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Sodium in PDB 5oyj: Crystal Structure of Vegfr-2 Domains 4-5 in Complex with Darpin D4B

Enzymatic activity of Crystal Structure of Vegfr-2 Domains 4-5 in Complex with Darpin D4B

All present enzymatic activity of Crystal Structure of Vegfr-2 Domains 4-5 in Complex with Darpin D4B:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Vegfr-2 Domains 4-5 in Complex with Darpin D4B, PDB code: 5oyj was solved by C.L.Piscitelli, K.M.Thieltges, S.Markovic-Mueller, H.K.Binz, K.Ballmer-Hofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.75 / 2.38
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 109.489, 164.559, 70.759, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.9

Other elements in 5oyj:

The structure of Crystal Structure of Vegfr-2 Domains 4-5 in Complex with Darpin D4B also contains other interesting chemical elements:

Arsenic (As) 1 atom
Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Vegfr-2 Domains 4-5 in Complex with Darpin D4B (pdb code 5oyj). 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 Vegfr-2 Domains 4-5 in Complex with Darpin D4B, PDB code: 5oyj:

Sodium binding site 1 out of 1 in 5oyj

Go back to Sodium Binding Sites List in 5oyj
Sodium binding site 1 out of 1 in the Crystal Structure of Vegfr-2 Domains 4-5 in Complex with Darpin D4B


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 Vegfr-2 Domains 4-5 in Complex with Darpin D4B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:63.9
occ:1.00
 O7 C:NAG603 2.2 74.1 1.0
O C:HOH743 2.3 64.3 1.0
O A:GLY146 2.5 62.0 1.0
OE1 A:GLN142 3.4 77.0 1.0
C7 C:NAG603 3.4 68.8 1.0
C A:GLY146 3.5 49.2 1.0
CD A:GLN142 3.8 69.5 1.0
CA A:GLY146 3.9 50.6 1.0
O3 C:NAG603 4.2 75.2 1.0
O C:HOH772 4.2 50.4 1.0
NE2 A:GLN142 4.2 65.9 1.0
N2 C:NAG603 4.3 59.8 1.0
C2 C:NAG603 4.3 61.8 1.0
C8 C:NAG603 4.4 70.3 1.0
OD2 A:ASP151 4.4 59.7 1.0
O6 C:NAG604 4.5 0.8 1.0
CG A:GLN142 4.6 58.2 1.0
N A:LYS147 4.7 51.0 1.0
C3 C:NAG603 4.9 70.0 1.0

Reference:

K.M.Thieltges, D.Avramovic, C.L.Piscitelli, S.Markovic-Mueller, H.K.Binz, K.Ballmer-Hofer. Characterization of A Drug-Targetable Allosteric Site Regulating Vascular Endothelial Growth Factor Signaling. Angiogenesis V. 21 533 2018.
ISSN: ESSN 1573-7209
PubMed: 29502220
DOI: 10.1007/S10456-018-9606-9
Page generated: Tue Dec 15 11:26:10 2020

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