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Calcium 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
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Vegfr-2 Domains 4-5 in Complex with Darpin D4B, PDB code: 5oyj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5oyj

Go back to Calcium Binding Sites List in 5oyj
Calcium binding site 1 out of 4 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 Calcium with other atoms in the Ca 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:Ca401

b:87.6
occ:1.00
 O A:GLY25 2.6 60.8 1.0
OD2 A:ASP27 2.6 75.3 1.0
O A:HOH558 3.0 68.1 1.0
C A:GLY25 3.6 56.6 1.0
O A:HOH571 3.7 80.9 1.0
CG A:ASP27 3.8 79.2 1.0
CA A:GLY25 4.1 54.3 1.0
OE2 A:GLU61 4.4 43.7 0.5
OD1 A:ASP27 4.6 78.7 1.0
N A:ASP27 4.7 58.2 1.0
N A:GLN26 4.8 57.1 1.0
CB A:ASP27 4.9 63.3 1.0
ND1 A:HIS59 4.9 39.8 1.0
CD A:GLU61 5.0 56.2 0.5

Calcium binding site 2 out of 4 in 5oyj

Go back to Calcium Binding Sites List in 5oyj
Calcium binding site 2 out of 4 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 Calcium with other atoms in the Ca binding site number 2 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:Ca402

b:64.8
occ:1.00
 O A:LEU100 2.3 43.9 1.0
O A:HOH526 2.4 47.4 1.0
O A:HOH553 2.6 53.9 1.0
O A:HOH560 3.0 55.6 1.0
C A:LEU100 3.3 49.2 1.0
CA A:LYS101 4.1 47.0 1.0
N A:LYS101 4.1 47.0 1.0
O A:HOH538 4.3 47.5 1.0
CA A:LEU100 4.3 44.1 1.0
O A:LYS101 4.3 44.2 1.0
C A:LYS101 4.4 45.7 1.0
N A:GLY103 4.5 41.7 1.0
CB A:LEU100 4.5 42.2 1.0
CA A:GLY103 4.6 32.9 1.0
OD1 A:ASN135 4.7 44.8 1.0

Calcium binding site 3 out of 4 in 5oyj

Go back to Calcium Binding Sites List in 5oyj
Calcium binding site 3 out of 4 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 Calcium with other atoms in the Ca binding site number 3 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:Ca403

b:0.1
occ:1.00
 OD2 A:ASP160 2.4 81.1 1.0
OE1 D:GLU326 2.5 1.0 1.0
O C:HOH776 3.0 52.4 1.0
CG A:ASP160 3.2 71.8 1.0
OD1 A:ASP160 3.3 82.2 1.0
CD D:GLU326 3.6 0.8 1.0
OE2 D:GLU326 4.0 0.4 1.0
O C:LYS406 4.1 47.6 1.0
O A:HOH550 4.3 58.7 1.0
O D:HOH748 4.6 65.2 1.0
CB A:ASP160 4.7 52.4 1.0
CG D:GLU326 4.9 0.0 1.0
C C:LYS406 5.0 44.5 1.0

Calcium binding site 4 out of 4 in 5oyj

Go back to Calcium Binding Sites List in 5oyj
Calcium binding site 4 out of 4 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 Calcium with other atoms in the Ca binding site number 4 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
C:Ca609

b:83.8
occ:1.00
 O A:HOH525 2.6 49.7 1.0
O A:HOH502 2.6 48.8 1.0
OE1 C:GLN409 3.3 65.8 1.0
O C:HOH729 3.3 66.9 1.0
OE1 A:GLU159 3.6 48.4 1.0
O A:GLY157 3.9 44.5 1.0
OE2 A:GLU159 3.9 48.3 1.0
O C:HOH792 3.9 70.2 1.0
CD C:GLN409 3.9 47.7 1.0
O C:LYS408 4.0 43.9 1.0
CD A:GLU159 4.2 40.0 1.0
CA A:GLY157 4.3 26.0 1.0
NE2 C:GLN409 4.3 53.6 1.0
CA C:GLN409 4.5 34.3 1.0
C A:GLY157 4.5 32.8 1.0
CB C:GLN409 5.0 41.1 1.0
C C:LYS408 5.0 33.8 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: Mon Jul 15 09:58:04 2024

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