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Calcium in PDB 7qbg: Tc:CD320 in Complex with Nanobody Tc-NB4

Protein crystallography data

The structure of Tc:CD320 in Complex with Nanobody Tc-NB4, PDB code: 7qbg 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) 48.92 / 2.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.339, 116.418, 125.498, 90, 90, 90
R / Rfree (%) 22.7 / 28.5

Other elements in 7qbg:

The structure of Tc:CD320 in Complex with Nanobody Tc-NB4 also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Tc:CD320 in Complex with Nanobody Tc-NB4 (pdb code 7qbg). 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-NB4, PDB code: 7qbg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7qbg

Go back to Calcium Binding Sites List in 7qbg
Calcium binding site 1 out of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB4


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-NB4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:70.2
occ:1.00
O B:TRP72 2.1 82.7 1.0
OD1 B:ASP75 2.1 76.6 1.0
O B:ASP77 2.2 69.8 1.0
OD2 B:ASP79 2.6 64.3 1.0
OD2 B:ASP85 2.6 75.2 1.0
OE2 B:GLU86 3.0 83.1 1.0
C B:TRP72 3.2 78.1 1.0
CG B:ASP75 3.3 77.1 1.0
C B:ASP77 3.3 70.3 1.0
CG B:ASP79 3.5 65.2 1.0
CG B:ASP85 3.6 80.3 1.0
CB B:ASP79 3.7 64.6 1.0
CB B:ASP85 3.8 84.8 1.0
N B:ASP79 3.8 64.1 1.0
CD B:GLU86 3.9 79.7 1.0
OD2 B:ASP75 3.9 77.4 1.0
CG B:GLU86 3.9 74.5 1.0
CA B:TRP72 4.0 78.6 1.0
CA B:ASP77 4.1 69.7 1.0
N B:ASP77 4.1 71.1 1.0
CB B:ASP77 4.2 70.6 1.0
N B:ARG73 4.2 78.4 1.0
CB B:TRP72 4.3 76.7 1.0
N B:LEU78 4.4 70.2 1.0
CB B:ASP75 4.4 76.6 1.0
CA B:ASP79 4.4 64.8 1.0
CA B:ARG73 4.5 85.8 1.0
N B:ASP75 4.6 80.5 1.0
CA B:LEU78 4.6 67.1 1.0
NZ C:LYS105 4.6 63.9 1.0
C B:LEU78 4.6 65.5 1.0
O B:ASP85 4.6 86.0 1.0
C B:ASP85 4.7 84.4 1.0
OD1 B:ASP79 4.7 62.6 1.0
OD1 B:ASP85 4.8 76.3 1.0
N B:CYS74 4.8 87.2 1.0
CA B:ASP85 4.9 83.0 1.0
C B:ARG73 4.9 90.9 1.0
CA B:ASP75 5.0 78.3 1.0

Calcium binding site 2 out of 6 in 7qbg

Go back to Calcium Binding Sites List in 7qbg
Calcium binding site 2 out of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB4


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-NB4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:50.1
occ:1.00
OD2 B:ASP163 1.8 50.4 1.0
OD1 B:ASP153 1.9 46.4 1.0
OD2 B:ASP157 2.2 49.7 1.0
O B:TRP150 2.3 46.4 1.0
O B:HIS155 2.4 49.1 1.0
CG B:ASP153 2.6 46.3 1.0
OE2 B:GLU164 2.9 52.4 1.0
OD2 B:ASP153 2.9 49.1 1.0
CG B:ASP163 3.1 51.5 1.0
CG B:ASP157 3.3 48.5 1.0
C B:TRP150 3.5 45.0 1.0
C B:HIS155 3.6 51.4 1.0
CD B:GLU164 3.7 52.4 1.0
CB B:ASP163 3.9 51.1 1.0
CB B:ASP153 3.9 48.0 1.0
N B:ASP157 4.0 51.4 1.0
OD1 B:ASP163 4.0 49.0 1.0
CB B:ASP157 4.0 42.0 1.0
N B:HIS155 4.1 51.3 1.0
CG B:GLU164 4.2 46.6 1.0
N B:ASP153 4.2 44.0 1.0
NZ C:LYS114 4.2 39.2 1.0
CB B:TRP150 4.2 46.8 1.0
OD1 B:ASP157 4.2 41.5 1.0
CA B:TRP150 4.3 47.1 1.0
CA B:HIS155 4.3 47.3 1.0
N B:ARG151 4.5 46.5 1.0
N B:PRO156 4.6 51.3 1.0
CA B:ASP153 4.6 51.2 1.0
CA B:PRO156 4.6 51.4 1.0
CA B:ARG151 4.7 52.3 1.0
CA B:ASP157 4.7 48.4 1.0
C B:PRO156 4.7 49.2 1.0
N B:CYS152 4.7 52.7 1.0
CB B:HIS155 4.7 51.9 1.0
OE1 B:GLU164 4.7 56.6 1.0
C B:ARG151 4.8 54.3 1.0
N B:GLY154 4.9 49.3 1.0
C B:ASP153 4.9 51.7 1.0

Calcium binding site 3 out of 6 in 7qbg

Go back to Calcium Binding Sites List in 7qbg
Calcium binding site 3 out of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB4


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-NB4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:47.8
occ:1.00
O D:HIS155 2.2 43.9 1.0
OD2 D:ASP157 2.3 46.5 1.0
O D:TRP150 2.3 52.5 1.0
OD1 D:ASP163 2.5 49.8 1.0
OD1 D:ASP153 2.6 45.7 1.0
OE2 D:GLU164 3.0 51.7 1.0
CG D:ASP157 3.2 46.3 1.0
CG D:ASP153 3.3 46.8 1.0
CG D:ASP163 3.4 53.7 1.0
C D:HIS155 3.4 49.1 1.0
OD2 D:ASP153 3.4 44.8 1.0
C D:TRP150 3.4 57.4 1.0
N D:ASP157 3.5 54.4 1.0
CB D:ASP157 3.7 40.8 1.0
CD D:GLU164 3.8 53.0 1.0
CB D:ASP163 3.8 57.2 1.0
CG D:GLU164 3.9 47.8 1.0
CB D:TRP150 4.1 42.9 1.0
CA D:TRP150 4.2 48.4 1.0
CA D:ASP157 4.2 47.9 1.0
N D:HIS155 4.3 46.3 1.0
OD1 D:ASP157 4.3 46.9 1.0
N D:PRO156 4.3 47.8 1.0
C D:PRO156 4.3 46.6 1.0
CA D:HIS155 4.3 45.2 1.0
CA D:PRO156 4.3 48.3 1.0
OD2 D:ASP163 4.4 55.5 1.0
N D:ARG151 4.4 56.0 1.0
N D:ASP153 4.5 45.8 1.0
CB D:ASP153 4.5 41.7 1.0
CA D:ARG151 4.7 54.9 1.0
CB D:HIS155 4.7 48.2 1.0
N D:CYS152 4.7 52.1 1.0
OE1 D:GLU164 4.8 62.5 1.0
NZ A:LYS114 4.8 45.0 1.0
C D:ARG151 4.9 56.6 1.0
C D:ASP163 5.0 53.5 1.0

Calcium binding site 4 out of 6 in 7qbg

Go back to Calcium Binding Sites List in 7qbg
Calcium binding site 4 out of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB4


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-NB4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:75.5
occ:1.00
O D:TRP72 2.3 75.8 1.0
OD2 D:ASP79 2.3 69.3 1.0
O D:ASP77 2.3 73.4 1.0
OD1 D:ASP75 2.3 76.0 1.0
OD2 D:ASP85 2.4 75.6 1.0
OE2 D:GLU86 2.8 77.7 1.0
CG D:ASP75 3.3 76.3 1.0
CG D:ASP79 3.4 70.7 1.0
CG D:ASP85 3.4 81.2 1.0
C D:TRP72 3.4 74.4 1.0
C D:ASP77 3.4 71.4 1.0
OD2 D:ASP75 3.6 75.7 1.0
CD D:GLU86 3.8 83.3 1.0
CB D:ASP85 3.8 80.7 1.0
CG D:GLU86 4.0 79.0 1.0
N D:ASP79 4.1 69.6 1.0
CA D:TRP72 4.1 72.5 1.0
N D:ASP77 4.1 71.9 1.0
CB D:ASP79 4.1 72.7 1.0
CA D:ASP77 4.2 70.7 1.0
CB D:TRP72 4.2 71.2 1.0
N D:ASP75 4.2 73.3 1.0
CB D:ASP77 4.3 72.8 1.0
OD1 D:ASP79 4.3 68.6 1.0
NZ A:LYS105 4.4 66.7 1.0
N D:CYS74 4.4 81.5 1.0
N D:LEU78 4.5 69.6 1.0
N D:ARG73 4.5 76.1 1.0
OD1 D:ASP85 4.5 80.0 1.0
CB D:ASP75 4.5 75.8 1.0
CA D:LEU78 4.7 70.0 1.0
CA D:ARG73 4.7 79.5 1.0
CA D:ASP79 4.7 70.4 1.0
CA D:ASP75 4.8 76.2 1.0
C D:LEU78 4.8 73.6 1.0
C D:ARG73 4.9 82.2 1.0
OE1 D:GLU86 4.9 86.1 1.0
C D:ASP75 5.0 77.6 1.0

Calcium binding site 5 out of 6 in 7qbg

Go back to Calcium Binding Sites List in 7qbg
Calcium binding site 5 out of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB4


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-NB4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:59.9
occ:1.00
OD2 E:ASP54 2.3 61.6 1.0
O E:GLY126 2.3 69.3 1.0
O E:GLN122 2.5 62.8 1.0
CG E:ASP54 3.1 61.9 1.0
C E:GLY126 3.3 66.9 1.0
OD1 E:ASP54 3.3 67.1 1.0
C E:GLN122 3.6 60.3 1.0
N E:SER124 3.8 55.3 1.0
O E:SER124 3.8 55.2 1.0
C E:SER124 3.9 66.8 1.0
C E:PRO123 3.9 69.9 1.0
N E:GLY126 3.9 68.7 1.0
CA E:SER124 4.0 66.8 1.0
O E:PRO123 4.0 79.0 1.0
CA E:GLY126 4.1 67.9 1.0
CB E:GLN122 4.1 61.4 1.0
N E:CYS127 4.2 68.5 1.0
CA E:CYS127 4.4 64.5 1.0
N E:PRO123 4.4 58.8 1.0
N E:ASN125 4.4 68.5 1.0
CA E:GLN122 4.5 56.5 1.0
C E:ASN125 4.5 67.0 1.0
OG E:SER74 4.5 70.7 1.0
CB E:ASP54 4.5 58.6 1.0
CA E:PRO123 4.6 60.6 1.0
OE1 E:GLN122 4.8 57.8 1.0
O E:ASN125 4.9 69.6 1.0
CD C:LYS81 4.9 61.7 1.0
CB E:SER73 4.9 79.8 1.0
CG E:GLN122 5.0 58.7 1.0

Calcium binding site 6 out of 6 in 7qbg

Go back to Calcium Binding Sites List in 7qbg
Calcium binding site 6 out of 6 in the Tc:CD320 in Complex with Nanobody Tc-NB4


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-NB4 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca201

b:56.0
occ:1.00
O G:SER124 2.3 59.8 1.0
O G:GLY126 2.3 78.4 1.0
O G:GLN122 2.3 56.1 1.0
OD2 G:ASP54 2.5 62.8 1.0
OD1 G:ASP54 2.9 77.4 1.0
CG G:ASP54 3.1 67.7 1.0
C G:GLY126 3.2 77.4 1.0
C G:SER124 3.4 58.2 1.0
C G:GLN122 3.6 50.7 1.0
O G:ASN125 3.8 80.4 1.0
N G:CYS127 3.9 84.1 1.0
N G:SER124 4.0 50.6 1.0
C G:PRO123 4.0 51.1 1.0
C G:ASN125 4.0 71.0 1.0
CA G:CYS127 4.0 80.4 1.0
CA G:SER124 4.2 52.0 1.0
CB G:GLN122 4.2 54.5 1.0
N G:GLY126 4.2 73.9 1.0
CA G:GLY126 4.3 76.6 1.0
CA G:PRO123 4.3 49.7 1.0
O G:PRO123 4.3 55.6 1.0
N G:PRO123 4.4 52.0 1.0
N G:ASN125 4.5 61.9 1.0
CA G:GLN122 4.5 47.5 1.0
CB G:SER74 4.6 79.2 1.0
CB G:ASP54 4.6 64.2 1.0
OE1 G:GLN122 4.6 65.7 1.0
CB G:SER124 4.6 51.2 1.0
CA G:ASN125 4.8 61.6 1.0
N G:SER74 4.8 84.2 1.0
OG G:SER73 4.8 101.8 1.0
CB G:CYS127 4.9 84.8 1.0
O G:HOH301 4.9 59.9 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 03:25:55 2024

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