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Sodium in PDB 5abd: Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu

Enzymatic activity of Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu

All present enzymatic activity of Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu, PDB code: 5abd was solved by J.-F.Gaucher, M.-B.Lascombe, M.Reille-Seroussi, N.Gagey-Eilstein, S.Broussy, P.Coric, B.Seijo, B.Gautier, W.-Q.Liu, F.Huguenot, N.Inguimbert, S.Bouaziz, M.Vidal, I.Broutin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.97 / 2.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 62.547, 66.189, 176.477, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.2

Other elements in 5abd:

The structure of Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu also contains other interesting chemical elements:

Copper (Cu) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu (pdb code 5abd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu, PDB code: 5abd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5abd

Go back to Sodium Binding Sites List in 5abd
Sodium binding site 1 out of 2 in the Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu


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-1 Domain 2 in Presence of Cu within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1227

b:47.1
occ:1.00
OH E:TYR220 2.5 36.5 1.0
O E:GLU137 2.8 36.3 1.0
O E:HOH2021 2.8 27.6 1.0
HB2 E:GLU137 2.8 50.9 1.0
O E:HOH2004 3.0 30.6 1.0
O E:PRO157 3.0 35.2 1.0
HA E:CYS158 3.1 37.4 1.0
HH12 E:ARG159 3.1 74.0 1.0
HE2 E:TYR220 3.2 31.2 1.0
HE1 E:TYR139 3.3 49.9 1.0
HG2 E:PRO157 3.4 41.5 1.0
CZ E:TYR220 3.5 30.7 1.0
HH11 E:ARG159 3.5 74.0 1.0
HD1 E:TYR139 3.6 45.3 1.0
NH1 E:ARG159 3.7 61.6 1.0
CE2 E:TYR220 3.7 26.0 1.0
C E:PRO157 3.7 32.2 1.0
HG1 E:THR218 3.7 30.5 1.0
CB E:GLU137 3.8 42.5 1.0
H E:GLU137 3.9 43.3 1.0
C E:GLU137 3.9 34.0 1.0
CA E:CYS158 4.0 31.1 1.0
CE1 E:TYR139 4.0 41.6 1.0
HB2 E:PRO157 4.1 40.5 1.0
HB3 E:GLU137 4.1 50.9 1.0
CD1 E:TYR139 4.2 37.8 1.0
N E:CYS158 4.2 30.2 1.0
CA E:GLU137 4.3 36.0 1.0
CG E:PRO157 4.3 34.5 1.0
OE1 E:GLU144 4.3 51.8 1.0
H E:ARG159 4.4 39.4 1.0
N E:GLU137 4.4 36.0 1.0
OG1 E:THR218 4.5 25.4 1.0
HB3 E:CYS158 4.5 39.6 1.0
HG22 E:THR218 4.6 35.4 1.0
CB E:PRO157 4.6 33.7 1.0
HG3 E:GLU137 4.6 65.6 1.0
CA E:PRO157 4.7 30.9 1.0
CE1 E:TYR220 4.7 31.2 1.0
CG E:GLU137 4.8 54.7 1.0
CB E:CYS158 4.8 33.0 1.0
HG3 E:PRO157 4.8 41.5 1.0
HB3 E:PHE135 4.9 35.9 1.0
HA E:MET138 4.9 36.5 1.0
CZ E:ARG159 4.9 66.9 1.0
N E:ARG159 4.9 32.9 1.0
H E:CYS158 4.9 36.3 1.0
C E:CYS158 5.0 32.5 1.0
HE1 E:TYR220 5.0 37.4 1.0
HG2 E:ARG159 5.0 64.9 1.0

Sodium binding site 2 out of 2 in 5abd

Go back to Sodium Binding Sites List in 5abd
Sodium binding site 2 out of 2 in the Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na1230

b:48.1
occ:1.00
OH X:TYR220 2.4 33.3 1.0
HE2 X:TYR139 2.7 67.3 1.0
O X:HOH2010 2.7 39.7 1.0
HE1 X:TYR220 3.0 35.2 1.0
HG2 X:PRO157 3.1 27.6 1.0
O X:GLU137 3.1 64.5 1.0
HB2 X:GLU137 3.2 75.2 1.0
HD2 X:TYR139 3.3 65.4 1.0
O X:PRO157 3.3 25.9 1.0
HA X:CYS158 3.4 26.5 1.0
CZ X:TYR220 3.4 28.4 1.0
CE2 X:TYR139 3.5 56.1 1.0
CE1 X:TYR220 3.5 29.3 1.0
HG1 X:THR218 3.6 34.7 1.0
O X:HOH2005 3.7 25.7 1.0
CD2 X:TYR139 3.7 54.5 1.0
O X:HOH2006 3.9 55.0 1.0
C X:PRO157 3.9 25.1 1.0
CB X:GLU137 4.0 62.6 1.0
CG X:PRO157 4.1 23.0 1.0
C X:GLU137 4.1 62.1 1.0
HB2 X:PRO157 4.1 25.6 1.0
HB3 X:GLU137 4.2 75.2 1.0
CA X:CYS158 4.2 22.1 1.0
OE1 X:GLU144 4.3 68.8 1.0
OG1 X:THR218 4.3 28.9 1.0
N X:CYS158 4.3 22.9 1.0
HB3 X:CYS158 4.5 26.7 1.0
HH X:TYR139 4.5 70.8 1.0
H X:GLU137 4.5 63.4 1.0
CB X:PRO157 4.5 21.3 1.0
HG3 X:PRO157 4.6 27.6 1.0
HG22 X:THR218 4.6 42.1 1.0
CA X:GLU137 4.6 58.6 1.0
HD2 X:PRO157 4.6 30.5 1.0
CE2 X:TYR220 4.7 26.5 1.0
CZ X:TYR139 4.7 57.0 1.0
CA X:PRO157 4.8 23.7 1.0
CD1 X:TYR220 4.9 27.1 1.0
CD X:PRO157 4.9 25.4 1.0
CB X:CYS158 4.9 22.3 1.0
H X:TYR139 4.9 85.6 1.0
H X:ARG159 4.9 26.9 1.0
CD X:GLU137 4.9 82.6 1.0
HE2 X:TYR220 4.9 31.8 1.0
HA X:MET138 5.0 95.0 1.0

Reference:

J.-F.Gaucher, M.Reille-Seroussi, N.Gagey-Eilstein, S.Broussy, P.Coric, B.Seijo, M.-B.Lascombe, B.Gautier, W.-Q.Liu, F.Huguenot, N.Inguimbert, S.Bouaziz, M.Vidal, I.Broutin. Biophysical Studies of the Induced Dimerization of Human Vegf R Receptor 1 Binding Domain By Divalent Metals Competing with Vegf-A Plos One V. 11 67755 2016.
ISSN: ESSN 1932-6203
PubMed: 27942001
DOI: 10.1371/JOURNAL.PONE.0167755
Page generated: Tue Dec 15 10:19:01 2020

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