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Calcium in PDB 4yge: Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2

Protein crystallography data

The structure of Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2, PDB code: 4yge 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 / 3.05
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.128, 113.128, 157.602, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 21.1

Other elements in 4yge:

The structure of Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2 (pdb code 4yge). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2, PDB code: 4yge:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4yge

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Calcium binding site 1 out of 9 in the Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2


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, Trigonal Calcium-Bound Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:31.5
occ:1.00
 OD1 A:ASN156 2.0 34.3 1.0
OD1 A:ASP181 2.3 37.9 1.0
OD1 A:ASP152 2.4 27.2 1.0
O A:PHE154 2.5 23.6 1.0
OD2 A:ASP152 2.8 27.2 1.0
CG A:ASP152 2.9 25.1 1.0
CG A:ASN156 3.2 30.0 1.0
CG A:ASP181 3.5 38.2 1.0
C A:PHE154 3.7 26.4 1.0
ND2 A:ASN156 4.0 27.7 1.0
CB A:ASN156 4.2 32.4 1.0
N A:ASN156 4.2 32.1 1.0
OD2 A:ASP181 4.3 38.6 1.0
O A:HIS178 4.3 58.7 1.0
CB A:ASP181 4.3 39.0 1.0
CB A:PHE154 4.4 23.9 1.0
CA A:PHE154 4.4 24.0 1.0
CA A:ASP181 4.4 38.6 1.0
CE1 A:HIS178 4.4 60.2 1.0
CB A:ASP152 4.4 23.9 1.0
N A:PHE154 4.5 23.1 1.0
N A:ASP155 4.7 30.0 1.0
ND1 A:HIS178 4.7 60.7 1.0
ND2 A:ASN162 4.8 28.3 1.0
CZ A:PHE138 4.8 24.9 1.0
OH A:TYR176 4.8 36.4 1.0
CA A:ASN156 4.9 32.6 1.0
CD2 A:PHE154 4.9 23.4 1.0
O A:ASP121 4.9 27.2 1.0

Calcium binding site 2 out of 9 in 4yge

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Calcium binding site 2 out of 9 in the Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2


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, Trigonal Calcium-Bound Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:49.7
occ:1.00
 OD1 A:ASN162 2.2 31.5 1.0
OD1 A:ASN161 2.4 43.8 1.0
OD1 A:ASP157 2.4 44.5 1.0
OD2 A:ASP181 2.4 38.6 1.0
OD1 A:ASP155 2.8 39.3 1.0
CG A:ASP157 3.1 42.8 1.0
CG A:ASN161 3.2 40.2 1.0
CG A:ASP181 3.3 38.2 1.0
OD2 A:ASP157 3.3 40.5 1.0
CG A:ASN162 3.4 29.4 1.0
CB A:ASP181 3.6 39.0 1.0
ND2 A:ASN161 3.6 40.2 1.0
ND2 A:ASN162 3.9 28.3 1.0
CG A:ASP155 4.0 37.9 1.0
CA A:ASP155 4.3 32.3 1.0
OD1 A:ASP181 4.4 37.9 1.0
O A:ASN161 4.4 36.6 1.0
CB A:ASP157 4.5 38.3 1.0
C A:ASN161 4.5 36.5 1.0
N A:ASP157 4.6 34.9 1.0
CB A:ASN162 4.6 30.2 1.0
CB A:ASN161 4.6 38.8 1.0
CB A:ASP155 4.7 34.2 1.0
C A:ASP155 4.7 32.9 1.0
CB A:LYS159 4.8 51.3 1.0
N A:ASN161 4.8 38.9 1.0
N A:LYS159 4.8 43.7 1.0
N A:ASN156 4.8 32.1 1.0
N A:ASN162 4.8 34.1 1.0
CG A:LYS159 4.9 59.7 1.0
CA A:ASN161 4.9 36.9 1.0
CA A:ASP157 4.9 36.4 1.0
OD2 A:ASP155 4.9 39.2 1.0
O A:ASN180 5.0 43.0 1.0

Calcium binding site 3 out of 9 in 4yge

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Calcium binding site 3 out of 9 in the Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2


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, Trigonal Calcium-Bound Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:60.0
occ:1.00
 O B:TYR135 2.4 51.4 1.0
OD1 B:ASP133 2.4 52.6 1.0
OD1 B:ASN131 2.4 57.0 1.0
OD1 B:ASP129 2.5 43.3 1.0
OE1 B:GLU140 2.7 73.1 1.0
CG B:ASP133 3.3 55.0 1.0
C B:TYR135 3.3 51.9 1.0
CG B:ASN131 3.4 61.4 1.0
CD B:GLU140 3.4 70.5 1.0
OE2 B:GLU140 3.4 80.3 1.0
OD2 B:ASP133 3.4 56.7 1.0
ND2 B:ASN131 3.6 65.5 1.0
CG B:ASP129 3.6 54.2 1.0
CA B:ILE136 4.2 52.4 1.0
CA B:TYR135 4.2 51.4 1.0
CB B:TYR135 4.2 48.1 1.0
N B:ILE136 4.2 53.5 1.0
N B:TYR135 4.3 50.4 1.0
OD2 B:ASP137 4.4 67.3 1.0
OD2 B:ASP129 4.4 42.9 1.0
CB B:ASP129 4.6 63.1 1.0
N B:ASP137 4.6 52.3 1.0
CB B:ASP133 4.6 52.2 1.0
CA B:ASP129 4.7 68.9 1.0
N B:ASP133 4.7 51.5 1.0
N B:ASN131 4.8 62.1 1.0
CB B:ASN131 4.8 58.1 1.0
CG B:GLU140 4.8 63.4 1.0
C B:ILE136 4.8 53.7 1.0
N B:LYS130 4.9 66.9 1.0
C B:ASP129 4.9 66.5 1.0

Calcium binding site 4 out of 9 in 4yge

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Calcium binding site 4 out of 9 in the Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2


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, Trigonal Calcium-Bound Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:38.1
occ:1.00
 OD1 B:ASP83 2.3 64.5 1.0
O B:LEU87 2.3 37.6 1.0
OD1 B:ASN85 2.4 42.0 1.0
OD1 B:ASP81 2.5 34.0 1.0
OE1 B:GLU92 2.5 34.1 1.0
OE2 B:GLU92 2.6 39.1 1.0
CD B:GLU92 2.8 37.4 1.0
CG B:ASP83 3.2 52.1 1.0
CG B:ASN85 3.2 43.2 1.0
OD2 B:ASP83 3.3 52.6 1.0
ND2 B:ASN85 3.4 44.1 1.0
C B:LEU87 3.5 39.7 1.0
CG B:ASP81 3.7 34.6 1.0
OD2 B:ASP89 3.8 45.4 1.0
N B:LEU87 4.2 43.8 1.0
CG B:GLU92 4.3 35.0 1.0
CA B:LEU87 4.3 42.3 1.0
N B:LEU88 4.4 39.7 1.0
CA B:LEU88 4.4 39.9 1.0
CA B:ASP81 4.4 35.0 1.0
CB B:ASN85 4.5 43.4 1.0
N B:ASP89 4.6 45.9 1.0
OD2 B:ASP81 4.6 30.9 1.0
CB B:ASP81 4.6 34.7 1.0
CB B:ASP83 4.6 45.5 1.0
N B:ASP83 4.6 37.3 1.0
N B:ASN85 4.6 45.2 1.0
CB B:LEU87 4.6 47.0 1.0
C B:ASP81 4.7 34.5 1.0
NZ A:LYS53 4.8 35.4 1.0
CG B:ASP89 4.8 46.1 1.0
N B:GLY84 4.9 36.6 1.0
N B:TYR82 4.9 34.2 1.0
CA B:ASP83 5.0 39.8 1.0
C B:LEU88 5.0 42.2 1.0

Calcium binding site 5 out of 9 in 4yge

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Calcium binding site 5 out of 9 in the Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2


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 Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:56.4
occ:1.00
 O C:PRO136 3.9 33.5 1.0
CB C:HIS178 4.2 53.8 1.0
CZ C:PHE138 4.3 33.1 1.0
CE2 C:PHE138 4.4 34.5 1.0
CE1 C:PHE138 4.4 32.0 1.0
N C:PHE138 4.5 28.7 1.0
OD1 C:ASP121 4.6 48.7 1.0
CG C:HIS178 4.6 53.2 1.0
CD2 C:PHE138 4.7 33.6 1.0
CG C:ASP121 4.7 49.1 1.0
CD1 C:PHE138 4.7 30.8 1.0
ND1 C:HIS178 4.7 55.1 1.0
CB C:ASP121 4.7 42.2 1.0
CG C:PHE138 4.8 30.0 1.0

Calcium binding site 6 out of 9 in 4yge

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Calcium binding site 6 out of 9 in the Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2


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 Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:28.1
occ:1.00
 O D:LEU87 2.3 41.5 1.0
OD1 D:ASP83 2.3 44.0 1.0
OD1 D:ASN85 2.3 37.3 1.0
OD1 D:ASP81 2.3 65.8 1.0
OE1 D:GLU92 2.4 26.7 1.0
OE2 D:GLU92 2.6 30.0 1.0
CD D:GLU92 2.8 27.8 1.0
CG D:ASN85 3.2 38.0 1.0
CG D:ASP83 3.2 40.5 1.0
OD2 D:ASP83 3.4 37.1 1.0
C D:LEU87 3.4 41.1 1.0
ND2 D:ASN85 3.5 39.4 1.0
CG D:ASP81 3.6 58.2 1.0
OD2 D:ASP89 3.9 48.2 1.0
N D:LEU87 4.2 42.4 1.0
CG D:GLU92 4.3 26.9 1.0
CA D:ASP81 4.3 44.9 1.0
CA D:LEU87 4.3 43.0 1.0
N D:LEU88 4.3 37.9 1.0
CA D:LEU88 4.4 38.7 1.0
CB D:ASP81 4.4 49.0 1.0
OD2 D:ASP81 4.4 57.8 1.0
CB D:ASN85 4.5 39.0 1.0
N D:ASN85 4.6 45.1 1.0
N D:ASP83 4.6 39.8 1.0
CB D:ASP83 4.6 39.4 1.0
C D:ASP81 4.6 42.4 1.0
N D:ASP89 4.6 35.8 1.0
CB D:LEU87 4.7 44.7 1.0
N D:TYR82 4.8 39.9 1.0
N D:GLY84 4.8 43.8 1.0
NZ C:LYS53 4.9 27.9 1.0
CG D:ASP89 4.9 42.5 1.0
CA D:ASP83 5.0 38.4 1.0
CA D:ASN85 5.0 41.0 1.0
CD2 D:LEU88 5.0 42.4 1.0

Calcium binding site 7 out of 9 in 4yge

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Calcium binding site 7 out of 9 in the Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2


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 Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:45.6
occ:1.00
 OE1 D:GLU140 2.3 67.8 1.0
OD1 D:ASN131 2.4 71.5 1.0
OD1 D:ASP129 2.5 45.2 1.0
O D:TYR135 2.5 53.1 1.0
OD1 D:ASP133 2.7 36.8 1.0
CD D:GLU140 3.0 64.8 1.0
OE2 D:GLU140 3.1 66.0 1.0
CG D:ASN131 3.4 64.0 1.0
C D:TYR135 3.5 43.9 1.0
CG D:ASP133 3.5 38.4 1.0
CG D:ASP129 3.6 56.8 1.0
OD2 D:ASP133 3.7 34.3 1.0
ND2 D:ASN131 3.7 65.9 1.0
CA D:ILE136 4.0 43.9 1.0
OD2 D:ASP137 4.1 66.0 1.0
N D:ILE136 4.2 44.7 1.0
CA D:TYR135 4.4 41.0 1.0
CG D:GLU140 4.4 60.7 1.0
CB D:TYR135 4.5 40.6 1.0
CA D:ASP129 4.5 66.1 1.0
N D:ASP137 4.5 50.7 1.0
OD2 D:ASP129 4.5 47.5 1.0
CB D:ASP129 4.5 61.5 1.0
N D:TYR135 4.5 38.8 1.0
N D:LYS130 4.6 68.1 1.0
N D:ASN131 4.6 68.1 1.0
C D:ILE136 4.7 45.5 1.0
C D:ASP129 4.7 69.2 1.0
CB D:ASN131 4.8 64.3 1.0
N D:ASP133 4.8 40.2 1.0
CB D:ASP133 4.9 38.4 1.0

Calcium binding site 8 out of 9 in 4yge

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Calcium binding site 8 out of 9 in the Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2


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 Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca501

b:22.4
occ:1.00
 O F:LEU87 2.3 28.1 1.0
OE1 F:GLU92 2.3 21.8 1.0
OD1 F:ASP83 2.4 37.4 1.0
OD1 F:ASN85 2.5 28.6 1.0
OD1 F:ASP81 2.5 25.4 1.0
OE2 F:GLU92 2.6 21.8 1.0
CD F:GLU92 2.7 22.3 1.0
CG F:ASP83 3.2 34.4 1.0
CG F:ASN85 3.3 28.5 1.0
OD2 F:ASP83 3.4 37.5 1.0
C F:LEU87 3.4 27.6 1.0
ND2 F:ASN85 3.5 28.7 1.0
OD2 F:ASP89 3.7 27.1 1.0
CG F:ASP81 3.8 25.8 1.0
CG F:GLU92 4.2 21.5 1.0
N F:LEU87 4.3 31.1 1.0
N F:LEU88 4.3 26.8 1.0
CA F:LEU88 4.3 25.9 1.0
CA F:LEU87 4.3 29.1 1.0
CA F:ASP81 4.4 26.9 1.0
N F:ASP89 4.4 22.8 1.0
CB F:ASP81 4.6 25.7 1.0
CB F:ASP83 4.6 30.6 1.0
CB F:LEU87 4.6 28.9 1.0
CB F:ASN85 4.6 29.1 1.0
N F:ASP83 4.7 27.9 1.0
OD2 F:ASP81 4.7 24.6 1.0
CG F:ASP89 4.7 26.8 1.0
C F:ASP81 4.7 25.5 1.0
N F:ASN85 4.7 31.9 1.0
NZ E:LYS53 4.8 23.9 1.0
N F:TYR82 4.9 25.3 1.0
C F:LEU88 4.9 25.2 1.0
N F:GLY84 5.0 27.2 1.0

Calcium binding site 9 out of 9 in 4yge

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Calcium binding site 9 out of 9 in the Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca502

b:32.8
occ:1.00
 OD1 F:ASN131 2.3 54.8 1.0
OD1 F:ASP129 2.5 35.4 1.0
O F:TYR135 2.5 32.1 1.0
OD1 F:ASP133 2.6 43.1 1.0
OE1 F:GLU140 2.6 37.1 1.0
OE2 F:GLU140 3.2 40.8 1.0
CD F:GLU140 3.2 38.9 1.0
CG F:ASN131 3.2 46.0 1.0
CG F:ASP133 3.4 39.4 1.0
ND2 F:ASN131 3.5 48.0 1.0
OD2 F:ASP133 3.5 37.3 1.0
C F:TYR135 3.5 34.4 1.0
CG F:ASP129 3.7 37.3 1.0
CA F:ILE136 4.2 38.0 1.0
OD2 F:ASP137 4.3 54.7 1.0
N F:ILE136 4.3 36.5 1.0
CA F:TYR135 4.4 34.3 1.0
CB F:TYR135 4.4 34.5 1.0
OD2 F:ASP129 4.5 32.3 1.0
N F:TYR135 4.5 35.3 1.0
CA F:ASP129 4.6 37.6 1.0
N F:ASN131 4.6 37.8 1.0
CB F:ASP129 4.6 37.5 1.0
N F:ASP137 4.6 36.7 1.0
CB F:ASN131 4.6 41.1 1.0
CG F:GLU140 4.6 39.8 1.0
CB F:ASP133 4.7 38.4 1.0
N F:ASP133 4.7 37.8 1.0
N F:LYS130 4.7 38.7 1.0
C F:ASP129 4.8 36.4 1.0
C F:ILE136 4.9 35.5 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 14:55:14 2024

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