Atomistry » Calcium » PDB 4zmp-5a3o » 4zmq
Atomistry »
  Calcium »
    PDB 4zmp-5a3o »
      4zmq »

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

Protein crystallography data

The structure of Crystal Structure of Human P-Cadherin (Ss-X-Dimer), PDB code: 4zmq 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) 39.72 / 2.20
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 182.090, 182.090, 41.040, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 23.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer) (pdb code 4zmq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer), PDB code: 4zmq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4zmq

Go back to Calcium Binding Sites List in 4zmq
Calcium binding site 1 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:34.3
occ:1.00
 OD2 A:ASP103 2.2 30.2 1.0
O A:HOH431 2.3 31.1 1.0
OD1 A:ASP67 2.3 33.7 1.0
OE1 A:GLU69 2.3 32.1 1.0
OE1 A:GLU11 2.3 31.1 1.0
O A:HOH500 2.5 29.5 1.0
CG A:ASP103 3.2 29.4 1.0
CD A:GLU11 3.3 31.4 1.0
CG A:ASP67 3.3 35.6 1.0
OD1 A:ASP103 3.4 29.3 1.0
CD A:GLU69 3.5 31.8 1.0
OE2 A:GLU11 3.7 31.5 1.0
OD2 A:ASP67 4.0 38.6 1.0
CA A:CA302 4.1 30.1 1.0
N A:ARG68 4.2 33.6 1.0
N A:GLU69 4.3 34.8 1.0
CA A:ASP67 4.3 34.4 1.0
ND2 A:ASN12 4.3 34.3 1.0
CB A:GLU69 4.3 33.9 1.0
NE2 A:HIS104 4.3 36.8 1.0
CB A:ASP67 4.3 35.1 1.0
OD1 A:ASN12 4.3 35.8 1.0
OE2 A:GLU69 4.4 33.3 1.0
CG A:GLU69 4.4 32.3 1.0
C A:ASP67 4.5 33.5 1.0
CB A:ASP103 4.6 28.5 1.0
CG A:GLU11 4.6 31.4 1.0
CG A:ASN12 4.7 35.4 1.0
CD2 A:HIS104 4.9 36.5 1.0
CA A:GLU69 4.9 36.5 1.0

Calcium binding site 2 out of 8 in 4zmq

Go back to Calcium Binding Sites List in 4zmq
Calcium binding site 2 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:30.1
occ:1.00
 OD1 A:ASP103 2.3 29.3 1.0
OE2 A:GLU11 2.4 31.5 1.0
OD1 A:ASP100 2.4 32.1 1.0
OD1 A:ASP136 2.4 27.0 1.0
OE2 A:GLU69 2.4 33.3 1.0
O A:GLN101 2.5 29.6 1.0
OE1 A:GLU69 2.8 32.1 1.0
CD A:GLU69 3.0 31.8 1.0
CG A:ASP100 3.2 31.2 1.0
CG A:ASP103 3.4 29.4 1.0
CD A:GLU11 3.5 31.4 1.0
CG A:ASP136 3.5 27.9 1.0
OD2 A:ASP100 3.5 29.0 1.0
C A:GLN101 3.7 28.2 1.0
OE1 A:GLU11 3.9 31.1 1.0
N A:GLN101 3.9 31.1 1.0
OD2 A:ASP103 3.9 30.2 1.0
N A:ASP103 4.0 26.9 1.0
CB A:ASP136 4.1 28.1 1.0
CD2 A:HIS104 4.1 36.5 1.0
CA A:CA301 4.1 34.3 1.0
CA A:ASP136 4.3 29.8 1.0
NE A:ARG68 4.4 34.1 1.0
CA A:GLN101 4.4 28.5 1.0
OD2 A:ASP136 4.5 27.8 1.0
CB A:ASP100 4.5 31.9 1.0
CG A:GLU69 4.5 32.3 1.0
CB A:ASP103 4.6 28.5 1.0
N A:ASN102 4.7 28.1 1.0
CA A:ASP100 4.7 31.5 1.0
NE2 A:HIS104 4.7 36.8 1.0
NH2 A:ARG68 4.7 36.7 1.0
CG A:GLU11 4.7 31.4 1.0
CA A:ASP103 4.8 29.4 1.0
C A:ASP100 4.8 31.6 1.0
CA A:ASN102 4.8 27.4 1.0
C A:ASN102 5.0 28.1 1.0

Calcium binding site 3 out of 8 in 4zmq

Go back to Calcium Binding Sites List in 4zmq
Calcium binding site 3 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:26.2
occ:1.00
 O A:HIS104 2.3 29.6 1.0
OD1 A:ASN102 2.3 27.0 1.0
OD2 A:ASP136 2.3 27.8 1.0
O A:ASN143 2.4 23.1 1.0
OD2 A:ASP195 2.4 26.3 1.0
OD2 A:ASP134 2.4 27.4 1.0
OD1 A:ASP134 2.5 28.1 1.0
CG A:ASP134 2.8 27.3 1.0
CG A:ASP136 3.4 27.9 1.0
CG A:ASP195 3.4 24.9 1.0
CG A:ASN102 3.5 26.8 1.0
C A:HIS104 3.5 33.3 1.0
C A:ASN143 3.5 24.8 1.0
CB A:ASP195 3.7 24.3 1.0
CB A:ASP136 3.8 28.1 1.0
ND2 A:ASN102 4.0 25.9 1.0
O A:HOH437 4.2 30.3 1.0
CA A:HIS104 4.3 34.5 1.0
N A:HIS104 4.3 33.7 1.0
CB A:ASP134 4.3 27.0 1.0
CA A:ASN143 4.3 24.3 1.0
N A:GLY144 4.4 25.5 1.0
CB A:ASN143 4.5 25.1 1.0
N A:LYS105 4.5 33.0 1.0
CB A:HIS104 4.5 34.5 1.0
OD1 A:ASP136 4.5 27.0 1.0
OD1 A:ASP195 4.5 25.5 1.0
CA A:GLY144 4.5 25.7 1.0
CA A:LYS105 4.6 33.8 1.0
CB A:ASN102 4.7 27.3 1.0
CA A:ASN102 4.7 27.4 1.0
N A:ASP136 4.8 30.4 1.0
C A:LYS105 4.8 29.9 1.0
C A:ASN102 4.9 28.1 1.0
CA A:ASP136 4.9 29.8 1.0
CD A:PRO106 4.9 25.3 1.0
N A:PRO106 4.9 26.6 1.0

Calcium binding site 4 out of 8 in 4zmq

Go back to Calcium Binding Sites List in 4zmq
Calcium binding site 4 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:60.5
occ:1.00
 O A:GLU69 2.6 39.9 1.0
O A:HOH444 2.6 47.5 1.0
C A:GLU69 3.8 38.2 1.0
O A:GLU70 4.4 47.8 1.0
CA A:GLU70 4.5 44.9 1.0
N A:GLU70 4.6 40.7 1.0
CA A:GLU69 4.8 36.5 1.0
C A:GLU70 4.8 45.2 1.0
O A:HOH506 5.0 45.2 1.0

Calcium binding site 5 out of 8 in 4zmq

Go back to Calcium Binding Sites List in 4zmq
Calcium binding site 5 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer)


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 Human P-Cadherin (Ss-X-Dimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:65.8
occ:1.00
 OD1 A:ASP213 2.7 55.2 1.0
OXT A:ASP213 3.5 42.7 1.0
CA A:ASP213 4.0 44.7 1.0
CG A:ASP213 4.0 55.9 1.0
C A:ASP213 4.2 43.5 1.0
O A:HOH468 4.5 34.2 1.0
CB A:ASP213 4.6 48.9 1.0
O A:LEU212 4.6 36.3 1.0
OD2 A:ASP213 5.0 61.0 1.0

Calcium binding site 6 out of 8 in 4zmq

Go back to Calcium Binding Sites List in 4zmq
Calcium binding site 6 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer)


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 Human P-Cadherin (Ss-X-Dimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:26.3
occ:1.00
 OE1 B:GLU69 2.2 27.9 1.0
OD1 B:ASP67 2.2 29.3 1.0
OD2 B:ASP103 2.3 28.5 1.0
OE1 B:GLU11 2.3 28.2 1.0
O B:HOH420 2.3 26.0 1.0
O B:HOH484 2.3 28.4 1.0
CG B:ASP103 3.1 26.8 1.0
CG B:ASP67 3.2 29.7 1.0
CD B:GLU11 3.3 29.3 1.0
OD1 B:ASP103 3.3 26.7 1.0
CD B:GLU69 3.5 27.1 1.0
OE2 B:GLU11 3.7 29.7 1.0
OD2 B:ASP67 3.9 30.2 1.0
CA B:CA302 4.1 28.2 1.0
CB B:ASP67 4.2 30.0 1.0
NE2 B:HIS104 4.2 35.3 1.0
CA B:ASP67 4.2 28.0 1.0
N B:ARG68 4.2 29.1 1.0
OE2 B:GLU69 4.3 26.4 1.0
ND2 B:ASN12 4.3 29.6 1.0
OD1 B:ASN12 4.3 31.0 1.0
N B:GLU69 4.3 31.5 1.0
CB B:GLU69 4.4 30.1 1.0
CG B:GLU69 4.4 29.4 1.0
C B:ASP67 4.5 27.4 1.0
CB B:ASP103 4.5 26.5 1.0
CG B:GLU11 4.6 27.3 1.0
CG B:ASN12 4.8 28.3 1.0
CD2 B:HIS104 4.8 32.8 1.0
CB B:GLU11 5.0 27.5 1.0

Calcium binding site 7 out of 8 in 4zmq

Go back to Calcium Binding Sites List in 4zmq
Calcium binding site 7 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human P-Cadherin (Ss-X-Dimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:28.2
occ:1.00
 OD1 B:ASP100 2.3 31.2 1.0
OD1 B:ASP103 2.3 26.7 1.0
O B:GLN101 2.3 25.8 1.0
OD1 B:ASP136 2.3 30.4 1.0
OE2 B:GLU69 2.3 26.4 1.0
OE2 B:GLU11 2.4 29.7 1.0
OE1 B:GLU69 2.9 27.9 1.0
CD B:GLU69 3.0 27.1 1.0
CG B:ASP100 3.2 32.1 1.0
CG B:ASP136 3.4 31.6 1.0
CD B:GLU11 3.4 29.3 1.0
CG B:ASP103 3.4 26.8 1.0
C B:GLN101 3.5 26.4 1.0
OD2 B:ASP100 3.7 29.3 1.0
OE1 B:GLU11 3.8 28.2 1.0
N B:GLN101 3.8 24.8 1.0
N B:ASP103 4.0 26.7 1.0
OD2 B:ASP103 4.0 28.5 1.0
CD2 B:HIS104 4.0 32.8 1.0
CB B:ASP136 4.0 31.0 1.0
CA B:CA301 4.1 26.3 1.0
CA B:ASP136 4.3 31.1 1.0
OD2 B:ASP136 4.3 31.5 1.0
CA B:GLN101 4.3 24.9 1.0
CG B:GLU69 4.4 29.4 1.0
CB B:ASP100 4.5 30.0 1.0
NE B:ARG68 4.5 33.4 1.0
CB B:ASP103 4.6 26.5 1.0
N B:ASN102 4.6 24.8 1.0
CA B:ASP100 4.6 28.8 1.0
NH2 B:ARG68 4.6 34.9 1.0
NE2 B:HIS104 4.6 35.3 1.0
CA B:ASP103 4.7 29.0 1.0
C B:ASP100 4.7 26.0 1.0
CG B:GLU11 4.7 27.3 1.0
CA B:ASN102 4.8 25.9 1.0
C B:ASN102 4.9 24.4 1.0
CB B:GLN101 4.9 28.0 1.0

Calcium binding site 8 out of 8 in 4zmq

Go back to Calcium Binding Sites List in 4zmq
Calcium binding site 8 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human P-Cadherin (Ss-X-Dimer) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:29.4
occ:1.00
 OD1 B:ASN102 2.3 29.8 1.0
O B:HIS104 2.3 27.8 1.0
O B:ASN143 2.4 28.5 1.0
OD2 B:ASP136 2.4 31.5 1.0
OD1 B:ASP134 2.4 31.5 1.0
OD2 B:ASP195 2.5 26.6 1.0
OD2 B:ASP134 2.5 32.4 1.0
CG B:ASP134 2.8 32.3 1.0
CG B:ASN102 3.4 25.9 1.0
CG B:ASP195 3.4 27.3 1.0
CG B:ASP136 3.5 31.6 1.0
C B:HIS104 3.5 30.6 1.0
C B:ASN143 3.6 29.3 1.0
CB B:ASP195 3.7 28.0 1.0
CB B:ASP136 3.8 31.0 1.0
ND2 B:ASN102 3.9 25.4 1.0
N B:HIS104 4.2 32.8 1.0
O B:HOH406 4.2 26.0 1.0
CA B:HIS104 4.2 34.0 1.0
CB B:ASP134 4.3 31.8 1.0
CA B:ASN143 4.4 29.3 1.0
N B:GLY144 4.5 29.8 1.0
OD1 B:ASP195 4.5 28.4 1.0
CB B:ASN143 4.5 27.0 1.0
N B:LYS105 4.5 29.5 1.0
CB B:HIS104 4.5 32.7 1.0
OD1 B:ASP136 4.6 30.4 1.0
CB B:ASN102 4.6 25.9 1.0
CA B:GLY144 4.6 30.7 1.0
CA B:ASN102 4.7 25.9 1.0
CA B:LYS105 4.7 34.4 1.0
C B:ASN102 4.8 24.4 1.0
C B:LYS105 4.9 33.5 1.0
N B:ASP136 4.9 33.7 1.0
N B:PRO106 4.9 33.2 1.0
CD B:PRO106 4.9 33.3 1.0
CA B:ASP136 5.0 31.1 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: Sun Jul 14 15:54:39 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy