Sodium » PDB 5bpl-5ccx » 5c7g
Atomistry »
  Sodium »
    PDB 5bpl-5ccx »
      5c7g »

Sodium in PDB 5c7g: Crystal Structure of the B1 Domain of Human Neuropilin-1 in Complex with A Bicine Molecule

Protein crystallography data

The structure of Crystal Structure of the B1 Domain of Human Neuropilin-1 in Complex with A Bicine Molecule, PDB code: 5c7g was solved by C.Didierjean, C.Jelsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.28 / 1.45
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.280, 62.280, 85.960, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 17.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the B1 Domain of Human Neuropilin-1 in Complex with A Bicine Molecule (pdb code 5c7g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the B1 Domain of Human Neuropilin-1 in Complex with A Bicine Molecule, PDB code: 5c7g:

Sodium binding site 1 out of 1 in 5c7g

Go back to Sodium Binding Sites List in 5c7g
Sodium binding site 1 out of 1 in the Crystal Structure of the B1 Domain of Human Neuropilin-1 in Complex with A Bicine Molecule


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 the B1 Domain of Human Neuropilin-1 in Complex with A Bicine Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:17.4
occ:1.00
O A:HOH331 2.1 17.6 1.0
O A:HOH432 2.1 18.9 1.0
O A:HOH365 2.1 19.2 1.0
HO6 A:BCN201 2.1 21.4 1.0
O A:HOH396 2.1 18.5 1.0
O6 A:BCN201 2.1 17.8 1.0
O A:HOH496 2.1 19.6 1.0
H62 A:BCN201 3.1 20.6 1.0
C6 A:BCN201 3.2 17.2 1.0
HH A:TYR81 3.7 20.9 1.0
HE1 A:TYR81 3.8 20.1 1.0
H51 A:BCN201 3.8 23.0 1.0
H61 A:BCN201 3.9 20.6 1.0
C5 A:BCN201 4.1 19.2 1.0
O A:HOH470 4.2 22.6 1.0
O4 A:BCN201 4.2 19.8 1.0
OD2 A:ASP48 4.3 20.0 1.0
O A:HOH306 4.3 27.6 1.0
H42 A:BCN201 4.3 26.3 1.0
O A:HOH440 4.3 17.3 1.0
HA3 A:GLY142 4.4 20.9 1.0
O A:THR141 4.5 18.3 1.0
OH A:TYR81 4.5 17.4 1.0
CE1 A:TYR81 4.6 16.8 1.0
HE2 A:LYS79 4.7 26.1 1.0
N1 A:BCN201 4.7 16.7 1.0
HO4 A:BCN201 4.8 23.7 1.0
C4 A:BCN201 4.8 21.9 1.0
H52 A:BCN201 4.9 23.0 1.0

Reference:

M.Richard, N.Pelligrini Moise, C.Jelsch, B.Maigret, C.Didierjean, X.Manival, C.Charron. Design, Synthesis and Biological Evaluation of New Peptidomimetic Compounds Targeting Nrp-1 Receptor to Be Published To Be Published.
Page generated: Mon Oct 7 20:15:29 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy