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Calcium in PDB 6ztb: Crystal Structure of Human P-Cadherin EC1_EC2

Protein crystallography data

The structure of Crystal Structure of Human P-Cadherin EC1_EC2, PDB code: 6ztb 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) 57.55 / 1.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.889, 76.522, 46.208, 90, 107.79, 90
R / Rfree (%) 19.8 / 21.4

Other elements in 6ztb:

The structure of Crystal Structure of Human P-Cadherin EC1_EC2 also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin EC1_EC2 (pdb code 6ztb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Human P-Cadherin EC1_EC2, PDB code: 6ztb:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6ztb

Go back to Calcium Binding Sites List in 6ztb
Calcium binding site 1 out of 3 in the Crystal Structure of Human P-Cadherin EC1_EC2


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 Human P-Cadherin EC1_EC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca401

b:17.9
occ:1.00
OD2 I:ASP302 2.3 20.6 1.0
OD2 I:ASP243 2.3 18.1 1.0
O I:HIS211 2.3 21.5 1.0
OD1 I:ASN209 2.4 21.3 1.0
OD2 I:ASP241 2.4 19.0 1.0
O I:ASN250 2.4 18.9 1.0
OD1 I:ASP241 2.5 18.6 1.0
CG I:ASP241 2.8 17.9 1.0
CG I:ASP302 3.3 21.9 1.0
CG I:ASP243 3.4 16.9 1.0
C I:HIS211 3.5 21.3 1.0
CG I:ASN209 3.5 22.1 1.0
C I:ASN250 3.6 20.0 1.0
CB I:ASP302 3.7 18.9 1.0
CB I:ASP243 3.7 17.3 1.0
ND2 I:ASN209 4.1 24.0 1.0
N I:HIS211 4.2 18.6 1.0
O I:HOH585 4.2 29.2 1.0
CA I:HIS211 4.3 19.3 1.0
CB I:ASP241 4.3 19.3 1.0
CB I:HIS211 4.4 19.9 1.0
N I:GLY251 4.4 17.9 1.0
OD1 I:ASP302 4.4 22.9 1.0
CA I:ASN250 4.5 18.1 1.0
CA I:GLY251 4.5 17.5 1.0
N I:LYS212 4.5 20.2 1.0
OD1 I:ASP243 4.5 17.9 1.0
CA I:LYS212 4.7 18.6 1.0
CB I:ASN209 4.7 19.9 1.0
CA I:ASN209 4.8 20.2 1.0
CB I:ASN250 4.8 19.4 1.0
N I:ASP243 4.8 18.4 1.0
C I:LYS212 4.8 20.5 1.0
CA I:ASP243 4.9 16.9 1.0
C I:ASN209 4.9 23.9 1.0

Calcium binding site 2 out of 3 in 6ztb

Go back to Calcium Binding Sites List in 6ztb
Calcium binding site 2 out of 3 in the Crystal Structure of Human P-Cadherin EC1_EC2


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 Human P-Cadherin EC1_EC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca402

b:20.4
occ:0.87
OE1 I:GLU176 2.3 19.4 1.0
OD2 I:ASP210 2.3 21.3 1.0
OE1 I:GLU118 2.3 18.1 1.0
O I:HOH528 2.4 21.6 1.0
O I:HOH727 2.4 25.8 1.0
OD1 I:ASP174 2.4 21.3 1.0
CG I:ASP210 3.1 20.4 1.0
OD1 I:ASP210 3.3 19.4 1.0
CG I:ASP174 3.3 24.0 1.0
CD I:GLU118 3.3 18.3 1.0
CD I:GLU176 3.5 19.7 1.0
OE2 I:GLU118 3.7 18.8 1.0
OD2 I:ASP174 3.9 26.4 1.0
CE1 I:HIS211 4.0 23.2 1.0
CA I:CA403 4.0 17.4 1.0
O I:HOH569 4.1 35.2 1.0
N I:ARG175 4.1 17.9 1.0
CA I:ASP174 4.1 18.8 1.0
CB I:ASP174 4.1 20.5 1.0
N I:GLU176 4.2 18.9 1.0
OD1 I:ASN119 4.3 20.5 1.0
ND2 I:ASN119 4.3 20.3 1.0
OE2 I:GLU176 4.4 19.6 1.0
CB I:GLU176 4.4 20.3 1.0
C I:ASP174 4.4 19.7 1.0
CG I:GLU176 4.5 20.4 1.0
O I:HOH755 4.5 52.4 1.0
CG I:GLU118 4.6 18.6 1.0
O I:HOH581 4.6 39.2 1.0
CB I:ASP210 4.6 20.4 1.0
ND1 I:HIS211 4.6 23.4 1.0
CG I:ASN119 4.8 18.5 1.0
O I:HOH504 4.8 44.2 1.0
CA I:GLU176 4.9 19.6 1.0
CB I:GLU118 5.0 17.0 1.0

Calcium binding site 3 out of 3 in 6ztb

Go back to Calcium Binding Sites List in 6ztb
Calcium binding site 3 out of 3 in the Crystal Structure of Human P-Cadherin EC1_EC2


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 Human P-Cadherin EC1_EC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca403

b:17.4
occ:1.00
OD1 I:ASP243 2.3 17.9 1.0
OE2 I:GLU118 2.3 18.8 1.0
OD1 I:ASP207 2.3 18.3 1.0
OD1 I:ASP210 2.3 19.4 1.0
OE2 I:GLU176 2.4 19.6 1.0
O I:GLN208 2.5 18.5 1.0
OE1 I:GLU176 2.8 19.4 1.0
CD I:GLU176 2.9 19.7 1.0
CG I:ASP207 3.4 16.7 1.0
CD I:GLU118 3.4 18.3 1.0
CG I:ASP243 3.4 16.9 1.0
CG I:ASP210 3.5 20.4 1.0
C I:GLN208 3.7 19.7 1.0
OE1 I:GLU118 3.8 18.1 1.0
OD2 I:ASP207 3.9 18.1 1.0
N I:GLN208 3.9 17.7 1.0
CA I:CA402 4.0 20.4 0.9
OD2 I:ASP210 4.1 21.3 1.0
CB I:ASP243 4.1 17.3 1.0
N I:ASP210 4.1 19.2 1.0
ND1 I:HIS211 4.1 23.4 1.0
CA I:ASP243 4.3 16.9 1.0
CG I:GLU176 4.4 20.4 1.0
CA I:GLN208 4.4 18.3 1.0
OD2 I:ASP243 4.4 18.1 1.0
NE I:ARG175 4.5 20.9 1.0
CB I:ASP207 4.6 17.7 1.0
CB I:ASP210 4.6 20.4 1.0
CE1 I:HIS211 4.6 23.2 1.0
CA I:ASP207 4.7 16.2 1.0
NH2 I:ARG175 4.7 20.4 1.0
CG I:GLU118 4.7 18.6 1.0
N I:ASN209 4.7 20.2 1.0
CA I:ASP210 4.8 19.1 1.0
C I:ASP207 4.8 18.3 1.0
CA I:ASN209 4.9 20.2 1.0
CB I:ARG175 5.0 18.3 1.0
C I:ASN209 5.0 23.9 1.0
N I:ASP243 5.0 18.4 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 22:46:38 2024

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