Sodium 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:

Calcium (Ca) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Human P-Cadherin EC1_EC2, PDB code: 6ztb:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6ztb

Go back to Sodium Binding Sites List in 6ztb
Sodium binding site 1 out of 4 in the Crystal Structure of Human P-Cadherin EC1_EC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na404

b:29.0
occ:1.00
O I:ASP243 2.3 18.8 1.0
O I:HOH606 2.4 22.0 1.0
O I:HOH760 2.5 35.2 1.0
O I:ASP241 2.6 19.4 1.0
O I:HOH714 3.3 21.2 1.0
C I:ASP243 3.5 19.0 1.0
O I:HOH715 3.7 41.8 1.0
C I:ASP241 3.8 18.9 1.0
C I:GLU242 3.8 19.2 1.0
O I:GLU242 3.9 19.6 1.0
O I:HOH662 4.0 20.6 1.0
N I:ASP243 4.0 18.4 1.0
CA I:GLU242 4.2 17.9 1.0
N I:ALA245 4.3 18.9 1.0
CA I:ASP243 4.4 16.9 1.0
CA I:GLY251 4.4 17.5 1.0
CB I:ALA245 4.4 19.4 1.0
O I:HOH789 4.5 28.8 1.0
O I:GLY251 4.5 18.8 1.0
N I:GLU242 4.5 18.7 1.0
N I:ASP244 4.5 17.8 1.0
O I:HOH811 4.6 26.4 1.0
C I:ASP244 4.6 20.2 1.0
CA I:ASP244 4.6 17.9 1.0
O I:HOH818 4.9 49.7 1.0
CA I:ASP241 4.9 18.1 1.0
C I:GLY251 4.9 19.7 1.0
O I:HOH791 4.9 34.8 1.0

Sodium binding site 2 out of 4 in 6ztb

Go back to Sodium Binding Sites List in 6ztb
Sodium binding site 2 out of 4 in the Crystal Structure of Human P-Cadherin EC1_EC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na405

b:25.6
occ:1.00
O I:SER223 2.3 25.5 1.0
O I:VAL234 2.3 24.7 1.0
O I:HOH686 2.4 33.7 1.0
O I:HOH618 2.4 27.1 1.0
O I:HOH675 2.4 27.8 1.0
O I:HOH737 2.5 36.1 1.0
C I:VAL234 3.4 24.9 1.0
C I:SER223 3.5 24.6 1.0
N I:SER223 3.9 23.2 1.0
CA I:VAL234 3.9 22.6 1.0
O I:HOH795 4.0 45.8 1.0
OG I:SER223 4.2 30.8 1.0
CA I:SER223 4.3 23.5 1.0
N I:VAL224 4.5 24.6 1.0
O I:HOH787 4.5 35.5 1.0
O I:HOH814 4.5 43.4 1.0
O I:SER233 4.6 25.2 1.0
N I:MET235 4.6 21.4 1.0
CA I:VAL224 4.6 24.3 1.0
CG1 I:VAL234 4.6 23.6 1.0
O I:HOH729 4.8 22.6 1.0
CB I:SER223 4.9 26.9 1.0
CB I:VAL234 4.9 23.9 1.0
CB I:VAL224 5.0 26.3 1.0
N I:VAL234 5.0 22.1 1.0

Sodium binding site 3 out of 4 in 6ztb

Go back to Sodium Binding Sites List in 6ztb
Sodium binding site 3 out of 4 in the Crystal Structure of Human P-Cadherin EC1_EC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na406

b:34.1
occ:1.00
O I:HOH724 2.4 40.0 1.0
O I:HOH773 2.4 35.8 1.0
O I:ASN119 2.4 21.0 1.0
C I:ASN119 3.7 19.8 1.0
O I:HOH595 4.1 24.4 1.0
CB I:ASN119 4.1 18.7 1.0
C I:GLY120 4.5 21.5 1.0
N I:LYS121 4.5 21.4 1.0
O I:HOH551 4.5 22.9 1.0
CA I:ASN119 4.5 18.0 1.0
N I:GLY120 4.7 18.9 1.0
CA I:GLY120 4.7 19.4 1.0
O I:HOH782 4.7 35.8 1.0
O I:HOH732 4.8 21.6 1.0
O I:GLY120 4.9 21.4 1.0
CB I:LYS121 4.9 25.1 1.0
O I:HOH719 4.9 29.0 1.0
CA I:LYS121 5.0 22.3 1.0

Sodium binding site 4 out of 4 in 6ztb

Go back to Sodium Binding Sites List in 6ztb
Sodium binding site 4 out of 4 in the Crystal Structure of Human P-Cadherin EC1_EC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human P-Cadherin EC1_EC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na407

b:41.9
occ:1.00
O I:LEU286 2.4 32.5 1.0
O I:GLU226 2.8 35.2 1.0
O I:HOH689 3.3 61.0 1.0
N I:LEU286 3.4 28.4 1.0
C I:LEU286 3.5 32.4 1.0
C I:GLY285 3.7 31.5 1.0
C I:GLU226 3.8 35.5 1.0
N I:GLY285 3.9 27.5 1.0
CA I:LEU286 4.0 28.5 1.0
CA I:GLY285 4.0 26.8 1.0
CA I:GLY227 4.4 32.1 1.0
O I:GLY285 4.4 32.5 1.0
CB I:LEU286 4.4 28.4 1.0
N I:GLY227 4.5 32.5 1.0
O I:HOH516 4.5 33.9 1.0
CB I:GLU226 4.5 33.3 1.0
N I:ASP287 4.6 28.8 1.0
CA I:GLU226 4.7 30.8 1.0
CA I:ASP287 5.0 28.9 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: Mon Jul 12 15:53:45 2021

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