Calcium in PDB 7deo: Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv
Protein crystallography data
The structure of Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv, PDB code: 7deo
was solved by
D.Fu,
G.Zhang,
X.Li,
Z.Rao,
Y.Guo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.49 /
2.50
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
156.08,
160.609,
42.239,
90,
90,
90
|
R / Rfree (%)
|
18.7 /
23.2
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv
(pdb code 7deo). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv, PDB code: 7deo:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 7deo
Go back to
Calcium Binding Sites List in 7deo
Calcium binding site 1 out
of 2 in the Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv
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 Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:20.5
occ:1.00
|
O
|
A:ARG104
|
2.2
|
16.0
|
1.0
|
O
|
A:PRO100
|
2.3
|
17.6
|
1.0
|
O
|
A:HOH686
|
2.3
|
22.9
|
1.0
|
OD1
|
A:ASP99
|
2.4
|
20.6
|
1.0
|
O
|
A:GLY102
|
2.4
|
16.1
|
1.0
|
O
|
A:HOH690
|
2.5
|
16.0
|
1.0
|
C
|
A:ARG104
|
3.4
|
16.8
|
1.0
|
C
|
A:GLY102
|
3.5
|
17.9
|
1.0
|
C
|
A:PRO100
|
3.5
|
18.2
|
1.0
|
CG
|
A:ASP99
|
3.5
|
21.4
|
1.0
|
N
|
A:GLY102
|
3.8
|
21.1
|
1.0
|
O
|
A:HOH691
|
3.9
|
28.7
|
1.0
|
O
|
A:HOH642
|
3.9
|
20.7
|
1.0
|
C
|
A:PRO101
|
4.0
|
23.4
|
1.0
|
N
|
A:PRO100
|
4.1
|
19.2
|
1.0
|
OD2
|
A:ASP99
|
4.1
|
19.4
|
1.0
|
N
|
A:ARG104
|
4.2
|
19.2
|
1.0
|
CA
|
A:GLY102
|
4.2
|
17.0
|
1.0
|
CA
|
A:ARG104
|
4.3
|
17.8
|
1.0
|
C
|
A:LEU103
|
4.3
|
20.2
|
1.0
|
O
|
A:PRO101
|
4.4
|
20.2
|
1.0
|
C
|
A:ASP99
|
4.4
|
22.3
|
1.0
|
CA
|
A:PRO100
|
4.4
|
20.7
|
1.0
|
N
|
A:PHE105
|
4.4
|
19.4
|
1.0
|
N
|
A:PRO101
|
4.5
|
19.4
|
1.0
|
CD
|
A:PRO100
|
4.5
|
20.2
|
1.0
|
CA
|
A:PRO101
|
4.5
|
21.7
|
1.0
|
N
|
A:LEU103
|
4.5
|
17.1
|
1.0
|
O
|
A:LEU103
|
4.5
|
22.6
|
1.0
|
CA
|
A:PHE105
|
4.5
|
21.5
|
1.0
|
CG
|
A:PRO100
|
4.6
|
22.5
|
1.0
|
CB
|
A:ASP99
|
4.7
|
17.9
|
1.0
|
O
|
A:ASP99
|
4.7
|
19.6
|
1.0
|
N
|
A:ARG106
|
4.8
|
23.9
|
1.0
|
CA
|
A:LEU103
|
4.8
|
19.9
|
1.0
|
C
|
A:PHE105
|
4.8
|
24.2
|
1.0
|
CA
|
A:ASP99
|
4.9
|
17.5
|
1.0
|
CB
|
A:PRO100
|
5.0
|
19.6
|
1.0
|
|
Calcium binding site 2 out
of 2 in 7deo
Go back to
Calcium Binding Sites List in 7deo
Calcium binding site 2 out
of 2 in the Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv
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 Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca501
b:27.1
occ:1.00
|
O
|
C:ARG104
|
2.3
|
23.6
|
1.0
|
O
|
C:PRO100
|
2.3
|
18.6
|
1.0
|
O
|
C:GLY102
|
2.3
|
24.6
|
1.0
|
O
|
C:HOH666
|
2.3
|
24.1
|
1.0
|
OD1
|
C:ASP99
|
2.5
|
28.0
|
1.0
|
O
|
C:HOH660
|
3.0
|
30.3
|
1.0
|
C
|
C:GLY102
|
3.4
|
23.3
|
1.0
|
C
|
C:ARG104
|
3.5
|
26.3
|
1.0
|
C
|
C:PRO100
|
3.5
|
23.8
|
1.0
|
CG
|
C:ASP99
|
3.6
|
29.6
|
1.0
|
N
|
C:GLY102
|
3.7
|
28.0
|
1.0
|
O
|
D:HOH1128
|
3.8
|
23.7
|
1.0
|
C
|
C:PRO101
|
3.9
|
27.0
|
1.0
|
N
|
C:PRO100
|
4.0
|
25.5
|
1.0
|
N
|
C:ARG104
|
4.1
|
27.1
|
1.0
|
CA
|
C:GLY102
|
4.1
|
23.7
|
1.0
|
C
|
C:LEU103
|
4.2
|
25.6
|
1.0
|
OD2
|
C:ASP99
|
4.2
|
31.5
|
1.0
|
C
|
C:ASP99
|
4.2
|
23.3
|
1.0
|
CA
|
C:ARG104
|
4.3
|
25.6
|
1.0
|
O
|
C:PRO101
|
4.3
|
21.3
|
1.0
|
CA
|
C:PRO100
|
4.4
|
25.9
|
1.0
|
O
|
C:LEU103
|
4.4
|
29.4
|
1.0
|
N
|
C:PRO101
|
4.4
|
24.8
|
1.0
|
N
|
C:LEU103
|
4.4
|
22.3
|
1.0
|
CA
|
C:PRO101
|
4.5
|
23.3
|
1.0
|
O
|
D:HOH1170
|
4.5
|
38.0
|
1.0
|
N
|
C:PHE105
|
4.5
|
25.3
|
1.0
|
O
|
C:ASP99
|
4.5
|
20.6
|
1.0
|
CA
|
C:PHE105
|
4.6
|
29.8
|
1.0
|
CD
|
C:PRO100
|
4.6
|
28.2
|
1.0
|
CB
|
C:ASP99
|
4.7
|
23.0
|
1.0
|
CA
|
C:LEU103
|
4.8
|
26.5
|
1.0
|
CG
|
C:PRO100
|
4.9
|
25.9
|
1.0
|
CA
|
C:ASP99
|
4.9
|
24.2
|
1.0
|
N
|
C:ARG106
|
4.9
|
25.0
|
1.0
|
|
Reference:
D.Fu,
G.Zhang,
X.Li,
Z.Rao,
Y.Guo.
Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv To Be Published.
Page generated: Sat Apr 17 14:08:28 2021
|