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:
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: Wed Jul 31 03:47:35 2024
|