Atomistry » Calcium » PDB 4y9p-4yty » 4ygb
Atomistry »
  Calcium »
    PDB 4y9p-4yty »
      4ygb »

Calcium in PDB 4ygb: Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Free Form

Protein crystallography data

The structure of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Free Form, PDB code: 4ygb was solved by T.Satoh, M.Nishio, M.Yagi-Utsumi, K.Suzuki, T.Anzai, T.Mizushima, Y.Kamiya, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.924, 116.930, 58.065, 90.00, 120.13, 90.00
R / Rfree (%) 18 / 19.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Free Form (pdb code 4ygb). 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 Ergic-53/MCFD2, Monoclinic Calcium-Free Form, PDB code: 4ygb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4ygb

Go back to Calcium Binding Sites List in 4ygb
Calcium binding site 1 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Free Form


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 Ergic-53/MCFD2, Monoclinic Calcium-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:20.5
occ:1.00
 O B:LEU87 2.2 23.6 1.0
OD1 B:ASP81 2.3 23.7 1.0
OD1 B:ASP83 2.3 20.7 1.0
O B:HOH621 2.4 22.8 1.0
OD1 B:ASN85 2.4 23.0 1.0
OE1 B:GLU92 2.5 21.2 1.0
OE2 B:GLU92 2.5 21.5 1.0
CD B:GLU92 2.9 21.9 1.0
CG B:ASP83 3.3 23.8 1.0
CG B:ASN85 3.4 24.1 1.0
C B:LEU87 3.5 24.4 1.0
CG B:ASP81 3.5 23.2 1.0
OD2 B:ASP83 3.7 24.4 1.0
ND2 B:ASN85 3.8 25.4 1.0
N B:LEU87 4.2 22.5 1.0
CA B:ASP81 4.2 21.4 1.0
N B:ASN85 4.3 23.5 1.0
CA B:LEU87 4.3 22.6 1.0
CG B:GLU92 4.3 20.7 1.0
CB B:ASP81 4.3 22.7 1.0
OD2 B:ASP81 4.4 23.2 1.0
N B:LEU88 4.4 21.9 1.0
OD2 B:ASP89 4.4 24.4 1.0
CA B:LEU88 4.4 22.3 1.0
N B:ASP83 4.5 22.1 1.0
C B:ASP81 4.5 22.0 1.0
CB B:ASN85 4.6 25.0 1.0
CB B:ASP83 4.6 24.0 1.0
CB B:LEU87 4.6 24.8 1.0
N B:GLY84 4.7 22.5 1.0
N B:TYR82 4.7 21.8 1.0
N B:ASP89 4.8 21.5 1.0
CA B:ASN85 4.8 23.7 1.0
N B:ASN86 4.8 24.1 1.0
O B:HOH612 4.8 24.6 1.0
CA B:ASP83 4.9 23.7 1.0
C B:ASN85 4.9 24.4 1.0
O B:ASP81 5.0 22.5 1.0

Calcium binding site 2 out of 4 in 4ygb

Go back to Calcium Binding Sites List in 4ygb
Calcium binding site 2 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Free Form


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 Ergic-53/MCFD2, Monoclinic Calcium-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:26.8
occ:1.00
 O B:TYR135 2.3 24.7 1.0
OD1 B:ASN131 2.3 29.8 1.0
OD1 B:ASP129 2.3 29.7 1.0
O B:HOH627 2.4 35.2 1.0
OD1 B:ASP133 2.4 26.8 1.0
OE1 B:GLU140 2.5 27.6 1.0
OE2 B:GLU140 2.5 27.0 1.0
CD B:GLU140 2.9 30.0 1.0
CG B:ASP133 3.3 26.5 1.0
CG B:ASP129 3.4 28.7 1.0
C B:TYR135 3.5 25.4 1.0
CG B:ASN131 3.5 33.2 1.0
OD2 B:ASP133 3.6 30.7 1.0
ND2 B:ASN131 4.1 36.1 1.0
CA B:ASP129 4.1 29.5 1.0
N B:TYR135 4.2 22.6 1.0
OD2 B:ASP129 4.2 30.2 1.0
CB B:ASP129 4.2 29.4 1.0
CA B:TYR135 4.3 23.6 1.0
N B:ASP133 4.3 29.7 1.0
N B:ASN131 4.4 35.0 1.0
CG B:GLU140 4.4 28.0 1.0
N B:ILE136 4.4 23.7 1.0
C B:ASP129 4.5 31.5 1.0
N B:LYS130 4.5 31.9 1.0
CA B:ILE136 4.5 23.6 1.0
OD2 B:ASP137 4.5 38.3 1.0
CB B:TYR135 4.5 25.0 1.0
N B:ASP137 4.5 25.6 1.0
CB B:ASP133 4.5 27.7 1.0
N B:ASN132 4.7 32.2 1.0
CB B:ASN131 4.7 33.0 1.0
CA B:ASN131 4.8 33.4 1.0
CA B:ASP133 4.9 28.2 1.0
C B:ASN131 4.9 33.5 1.0
CG B:ASP137 5.0 34.0 1.0
C B:ILE136 5.0 23.9 1.0

Calcium binding site 3 out of 4 in 4ygb

Go back to Calcium Binding Sites List in 4ygb
Calcium binding site 3 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Free Form


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 Ergic-53/MCFD2, Monoclinic Calcium-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:20.7
occ:1.00
 O D:LEU87 2.2 23.5 1.0
OD1 D:ASP81 2.3 23.6 1.0
OD1 D:ASP83 2.4 21.0 1.0
OD1 D:ASN85 2.4 21.9 1.0
O D:HOH613 2.4 23.4 1.0
OE1 D:GLU92 2.5 21.7 1.0
OE2 D:GLU92 2.5 21.3 1.0
CD D:GLU92 2.8 21.3 1.0
CG D:ASP83 3.3 24.1 1.0
CG D:ASN85 3.4 23.2 1.0
C D:LEU87 3.5 24.7 1.0
CG D:ASP81 3.5 23.5 1.0
OD2 D:ASP83 3.7 25.0 1.0
ND2 D:ASN85 3.8 24.8 1.0
N D:LEU87 4.2 22.3 1.0
CA D:ASP81 4.2 21.2 1.0
N D:ASN85 4.3 22.6 1.0
CA D:LEU87 4.3 23.4 1.0
CG D:GLU92 4.3 19.8 1.0
CB D:ASP81 4.3 22.6 1.0
N D:LEU88 4.4 21.9 1.0
OD2 D:ASP81 4.4 23.0 1.0
OD2 D:ASP89 4.4 24.7 1.0
CA D:LEU88 4.4 21.8 1.0
C D:ASP81 4.5 22.4 1.0
N D:ASP83 4.5 21.5 1.0
CB D:ASN85 4.5 24.3 1.0
CB D:LEU87 4.6 24.7 1.0
CB D:ASP83 4.6 24.0 1.0
N D:GLY84 4.6 22.7 1.0
N D:TYR82 4.7 21.2 1.0
CA D:ASN85 4.7 23.1 1.0
N D:ASP89 4.8 20.3 1.0
O D:HOH614 4.8 23.9 1.0
N D:ASN86 4.8 24.3 1.0
CA D:ASP83 4.9 22.9 1.0
C D:ASN85 4.9 23.6 1.0
O D:ASP81 5.0 22.1 1.0

Calcium binding site 4 out of 4 in 4ygb

Go back to Calcium Binding Sites List in 4ygb
Calcium binding site 4 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Free Form


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 Ergic-53/MCFD2, Monoclinic Calcium-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:26.4
occ:1.00
 O D:TYR135 2.3 24.5 1.0
OD1 D:ASN131 2.3 29.9 1.0
OD1 D:ASP129 2.4 29.5 1.0
O D:HOH626 2.4 35.0 1.0
OD1 D:ASP133 2.5 25.6 1.0
OE1 D:GLU140 2.5 28.5 1.0
OE2 D:GLU140 2.5 28.2 1.0
CD D:GLU140 2.8 29.5 1.0
CG D:ASP133 3.3 25.6 1.0
CG D:ASP129 3.4 28.4 1.0
C D:TYR135 3.4 24.7 1.0
CG D:ASN131 3.5 33.8 1.0
OD2 D:ASP133 3.6 29.9 1.0
ND2 D:ASN131 4.1 36.0 1.0
CA D:ASP129 4.1 29.3 1.0
N D:TYR135 4.2 23.4 1.0
CB D:ASP129 4.3 28.5 1.0
OD2 D:ASP129 4.3 29.1 1.0
CA D:TYR135 4.3 24.3 1.0
CG D:GLU140 4.4 28.5 1.0
N D:ASP133 4.4 29.2 1.0
N D:ASN131 4.4 34.4 1.0
N D:ILE136 4.4 23.9 1.0
C D:ASP129 4.5 30.9 1.0
CA D:ILE136 4.5 23.8 1.0
N D:LYS130 4.5 33.1 1.0
OD2 D:ASP137 4.5 36.9 1.0
N D:ASP137 4.5 25.1 1.0
CB D:TYR135 4.5 26.0 1.0
CB D:ASP133 4.6 27.8 1.0
O D:HOH632 4.6 43.7 1.0
N D:ASN132 4.7 31.0 1.0
CB D:ASN131 4.7 33.4 1.0
CA D:ASN131 4.8 33.1 1.0
C D:ASN131 4.9 32.8 1.0
CA D:ASP133 4.9 28.0 1.0
CG D:ASP137 4.9 32.5 1.0
C D:ILE136 5.0 23.6 1.0

Reference:

T.Satoh, M.Nishio, M.Yagi-Utsumi, K.Suzuki, T.Anzai, T.Mizushima, Y.Kamiya, K.Kato. Interaction Mode of Coagulation Factors V and VIII with the Cargo Receptor MCFD2/Ergic-53 Complex To Be Published.
Page generated: Sun Jul 14 14:54:26 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy