Calcium in PDB 7qbd: Tc:CD320 in Complex with Nanobody Tc-NB26
Protein crystallography data
The structure of Tc:CD320 in Complex with Nanobody Tc-NB26, PDB code: 7qbd
was solved by
J.S.Bloch,
K.P.Locher,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.14 /
4.18
|
|
Space group
|
P 43 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
102.129,
102.129,
360.998,
90,
90,
90
|
|
R / Rfree (%)
|
26.2 /
27.2
|
Other elements in 7qbd:
The structure of Tc:CD320 in Complex with Nanobody Tc-NB26 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Tc:CD320 in Complex with Nanobody Tc-NB26
(pdb code 7qbd). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Tc:CD320 in Complex with Nanobody Tc-NB26, PDB code: 7qbd:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 7qbd
Go back to
Calcium Binding Sites List in 7qbd
Calcium binding site 1 out
of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB26
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Tc:CD320 in Complex with Nanobody Tc-NB26 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:214.8
occ:1.00
|
N
|
A:ASN267
|
3.2
|
203.6
|
1.0
|
|
NE2
|
A:GLN389
|
3.2
|
187.2
|
1.0
|
|
N33
|
A:CNC501
|
3.3
|
167.0
|
1.0
|
|
O
|
A:ALA264
|
3.4
|
194.8
|
1.0
|
|
CB
|
A:ASN267
|
3.4
|
192.8
|
1.0
|
|
N
|
A:GLN266
|
3.4
|
194.7
|
1.0
|
|
OH
|
A:TYR226
|
3.6
|
179.5
|
1.0
|
|
CZ
|
A:TYR226
|
3.9
|
169.9
|
1.0
|
|
CA
|
A:ASN267
|
3.9
|
194.7
|
1.0
|
|
CE1
|
A:TYR226
|
3.9
|
169.6
|
1.0
|
|
CA
|
A:GLN266
|
4.1
|
195.0
|
1.0
|
|
CG
|
A:GLN389
|
4.1
|
169.6
|
1.0
|
|
C
|
A:GLN266
|
4.1
|
193.7
|
1.0
|
|
CB
|
A:GLN266
|
4.2
|
198.1
|
1.0
|
|
CD
|
A:GLN389
|
4.2
|
180.4
|
1.0
|
|
CA
|
A:PHE265
|
4.4
|
189.8
|
1.0
|
|
C
|
A:PHE265
|
4.4
|
189.6
|
1.0
|
|
C
|
A:ALA264
|
4.5
|
196.3
|
1.0
|
|
OD2
|
A:ASP393
|
4.5
|
194.5
|
1.0
|
|
CG
|
A:ASP393
|
4.6
|
195.3
|
1.0
|
|
CB
|
A:ASP393
|
4.6
|
188.1
|
1.0
|
|
C32
|
A:CNC501
|
4.6
|
162.5
|
1.0
|
|
CG
|
A:GLN266
|
4.7
|
199.2
|
1.0
|
|
CG
|
A:ASN267
|
4.7
|
189.1
|
1.0
|
|
CG
|
A:MET270
|
4.7
|
177.5
|
1.0
|
|
CE2
|
A:TYR226
|
4.7
|
167.8
|
1.0
|
|
O34
|
A:CNC501
|
4.8
|
162.2
|
1.0
|
|
CD1
|
A:TYR226
|
4.8
|
166.2
|
1.0
|
|
N
|
A:PHE265
|
4.9
|
194.5
|
1.0
|
|
CB
|
A:MET270
|
4.9
|
171.4
|
1.0
|
|
CB
|
A:GLN389
|
5.0
|
167.9
|
1.0
|
|
Calcium binding site 2 out
of 6 in 7qbd
Go back to
Calcium Binding Sites List in 7qbd
Calcium binding site 2 out
of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB26
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Tc:CD320 in Complex with Nanobody Tc-NB26 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca502
b:179.7
occ:1.00
|
N
|
B:ASN267
|
3.2
|
175.6
|
1.0
|
|
NE2
|
B:GLN389
|
3.2
|
156.3
|
1.0
|
|
N33
|
B:CNC501
|
3.3
|
150.1
|
1.0
|
|
O
|
B:ALA264
|
3.4
|
158.8
|
1.0
|
|
CB
|
B:ASN267
|
3.4
|
172.6
|
1.0
|
|
N
|
B:GLN266
|
3.4
|
170.6
|
1.0
|
|
OH
|
B:TYR226
|
3.6
|
149.5
|
1.0
|
|
CZ
|
B:TYR226
|
3.9
|
149.0
|
1.0
|
|
CA
|
B:ASN267
|
3.9
|
171.5
|
1.0
|
|
CE1
|
B:TYR226
|
3.9
|
148.0
|
1.0
|
|
CA
|
B:GLN266
|
4.1
|
175.4
|
1.0
|
|
CG
|
B:GLN389
|
4.1
|
150.2
|
1.0
|
|
C
|
B:GLN266
|
4.1
|
172.2
|
1.0
|
|
CB
|
B:GLN266
|
4.2
|
184.6
|
1.0
|
|
CD
|
B:GLN389
|
4.2
|
155.8
|
1.0
|
|
CA
|
B:PHE265
|
4.4
|
161.2
|
1.0
|
|
C
|
B:PHE265
|
4.4
|
163.8
|
1.0
|
|
C
|
B:ALA264
|
4.5
|
159.5
|
1.0
|
|
OD2
|
B:ASP393
|
4.5
|
173.9
|
1.0
|
|
CG
|
B:ASP393
|
4.6
|
175.4
|
1.0
|
|
CB
|
B:ASP393
|
4.6
|
174.2
|
1.0
|
|
C32
|
B:CNC501
|
4.6
|
144.5
|
1.0
|
|
CG
|
B:GLN266
|
4.7
|
186.0
|
1.0
|
|
CG
|
B:ASN267
|
4.7
|
171.3
|
1.0
|
|
CG
|
B:MET270
|
4.7
|
160.5
|
1.0
|
|
CE2
|
B:TYR226
|
4.7
|
156.5
|
1.0
|
|
O34
|
B:CNC501
|
4.8
|
135.8
|
1.0
|
|
CD1
|
B:TYR226
|
4.8
|
148.1
|
1.0
|
|
N
|
B:PHE265
|
4.9
|
159.8
|
1.0
|
|
CB
|
B:MET270
|
4.9
|
155.7
|
1.0
|
|
CB
|
B:GLN389
|
5.0
|
152.5
|
1.0
|
|
Calcium binding site 3 out
of 6 in 7qbd
Go back to
Calcium Binding Sites List in 7qbd
Calcium binding site 3 out
of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB26
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Tc:CD320 in Complex with Nanobody Tc-NB26 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca201
b:224.4
occ:1.00
|
OE2
|
C:GLU164
|
2.0
|
227.6
|
1.0
|
|
O
|
C:HIS155
|
2.3
|
218.2
|
1.0
|
|
OD1
|
C:ASP153
|
2.3
|
220.8
|
1.0
|
|
O
|
C:TRP150
|
2.3
|
223.7
|
1.0
|
|
OD2
|
C:ASP157
|
2.4
|
208.8
|
1.0
|
|
OD2
|
C:ASP163
|
2.4
|
227.2
|
1.0
|
|
CD
|
C:GLU164
|
2.9
|
227.0
|
1.0
|
|
CG
|
C:ASP153
|
3.2
|
217.8
|
1.0
|
|
CG
|
C:ASP157
|
3.5
|
212.3
|
1.0
|
|
C
|
C:HIS155
|
3.5
|
216.1
|
1.0
|
|
C
|
C:TRP150
|
3.5
|
219.2
|
1.0
|
|
OD2
|
C:ASP153
|
3.5
|
208.0
|
1.0
|
|
CG
|
C:ASP163
|
3.5
|
232.3
|
1.0
|
|
CG
|
C:GLU164
|
3.7
|
232.4
|
1.0
|
|
OE1
|
C:GLU164
|
3.8
|
231.9
|
1.0
|
|
N
|
C:ASP157
|
4.0
|
219.3
|
1.0
|
|
CB
|
C:TRP150
|
4.1
|
208.3
|
1.0
|
|
N
|
C:ASP153
|
4.1
|
217.5
|
1.0
|
|
N
|
C:HIS155
|
4.1
|
210.5
|
1.0
|
|
CB
|
C:ASP163
|
4.2
|
236.9
|
1.0
|
|
CA
|
C:TRP150
|
4.2
|
210.0
|
1.0
|
|
CB
|
C:ASP157
|
4.2
|
220.0
|
1.0
|
|
NZ
|
A:LYS114
|
4.3
|
192.2
|
1.0
|
|
CA
|
C:HIS155
|
4.3
|
211.3
|
1.0
|
|
OD1
|
C:ASP157
|
4.4
|
208.0
|
1.0
|
|
CB
|
C:ASP153
|
4.4
|
219.8
|
1.0
|
|
OD1
|
C:ASP163
|
4.5
|
232.9
|
1.0
|
|
N
|
C:PRO156
|
4.5
|
217.2
|
1.0
|
|
CA
|
C:PRO156
|
4.6
|
221.0
|
1.0
|
|
N
|
C:ARG151
|
4.6
|
222.0
|
1.0
|
|
N
|
C:CYS152
|
4.6
|
226.6
|
1.0
|
|
O
|
C:ASP163
|
4.6
|
242.1
|
1.0
|
|
CA
|
C:ASP153
|
4.7
|
216.9
|
1.0
|
|
C
|
C:PRO156
|
4.7
|
218.3
|
1.0
|
|
CA
|
C:ASP157
|
4.7
|
222.6
|
1.0
|
|
CB
|
C:HIS155
|
4.8
|
207.9
|
1.0
|
|
CA
|
C:ARG151
|
4.8
|
228.9
|
1.0
|
|
C
|
C:ARG151
|
4.8
|
227.6
|
1.0
|
|
N
|
C:GLY154
|
4.8
|
214.9
|
1.0
|
|
C
|
C:ASP163
|
4.8
|
242.7
|
1.0
|
|
C
|
C:ASP153
|
5.0
|
210.6
|
1.0
|
|
Calcium binding site 4 out
of 6 in 7qbd
Go back to
Calcium Binding Sites List in 7qbd
Calcium binding site 4 out
of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB26
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Tc:CD320 in Complex with Nanobody Tc-NB26 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca202
b:251.9
occ:1.00
|
OE2
|
C:GLU86
|
2.2
|
257.7
|
1.0
|
|
O
|
C:ASP77
|
2.4
|
241.0
|
1.0
|
|
O
|
C:TRP72
|
2.4
|
259.8
|
1.0
|
|
OD1
|
C:ASP75
|
2.4
|
253.6
|
1.0
|
|
OD2
|
C:ASP85
|
2.5
|
258.3
|
1.0
|
|
OD2
|
C:ASP79
|
2.5
|
252.3
|
1.0
|
|
CD
|
C:GLU86
|
3.2
|
256.4
|
1.0
|
|
C
|
C:ASP77
|
3.4
|
238.2
|
1.0
|
|
CG
|
C:ASP79
|
3.4
|
248.6
|
1.0
|
|
CG
|
C:ASP85
|
3.5
|
261.1
|
1.0
|
|
CG
|
C:ASP75
|
3.5
|
252.3
|
1.0
|
|
C
|
C:TRP72
|
3.5
|
258.6
|
1.0
|
|
CB
|
C:ASP85
|
3.9
|
264.3
|
1.0
|
|
CB
|
C:ASP79
|
3.9
|
248.3
|
1.0
|
|
N
|
C:ASP79
|
3.9
|
240.5
|
1.0
|
|
CB
|
C:TRP72
|
4.0
|
245.8
|
1.0
|
|
OD2
|
C:ASP75
|
4.0
|
249.1
|
1.0
|
|
CG
|
C:GLU86
|
4.1
|
255.4
|
1.0
|
|
OE1
|
C:GLU86
|
4.1
|
254.2
|
1.0
|
|
CA
|
C:ASP77
|
4.1
|
240.0
|
1.0
|
|
N
|
C:ASP77
|
4.1
|
242.1
|
1.0
|
|
CA
|
C:TRP72
|
4.1
|
251.3
|
1.0
|
|
CB
|
C:ASP77
|
4.1
|
240.9
|
1.0
|
|
OD1
|
C:ASP79
|
4.4
|
244.2
|
1.0
|
|
N
|
C:LEU78
|
4.5
|
238.5
|
1.0
|
|
N
|
C:ASP75
|
4.5
|
257.3
|
1.0
|
|
OD1
|
C:ASP85
|
4.5
|
264.0
|
1.0
|
|
O
|
C:ASP85
|
4.6
|
267.8
|
1.0
|
|
CA
|
C:ASP79
|
4.6
|
244.2
|
1.0
|
|
CB
|
C:ASP75
|
4.6
|
254.7
|
1.0
|
|
N
|
C:ARG73
|
4.7
|
260.7
|
1.0
|
|
CA
|
C:LEU78
|
4.7
|
241.1
|
1.0
|
|
C
|
C:ASP85
|
4.7
|
268.2
|
1.0
|
|
C
|
C:LEU78
|
4.8
|
241.1
|
1.0
|
|
N
|
C:CYS74
|
4.8
|
267.2
|
1.0
|
|
CA
|
C:ASP75
|
4.9
|
254.5
|
1.0
|
|
C
|
C:ASP75
|
5.0
|
248.4
|
1.0
|
|
CA
|
C:ASP85
|
5.0
|
266.1
|
1.0
|
|
CA
|
C:ARG73
|
5.0
|
262.0
|
1.0
|
|
Calcium binding site 5 out
of 6 in 7qbd
Go back to
Calcium Binding Sites List in 7qbd
Calcium binding site 5 out
of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB26
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Tc:CD320 in Complex with Nanobody Tc-NB26 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca201
b:218.9
occ:1.00
|
OE2
|
D:GLU164
|
2.0
|
232.1
|
1.0
|
|
O
|
D:HIS155
|
2.3
|
217.9
|
1.0
|
|
OD1
|
D:ASP153
|
2.3
|
221.2
|
1.0
|
|
O
|
D:TRP150
|
2.3
|
217.1
|
1.0
|
|
OD2
|
D:ASP157
|
2.4
|
215.3
|
1.0
|
|
OD2
|
D:ASP163
|
2.4
|
221.5
|
1.0
|
|
CD
|
D:GLU164
|
3.0
|
225.8
|
1.0
|
|
CG
|
D:ASP153
|
3.2
|
216.1
|
1.0
|
|
CG
|
D:ASP157
|
3.5
|
216.5
|
1.0
|
|
C
|
D:HIS155
|
3.5
|
216.2
|
1.0
|
|
C
|
D:TRP150
|
3.5
|
215.7
|
1.0
|
|
OD2
|
D:ASP153
|
3.5
|
207.3
|
1.0
|
|
CG
|
D:ASP163
|
3.5
|
225.0
|
1.0
|
|
CG
|
D:GLU164
|
3.7
|
225.4
|
1.0
|
|
OE1
|
D:GLU164
|
3.9
|
216.5
|
1.0
|
|
N
|
D:ASP157
|
4.0
|
223.6
|
1.0
|
|
CB
|
D:TRP150
|
4.1
|
216.8
|
1.0
|
|
N
|
D:ASP153
|
4.1
|
220.6
|
1.0
|
|
N
|
D:HIS155
|
4.1
|
213.7
|
1.0
|
|
CB
|
D:ASP163
|
4.2
|
225.4
|
1.0
|
|
CA
|
D:TRP150
|
4.2
|
214.3
|
1.0
|
|
CB
|
D:ASP157
|
4.2
|
219.2
|
1.0
|
|
NZ
|
B:LYS114
|
4.3
|
209.4
|
1.0
|
|
CA
|
D:HIS155
|
4.3
|
213.4
|
1.0
|
|
OD1
|
D:ASP157
|
4.4
|
213.9
|
1.0
|
|
CB
|
D:ASP153
|
4.4
|
218.2
|
1.0
|
|
OD1
|
D:ASP163
|
4.5
|
226.8
|
1.0
|
|
N
|
D:PRO156
|
4.5
|
216.5
|
1.0
|
|
CA
|
D:PRO156
|
4.6
|
222.1
|
1.0
|
|
N
|
D:ARG151
|
4.6
|
216.1
|
1.0
|
|
N
|
D:CYS152
|
4.6
|
227.8
|
1.0
|
|
O
|
D:ASP163
|
4.6
|
237.8
|
1.0
|
|
CA
|
D:ASP153
|
4.7
|
218.6
|
1.0
|
|
C
|
D:PRO156
|
4.7
|
222.4
|
1.0
|
|
CA
|
D:ASP157
|
4.7
|
221.9
|
1.0
|
|
CB
|
D:HIS155
|
4.8
|
210.1
|
1.0
|
|
CA
|
D:ARG151
|
4.8
|
220.7
|
1.0
|
|
N
|
D:GLY154
|
4.8
|
215.2
|
1.0
|
|
C
|
D:ARG151
|
4.8
|
226.1
|
1.0
|
|
C
|
D:ASP163
|
4.8
|
235.3
|
1.0
|
|
C
|
D:ASP153
|
5.0
|
211.6
|
1.0
|
|
Calcium binding site 6 out
of 6 in 7qbd
Go back to
Calcium Binding Sites List in 7qbd
Calcium binding site 6 out
of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB26
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Tc:CD320 in Complex with Nanobody Tc-NB26 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca202
b:249.1
occ:1.00
|
OE2
|
D:GLU86
|
2.0
|
252.6
|
1.0
|
|
O
|
D:ASP77
|
2.4
|
236.6
|
1.0
|
|
O
|
D:TRP72
|
2.4
|
252.1
|
1.0
|
|
OD1
|
D:ASP75
|
2.4
|
246.8
|
1.0
|
|
OD2
|
D:ASP85
|
2.5
|
246.8
|
1.0
|
|
OD2
|
D:ASP79
|
2.5
|
237.1
|
1.0
|
|
CD
|
D:GLU86
|
3.1
|
254.7
|
1.0
|
|
C
|
D:ASP77
|
3.4
|
232.2
|
1.0
|
|
CG
|
D:ASP79
|
3.4
|
234.4
|
1.0
|
|
CG
|
D:ASP85
|
3.5
|
254.0
|
1.0
|
|
CG
|
D:ASP75
|
3.5
|
244.9
|
1.0
|
|
C
|
D:TRP72
|
3.5
|
247.6
|
1.0
|
|
CG
|
D:GLU86
|
3.8
|
256.5
|
1.0
|
|
CB
|
D:ASP85
|
3.9
|
262.2
|
1.0
|
|
CB
|
D:ASP79
|
3.9
|
238.5
|
1.0
|
|
N
|
D:ASP79
|
3.9
|
236.9
|
1.0
|
|
OE1
|
D:GLU86
|
4.0
|
251.9
|
1.0
|
|
CB
|
D:TRP72
|
4.0
|
233.4
|
1.0
|
|
OD2
|
D:ASP75
|
4.0
|
237.9
|
1.0
|
|
CA
|
D:ASP77
|
4.1
|
231.3
|
1.0
|
|
N
|
D:ASP77
|
4.1
|
235.1
|
1.0
|
|
CA
|
D:TRP72
|
4.1
|
239.1
|
1.0
|
|
CB
|
D:ASP77
|
4.1
|
230.6
|
1.0
|
|
OD1
|
D:ASP79
|
4.4
|
230.1
|
1.0
|
|
N
|
D:LEU78
|
4.5
|
231.3
|
1.0
|
|
N
|
D:ASP75
|
4.5
|
251.7
|
1.0
|
|
OD1
|
D:ASP85
|
4.5
|
253.5
|
1.0
|
|
O
|
D:ASP85
|
4.6
|
262.9
|
1.0
|
|
CA
|
D:ASP79
|
4.6
|
239.7
|
1.0
|
|
CB
|
D:ASP75
|
4.6
|
250.4
|
1.0
|
|
N
|
D:ARG73
|
4.7
|
249.5
|
1.0
|
|
CA
|
D:LEU78
|
4.7
|
233.9
|
1.0
|
|
C
|
D:ASP85
|
4.7
|
266.1
|
1.0
|
|
C
|
D:LEU78
|
4.8
|
234.3
|
1.0
|
|
N
|
D:CYS74
|
4.8
|
259.6
|
1.0
|
|
CA
|
D:ASP75
|
4.9
|
251.9
|
1.0
|
|
C
|
D:ASP75
|
5.0
|
244.8
|
1.0
|
|
CA
|
D:ASP85
|
5.0
|
264.4
|
1.0
|
|
CA
|
D:ARG73
|
5.0
|
254.4
|
1.0
|
|
Reference:
J.S.Bloch,
J.M.Sequeira,
A.S.Ramirez,
E.V.Quadros,
K.P.Locher.
Generation of Nanobodies Targeting the Human, Transcobalamin-Mediated Vitamin B 12 Uptake Route. Faseb J. V. 36 22222 2022.
ISSN: ESSN 1530-6860
PubMed: 35218573
DOI: 10.1096/FJ.202101376RR
Page generated: Fri Jul 19 03:25:16 2024
|
