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Calcium in PDB 6ztr: Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324)

Protein crystallography data

The structure of Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324), PDB code: 6ztr was solved by J.M.Rondeau, S.Lehmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.49 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 172.691, 77.795, 133.406, 90, 90, 90
R / Rfree (%) 19.2 / 22.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324) (pdb code 6ztr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324), PDB code: 6ztr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6ztr

Go back to Calcium Binding Sites List in 6ztr
Calcium binding site 1 out of 6 in the Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324)


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 the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca401

b:32.9
occ:1.00
 OD2 I:ASP302 2.3 34.8 1.0
OD2 I:ASP243 2.3 39.2 1.0
O I:HIS211 2.3 39.7 1.0
OD1 I:ASN209 2.3 43.5 1.0
OD1 I:ASP241 2.5 31.2 1.0
O I:ASN250 2.5 34.0 1.0
OD2 I:ASP241 2.5 41.8 1.0
CG I:ASP241 2.8 35.2 1.0
CG I:ASP302 3.3 36.1 1.0
CG I:ASP243 3.4 37.6 1.0
C I:HIS211 3.5 39.8 1.0
CG I:ASN209 3.5 35.7 1.0
C I:ASN250 3.6 32.8 1.0
CB I:ASP302 3.7 35.2 1.0
CB I:ASP243 3.8 34.1 1.0
O I:HOH507 4.0 39.8 1.0
ND2 I:ASN209 4.1 27.7 1.0
CA I:HIS211 4.3 33.7 1.0
N I:HIS211 4.3 33.6 1.0
OD1 I:ASP302 4.3 36.0 1.0
CB I:ASP241 4.3 34.5 1.0
CA I:ASN250 4.4 27.9 1.0
N I:GLY251 4.4 28.6 1.0
N I:LYS212 4.4 37.8 1.0
CB I:HIS211 4.4 33.4 1.0
OD1 I:ASP243 4.5 38.1 1.0
CA I:GLY251 4.5 29.7 1.0
CA I:LYS212 4.6 37.2 1.0
CB I:ASN250 4.7 30.0 1.0
CB I:ASN209 4.7 31.6 1.0
CA I:ASN209 4.7 32.5 1.0
C I:LYS212 4.8 41.1 1.0
N I:ASP243 4.8 34.6 1.0
N I:PRO213 4.9 37.5 1.0
CD I:PRO213 4.9 37.9 1.0
C I:ASN209 4.9 38.0 1.0
CA I:ASP243 4.9 33.4 1.0

Calcium binding site 2 out of 6 in 6ztr

Go back to Calcium Binding Sites List in 6ztr
Calcium binding site 2 out of 6 in the Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324)


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 the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca402

b:30.9
occ:1.00
 OD1 I:ASP207 2.3 33.4 1.0
OD1 I:ASP210 2.4 40.0 1.0
OE2 I:GLU118 2.4 32.8 1.0
OE2 I:GLU176 2.4 37.6 1.0
OD1 I:ASP243 2.4 38.1 1.0
O I:GLN208 2.5 34.0 1.0
CD I:GLU176 3.1 39.8 1.0
OE1 I:GLU176 3.2 32.6 1.0
CG I:ASP207 3.4 30.0 1.0
CG I:ASP210 3.5 40.3 1.0
CG I:ASP243 3.5 37.6 1.0
CD I:GLU118 3.6 32.0 1.0
C I:GLN208 3.6 34.4 1.0
N I:GLN208 3.8 28.6 1.0
OD2 I:ASP207 3.9 35.4 1.0
CB I:ASP243 4.0 34.1 1.0
OD2 I:ASP210 4.0 41.5 1.0
ND1 I:HIS211 4.0 38.3 1.0
N I:ASP210 4.1 35.3 1.0
OE1 I:GLU118 4.1 33.1 1.0
CA I:ASP243 4.2 33.4 1.0
CA I:CA403 4.3 32.6 1.0
NE I:ARG175 4.3 40.2 1.0
CA I:GLN208 4.3 26.6 1.0
OD2 I:ASP243 4.5 39.2 1.0
CE1 I:HIS211 4.5 37.9 1.0
CB I:ASP207 4.5 32.5 1.0
CG I:GLU176 4.6 40.5 1.0
CB I:ASP210 4.6 37.3 1.0
NH2 I:ARG175 4.6 34.5 1.0
CA I:ASP207 4.6 31.3 1.0
N I:ASN209 4.7 31.9 1.0
C I:ASP207 4.7 34.8 1.0
CA I:ASP210 4.8 36.2 1.0
CG I:GLU118 4.8 28.8 1.0
CA I:ASN209 4.9 32.5 1.0
CB I:GLN208 4.9 26.2 1.0
CZ I:ARG175 5.0 48.4 1.0

Calcium binding site 3 out of 6 in 6ztr

Go back to Calcium Binding Sites List in 6ztr
Calcium binding site 3 out of 6 in the Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca403

b:32.6
occ:1.00
 O I:HOH527 2.2 40.0 1.0
OD1 I:ASP174 2.2 41.8 1.0
OE1 I:GLU118 2.3 33.1 1.0
O I:HOH506 2.4 22.1 1.0
OD2 I:ASP210 2.4 41.5 1.0
OE1 I:GLU176 2.4 32.6 1.0
CD I:GLU118 3.2 32.0 1.0
CG I:ASP174 3.2 41.9 1.0
CG I:ASP210 3.3 40.3 1.0
OE2 I:GLU118 3.5 32.8 1.0
OD1 I:ASP210 3.5 40.0 1.0
CD I:GLU176 3.6 39.8 1.0
OD2 I:ASP174 3.9 43.8 1.0
CA I:ASP174 4.1 34.1 1.0
N I:ARG175 4.1 34.2 1.0
CB I:ASP174 4.1 35.3 1.0
N I:GLU176 4.1 36.6 1.0
OD1 I:ASN119 4.2 33.3 1.0
CE1 I:HIS211 4.2 37.9 1.0
CA I:CA402 4.3 30.9 1.0
ND2 I:ASN119 4.4 32.0 1.0
C I:ASP174 4.4 37.8 1.0
OE2 I:GLU176 4.4 37.6 1.0
CG I:GLU118 4.5 28.8 1.0
CB I:GLU176 4.5 38.8 1.0
O I:HOH517 4.6 66.2 1.0
CG I:GLU176 4.6 40.5 1.0
CB I:ASP210 4.7 37.3 1.0
CG I:ASN119 4.7 30.9 1.0
CA I:GLU176 4.8 37.9 1.0
ND1 I:HIS211 4.9 38.3 1.0
CA I:ARG175 4.9 34.6 1.0
CB I:GLU118 5.0 29.9 1.0

Calcium binding site 4 out of 6 in 6ztr

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Calcium binding site 4 out of 6 in the Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca401

b:33.4
occ:1.00
 OD1 J:ASP207 2.2 32.7 1.0
OD1 J:ASP210 2.3 37.5 1.0
OE2 J:GLU176 2.3 32.4 1.0
OD1 J:ASP243 2.3 32.2 1.0
OE2 J:GLU118 2.4 32.7 1.0
O J:GLN208 2.4 34.0 1.0
CD J:GLU176 3.1 47.3 1.0
OE1 J:GLU176 3.2 36.8 1.0
CG J:ASP207 3.3 31.6 1.0
CG J:ASP210 3.4 37.1 1.0
CG J:ASP243 3.4 29.8 1.0
CD J:GLU118 3.5 36.1 1.0
C J:GLN208 3.6 36.3 1.0
N J:GLN208 3.8 28.9 1.0
OD2 J:ASP207 3.9 33.2 1.0
OE1 J:GLU118 3.9 33.0 1.0
OD2 J:ASP210 3.9 33.4 1.0
ND1 J:HIS211 4.0 38.2 1.0
N J:ASP210 4.0 35.6 1.0
CB J:ASP243 4.0 32.5 1.0
CA J:CA402 4.2 34.8 1.0
CA J:ASP243 4.3 31.9 1.0
OD2 J:ASP243 4.3 32.7 1.0
CA J:GLN208 4.3 28.8 1.0
CE1 J:HIS211 4.5 38.2 1.0
CB J:ASP207 4.5 29.9 1.0
NE J:ARG175 4.5 34.0 1.0
CG J:GLU176 4.5 40.2 1.0
CB J:ASP210 4.5 37.3 1.0
N J:ASN209 4.6 28.8 1.0
CA J:ASP210 4.7 36.0 1.0
CA J:ASP207 4.7 27.8 1.0
NH2 J:ARG175 4.7 34.8 1.0
CG J:GLU118 4.7 32.5 1.0
C J:ASP207 4.7 31.6 1.0
CA J:ASN209 4.9 29.4 1.0
CB J:GLN208 5.0 29.9 1.0
C J:ASN209 5.0 36.3 1.0

Calcium binding site 5 out of 6 in 6ztr

Go back to Calcium Binding Sites List in 6ztr
Calcium binding site 5 out of 6 in the Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca402

b:34.8
occ:1.00
 OE1 J:GLU176 2.2 36.8 1.0
OD1 J:ASP174 2.2 36.3 1.0
OE1 J:GLU118 2.2 33.0 1.0
OD2 J:ASP210 2.3 33.4 1.0
O J:HOH558 2.3 31.1 1.0
O J:HOH511 2.4 32.6 1.0
CG J:ASP174 3.2 35.8 1.0
CG J:ASP210 3.3 37.1 1.0
CD J:GLU118 3.3 36.1 1.0
CD J:GLU176 3.4 47.3 1.0
OD1 J:ASP210 3.5 37.5 1.0
OE2 J:GLU118 3.7 32.7 1.0
OD2 J:ASP174 3.9 38.1 1.0
N J:ARG175 4.1 32.2 1.0
CB J:ASP174 4.1 34.4 1.0
CA J:ASP174 4.1 33.2 1.0
CA J:CA401 4.2 33.4 1.0
OD1 J:ASN119 4.2 34.1 1.0
OE2 J:GLU176 4.2 32.4 1.0
N J:GLU176 4.2 34.3 1.0
ND2 J:ASN119 4.3 33.2 1.0
CE1 J:HIS211 4.3 38.2 1.0
CB J:GLU176 4.4 36.8 1.0
C J:ASP174 4.4 35.6 1.0
CG J:GLU176 4.4 40.2 1.0
CG J:GLU118 4.5 32.5 1.0
CB J:ASP210 4.6 37.3 1.0
CG J:ASN119 4.7 36.7 1.0
CA J:GLU176 4.9 35.2 1.0
CB J:GLU118 4.9 26.9 1.0
CA J:ARG175 5.0 32.2 1.0
ND1 J:HIS211 5.0 38.2 1.0

Calcium binding site 6 out of 6 in 6ztr

Go back to Calcium Binding Sites List in 6ztr
Calcium binding site 6 out of 6 in the Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Anti-Human P-Cadherin Fab CQY684 in Complex with Human P-Cadherin(108-324) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca403

b:35.9
occ:1.00
 O J:HIS211 2.3 37.2 1.0
OD2 J:ASP302 2.3 38.5 1.0
OD1 J:ASN209 2.3 41.2 1.0
OD2 J:ASP243 2.4 32.7 1.0
OD1 J:ASP241 2.5 35.2 1.0
O J:ASN250 2.5 35.8 1.0
OD2 J:ASP241 2.6 43.1 1.0
CG J:ASP241 2.9 38.7 1.0
CG J:ASP302 3.3 40.9 1.0
CG J:ASP243 3.4 29.8 1.0
C J:HIS211 3.4 38.8 1.0
CG J:ASN209 3.5 40.6 1.0
C J:ASN250 3.6 35.2 1.0
CB J:ASP302 3.7 37.7 1.0
CB J:ASP243 3.8 32.5 1.0
ND2 J:ASN209 4.2 31.3 1.0
CA J:HIS211 4.2 34.9 1.0
N J:HIS211 4.2 35.4 1.0
O J:HOH502 4.3 43.4 1.0
OD1 J:ASP302 4.3 42.1 1.0
CB J:HIS211 4.4 33.9 1.0
CA J:ASN250 4.4 31.9 1.0
CB J:ASP241 4.4 36.8 1.0
N J:LYS212 4.4 38.4 1.0
N J:GLY251 4.5 30.0 1.0
OD1 J:ASP243 4.5 32.2 1.0
CB J:ASN250 4.6 31.3 1.0
CA J:LYS212 4.6 38.3 1.0
CA J:GLY251 4.6 29.8 1.0
CB J:ASN209 4.6 27.6 1.0
CA J:ASN209 4.7 29.4 1.0
N J:ASP243 4.8 34.1 1.0
C J:LYS212 4.8 43.5 1.0
C J:ASN209 4.8 36.3 1.0
CA J:ASP243 4.9 31.9 1.0
N J:PRO213 4.9 38.3 1.0
CD J:PRO213 4.9 38.5 1.0

Reference:

Q.Sheng, J.A.D'alessio, D.L.Menezes, C.Karim, Y.Tang, A.Tam, S.Clark, C.Ying, A.Connor, K.G.Mansfield, J.M.Rondeau, M.Ghoddusi, F.C.Geyer, J.Gu, M.E.Mclaughlin, R.Newcombe, G.Elliott, W.R.Tschantz, S.Lehmann, K.Miller, T.Huber, K.G.Rendahl, U.Jeffry, N.K.Pryer, E.Lees, P.Kwon, J.A.Abraham, J.S.Damiano, T.J.Abrams. PCA062, A P-Cadherin Targeting Antibody-Drug-Conjugate, Displays Potent Anti-Tumor Activity Against P-Cadherin-Expressing Malignancies. Mol.Cancer Ther. 2021.
ISSN: ESSN 1538-8514
PubMed: 33879555
DOI: 10.1158/1535-7163.MCT-20-0708
Page generated: Thu Jul 18 22:47:10 2024

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