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Copper 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:

Sodium (Na) 2 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 5 binding sites of Copper where determined in the Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu, PDB code: 5abd:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 5abd

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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
I:Cu1225

b:89.0
occ:0.48
NE2 I:HIS223 2.2 93.0 1.0
NE2 I:HIS147 2.3 90.5 1.0
HD2 I:HIS147 2.7 0.7 1.0
CD2 I:HIS147 2.8 86.4 1.0
CE1 I:HIS223 3.0 93.2 1.0
HE1 I:HIS223 3.0 0.8 1.0
CD2 I:HIS223 3.3 88.3 1.0
CE1 I:HIS147 3.5 91.8 1.0
HD2 I:HIS223 3.6 0.9 1.0
HG22 I:ILE145 3.9 70.3 1.0
HE1 I:HIS147 3.9 0.2 1.0
CG I:HIS147 4.1 82.6 1.0
ND1 I:HIS223 4.2 88.6 1.0
CG I:HIS223 4.4 83.2 1.0
ND1 I:HIS147 4.4 88.2 1.0
HG23 I:ILE145 4.5 70.3 1.0
CG2 I:ILE145 4.6 58.6 1.0
HD1 I:HIS223 4.9 0.4 1.0

Copper binding site 2 out of 5 in 5abd

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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
I:Cu1226

b:62.6
occ:1.00
NE2 I:HIS214 1.9 51.5 1.0
CE1 I:HIS214 2.7 51.5 1.0
HE1 I:HIS214 2.8 61.8 1.0
CD2 I:HIS214 3.0 49.5 1.0
HD2 I:HIS214 3.3 59.4 1.0
ND1 I:HIS214 3.9 48.9 1.0
CG I:HIS214 4.0 46.7 1.0
O I:ASN212 4.0 52.3 1.0
HD1 I:HIS214 4.6 58.7 1.0

Copper binding site 3 out of 5 in 5abd

Go back to Copper Binding Sites List in 5abd
Copper binding site 3 out of 5 in the Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cu1227

b:47.3
occ:1.00
NE2 E:HIS223 2.1 48.6 1.0
NE2 X:HIS223 2.1 42.4 1.0
NE2 X:HIS147 2.2 46.3 1.0
NE2 E:HIS147 2.2 49.4 1.0
HE1 X:HIS223 2.6 58.4 1.0
CE1 X:HIS223 2.7 48.7 1.0
CE1 E:HIS223 2.8 49.6 1.0
HE1 E:HIS223 2.8 59.5 1.0
CE1 X:HIS147 3.1 47.7 1.0
CD2 E:HIS147 3.1 44.4 1.0
HD2 E:HIS147 3.2 53.3 1.0
CD2 X:HIS147 3.2 40.4 1.0
HE1 X:HIS147 3.2 57.3 1.0
CD2 E:HIS223 3.2 45.0 1.0
CE1 E:HIS147 3.3 52.8 1.0
CD2 X:HIS223 3.4 37.7 1.0
HD2 X:HIS147 3.4 48.4 1.0
HE1 E:HIS147 3.5 63.4 1.0
HD2 E:HIS223 3.5 54.0 1.0
HG22 E:ILE145 3.6 38.4 1.0
HG22 X:ILE145 3.7 29.1 1.0
HD2 X:HIS223 3.8 45.2 1.0
ND1 X:HIS223 4.0 46.5 1.0
ND1 E:HIS223 4.0 49.5 1.0
HG23 E:ILE145 4.2 38.4 1.0
ND1 X:HIS147 4.2 43.3 1.0
CG E:HIS223 4.2 43.9 1.0
CG X:HIS147 4.3 37.1 1.0
CG2 E:ILE145 4.3 32.0 1.0
CG E:HIS147 4.3 45.2 1.0
CG X:HIS223 4.3 39.2 1.0
ND1 E:HIS147 4.3 50.3 1.0
CG2 X:ILE145 4.5 24.2 1.0
HD11 X:ILE145 4.5 42.8 1.0
HG23 X:ILE145 4.6 29.1 1.0
HG21 E:ILE145 4.6 38.4 1.0
HD1 X:HIS223 4.6 55.8 1.0
HG21 X:ILE145 4.7 29.1 1.0
HD11 E:ILE145 4.7 44.4 1.0
HD1 E:HIS223 4.7 59.5 1.0
HD1 X:HIS147 4.9 52.0 1.0

Copper binding site 4 out of 5 in 5abd

Go back to Copper Binding Sites List in 5abd
Copper binding site 4 out of 5 in the Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cu1228

b:37.2
occ:1.00
NE2 X:HIS214 1.9 35.6 1.0
CE1 X:HIS214 2.8 33.5 1.0
CD2 X:HIS214 2.9 31.3 1.0
O X:HOH2118 3.0 44.9 1.0
HE1 X:HIS214 3.0 40.2 1.0
HD2 X:HIS214 3.1 37.6 1.0
ND1 X:HIS214 4.0 32.6 1.0
CG X:HIS214 4.0 30.4 1.0
O X:ASN212 4.2 38.6 1.0
HD21 X:ASN212 4.5 76.5 1.0
ND2 X:ASN212 4.7 63.8 1.0
HD1 X:HIS214 4.7 39.1 1.0
HD22 X:ASN212 4.8 76.5 1.0
HB3 X:ASN212 4.9 56.6 1.0

Copper binding site 5 out of 5 in 5abd

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Vegfr-1 Domain 2 in Presence of Cu within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cu1229

b:42.0
occ:1.00
N X:ARG133 2.0 45.0 1.0
O X:ARG133 2.1 40.6 1.0
N X:GLY132 2.4 56.4 1.0
C X:ARG133 2.8 35.5 1.0
C X:GLY132 2.9 47.8 1.0
CA X:ARG133 2.9 38.5 1.0
O X:HOH2001 3.0 64.5 1.0
CA X:GLY132 3.0 53.7 1.0
HA3 X:GLY132 3.3 64.5 1.0
HG2 X:ARG133 3.3 64.4 1.0
HA X:ARG133 3.6 46.2 1.0
CG X:ARG133 3.8 53.6 1.0
HG3 X:ARG133 3.9 64.4 1.0
CB X:ARG133 3.9 41.1 1.0
HA2 X:GLY132 3.9 64.5 1.0
O X:HOH2002 4.0 40.7 1.0
O X:HOH2004 4.1 49.6 1.0
N X:PRO134 4.1 33.5 1.0
O X:GLY132 4.1 48.3 1.0
HB3 X:ARG133 4.4 49.4 1.0
HD2 X:PRO134 4.4 35.3 1.0
O X:PHE135 4.4 34.5 1.0
HB2 X:ARG133 4.7 49.4 1.0
CD X:PRO134 4.7 29.4 1.0
H X:PHE135 4.9 32.3 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: Sun Dec 13 11:16:53 2020

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