Atomistry » Calcium » PDB 4zmq-5a3y » 4zmv
Atomistry »
  Calcium »
    PDB 4zmq-5a3y »
      4zmv »

Calcium in PDB 4zmv: Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I)

Protein crystallography data

The structure of Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I), PDB code: 4zmv was solved by J.M.M.Caaveiro, S.Kudo, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.10 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.440, 98.910, 109.980, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 23.6

Other elements in 4zmv:

The structure of Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I) also contains other interesting chemical elements:

Nickel (Ni) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I) (pdb code 4zmv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I), PDB code: 4zmv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4zmv

Go back to Calcium Binding Sites List in 4zmv
Calcium binding site 1 out of 4 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I)


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 (Ss-X-Dimer Pocket I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:37.6
occ:1.00
OD1 A:ASN102 2.2 33.5 1.0
OD2 A:ASP134 2.4 45.8 1.0
O A:ASN143 2.4 33.2 1.0
O A:HIS104 2.4 44.1 1.0
OD2 A:ASP195 2.4 32.6 1.0
OD2 A:ASP136 2.5 40.8 1.0
OD1 A:ASP134 2.5 37.4 1.0
CG A:ASP134 2.8 41.3 1.0
CG A:ASP195 3.4 35.0 1.0
CG A:ASN102 3.4 32.8 1.0
CG A:ASP136 3.5 38.5 1.0
C A:HIS104 3.5 42.2 1.0
C A:ASN143 3.6 34.1 1.0
CB A:ASP195 3.8 34.5 1.0
CB A:ASP136 3.8 36.6 1.0
ND2 A:ASN102 4.1 31.7 1.0
N A:HIS104 4.2 39.5 1.0
CA A:HIS104 4.2 40.6 1.0
CB A:ASP134 4.4 39.5 1.0
CB A:HIS104 4.4 40.6 1.0
N A:GLY144 4.5 33.9 1.0
CA A:ASN143 4.5 35.1 1.0
OD1 A:ASP136 4.5 42.5 1.0
OD1 A:ASP195 4.5 36.6 1.0
CA A:GLY144 4.6 32.8 1.0
N A:LYS105 4.6 46.0 1.0
CA A:ASN102 4.6 30.9 1.0
CB A:ASN143 4.6 33.6 1.0
CB A:ASN102 4.6 31.8 1.0
CA A:LYS105 4.8 48.9 1.0
C A:ASN102 4.8 30.0 1.0
N A:ASP136 4.9 36.7 1.0
C A:LYS105 4.9 45.4 1.0
N A:PRO106 5.0 43.0 1.0
O A:ASN102 5.0 29.4 1.0

Calcium binding site 2 out of 4 in 4zmv

Go back to Calcium Binding Sites List in 4zmv
Calcium binding site 2 out of 4 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I)


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 (Ss-X-Dimer Pocket I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:35.8
occ:1.00
OD2 A:ASP103 2.2 30.4 1.0
OE2 A:GLU69 2.2 33.0 1.0
O A:GLN101 2.3 32.4 1.0
OE2 A:GLU11 2.3 38.1 1.0
OD1 A:ASP136 2.4 42.5 1.0
OD2 A:ASP100 2.5 29.5 1.0
OE1 A:GLU69 2.8 40.6 1.0
CD A:GLU69 2.8 40.3 1.0
CG A:ASP136 3.2 38.5 1.0
CG A:ASP103 3.3 32.3 1.0
CG A:ASP100 3.3 32.2 1.0
CD A:GLU11 3.4 34.6 1.0
C A:GLN101 3.5 34.0 1.0
OD1 A:ASP100 3.7 31.4 1.0
OD1 A:ASP103 3.7 35.1 1.0
CB A:ASP136 3.8 36.6 1.0
N A:GLN101 3.8 33.0 1.0
OE1 A:GLU11 3.9 32.7 1.0
N A:ASP103 4.0 31.2 1.0
OD2 A:ASP136 4.1 40.8 1.0
CA A:ASP136 4.1 36.6 1.0
ND1 A:HIS104 4.2 41.2 1.0
CG A:GLU69 4.3 41.0 1.0
CA A:GLN101 4.3 34.2 1.0
NE A:ARG68 4.4 37.9 1.0
CB A:ASP100 4.5 34.3 1.0
NH2 A:ARG68 4.5 36.4 1.0
N A:ASN102 4.5 30.8 1.0
CB A:ASP103 4.5 32.5 1.0
CA A:ASP100 4.6 33.1 1.0
CE1 A:HIS104 4.7 41.7 1.0
C A:ASP100 4.7 33.8 1.0
CG A:GLU11 4.7 34.5 1.0
CA A:ASN102 4.8 30.9 1.0
CA A:ASP103 4.8 33.5 1.0
C A:ASN102 4.9 30.0 1.0
N A:ASP136 5.0 36.7 1.0
CZ A:ARG68 5.0 37.4 1.0

Calcium binding site 3 out of 4 in 4zmv

Go back to Calcium Binding Sites List in 4zmv
Calcium binding site 3 out of 4 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I)


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 (Ss-X-Dimer Pocket I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:34.2
occ:1.00
OD2 B:ASP103 2.1 35.5 1.0
OD2 B:ASP100 2.3 32.9 1.0
OE2 B:GLU11 2.4 33.4 1.0
OD1 B:ASP136 2.4 38.5 1.0
O B:GLN101 2.4 31.8 1.0
OE2 B:GLU69 2.5 38.1 1.0
OE1 B:GLU69 2.7 40.4 1.0
CD B:GLU69 2.9 42.5 1.0
CG B:ASP136 3.2 37.0 1.0
CG B:ASP103 3.2 40.7 1.0
CG B:ASP100 3.3 36.8 1.0
CD B:GLU11 3.4 37.6 1.0
C B:GLN101 3.6 35.5 1.0
OE1 B:GLU11 3.7 39.6 1.0
OD1 B:ASP103 3.8 44.0 1.0
CB B:ASP136 3.8 35.2 1.0
OD1 B:ASP100 3.9 34.7 1.0
N B:GLN101 3.9 34.5 1.0
ND1 B:HIS104 4.0 45.6 1.0
OD2 B:ASP136 4.0 40.1 1.0
N B:ASP103 4.0 38.0 1.0
CA B:ASP136 4.1 35.2 1.0
CE1 B:HIS104 4.4 48.7 1.0
CA B:GLN101 4.4 36.9 1.0
CG B:GLU69 4.4 45.0 1.0
CB B:ASP103 4.5 39.8 1.0
CB B:ASP100 4.6 33.5 1.0
N B:ASN102 4.6 35.9 1.0
NE B:ARG68 4.7 35.1 1.0
CA B:ASP100 4.7 33.1 1.0
CA B:ASP103 4.7 38.9 1.0
CG B:GLU11 4.7 36.5 1.0
NH2 B:ARG68 4.8 36.0 1.0
CA B:ASN102 4.8 36.8 1.0
C B:ASP100 4.8 33.3 1.0
N B:ASP136 4.9 36.3 1.0
C B:ASN102 4.9 38.1 1.0

Calcium binding site 4 out of 4 in 4zmv

Go back to Calcium Binding Sites List in 4zmv
Calcium binding site 4 out of 4 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I)


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 Human P-Cadherin (Ss-X-Dimer Pocket I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:42.7
occ:1.00
OD1 B:ASN102 2.1 41.1 1.0
O B:HIS104 2.3 45.9 1.0
OD2 B:ASP134 2.4 42.6 1.0
O B:ASN143 2.4 34.3 1.0
OD2 B:ASP195 2.5 30.4 1.0
OD1 B:ASP134 2.5 41.9 1.0
OD2 B:ASP136 2.6 40.1 1.0
CG B:ASP134 2.8 42.9 1.0
CG B:ASN102 3.3 41.8 1.0
CG B:ASP195 3.3 32.9 1.0
C B:HIS104 3.5 45.9 1.0
CG B:ASP136 3.6 37.0 1.0
C B:ASN143 3.6 35.5 1.0
CB B:ASP195 3.7 32.4 1.0
ND2 B:ASN102 3.9 40.8 1.0
CB B:ASP136 4.0 35.2 1.0
O B:HOH411 4.1 37.9 1.0
CA B:HIS104 4.3 44.4 1.0
N B:HIS104 4.3 40.5 1.0
CB B:ASP134 4.3 40.4 1.0
OD1 B:ASP195 4.4 35.0 1.0
CA B:ASN143 4.4 37.6 1.0
N B:LYS105 4.5 49.9 1.0
CB B:ASN102 4.5 37.9 1.0
N B:GLY144 4.5 36.1 1.0
CA B:ASN102 4.6 36.8 1.0
CB B:HIS104 4.6 45.4 1.0
OD1 B:ASP136 4.6 38.5 1.0
CA B:GLY144 4.6 34.7 1.0
CA B:LYS105 4.6 51.4 1.0
CB B:ASN143 4.6 38.3 1.0
C B:LYS105 4.7 44.5 1.0
C B:ASN102 4.8 38.1 1.0
N B:PRO106 4.8 41.3 1.0
N B:ASP136 5.0 36.3 1.0

Reference:

S.Kudo, J.M.Caaveiro, K.Tsumoto. Adhesive Dimerization of Human P-Cadherin Catalyzed By A Chaperone-Like Mechanism Structure V. 24 1523 2016.
ISSN: ISSN 0969-2126
PubMed: 27545624
DOI: 10.1016/J.STR.2016.07.002
Page generated: Wed Jul 9 03:45:49 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy