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Calcium in PDB 3a4u: Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53

Protein crystallography data

The structure of Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53, PDB code: 3a4u was solved by M.Nishio, Y.Kamiya, T.Mizushima, S.Wakatsuki, H.Sasakawa, K.Yamamoto, S.Uchiyama, M.Noda, A.R.Mckay, K.Fukui, H.P.Hauri, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.81 / 1.84
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 59.410, 59.410, 198.842, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 20

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53 (pdb code 3a4u). 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 MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53, PDB code: 3a4u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3a4u

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Calcium binding site 1 out of 4 in the Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53


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 MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca286

b:13.8
occ:1.00
OD1 A:ASP181 2.3 15.3 1.0
O A:PHE154 2.3 15.6 1.0
OD1 A:ASN156 2.3 17.2 1.0
O A:HOH4 2.4 12.2 1.0
OD1 A:ASP152 2.4 13.6 1.0
O A:HOH14 2.5 14.6 1.0
OD2 A:ASP152 2.5 14.8 1.0
CG A:ASP152 2.8 13.4 1.0
CG A:ASP181 3.3 16.7 1.0
CG A:ASN156 3.5 18.8 1.0
C A:PHE154 3.5 16.4 1.0
OD2 A:ASP181 4.0 18.3 1.0
N A:ASN156 4.1 18.4 1.0
CB A:ASN156 4.1 19.0 1.0
CB A:ASP181 4.2 16.7 1.0
CA A:PHE154 4.2 16.2 1.0
N A:PHE154 4.3 15.5 1.0
CB A:ASP152 4.3 12.0 1.0
CB A:PHE154 4.4 16.8 1.0
CA A:ASP181 4.4 16.9 1.0
O A:HIS178 4.5 20.5 1.0
ND2 A:ASN162 4.6 17.4 1.0
N A:ASP155 4.6 16.7 1.0
ND2 A:ASN156 4.6 18.6 1.0
OH A:TYR176 4.6 15.1 1.0
NE2 A:HIS178 4.7 27.7 1.0
CA A:ASN156 4.7 19.2 1.0
CZ A:PHE138 4.8 14.2 1.0
CE1 A:HIS178 4.8 27.8 1.0
CD2 A:PHE154 4.8 18.7 1.0
OD2 A:ASP121 4.8 22.8 1.0
CA A:ASP155 4.9 17.4 1.0
O A:ASP121 4.9 14.8 1.0
O A:HOH9 5.0 15.2 1.0
C A:ASP155 5.0 18.0 1.0
N A:ASP181 5.0 17.4 1.0

Calcium binding site 2 out of 4 in 3a4u

Go back to Calcium Binding Sites List in 3a4u
Calcium binding site 2 out of 4 in the Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53


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 MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca287

b:18.3
occ:1.00
OD2 A:ASP181 2.4 18.3 1.0
OD1 A:ASN161 2.4 19.5 1.0
OD1 A:ASN162 2.4 16.1 1.0
OD1 A:ASP155 2.4 17.4 1.0
O A:HOH308 2.5 20.2 1.0
O A:HOH30 2.5 21.1 1.0
OD1 A:ASP157 2.5 22.9 1.0
CG A:ASN161 3.3 20.9 1.0
CG A:ASP181 3.5 16.7 1.0
CG A:ASN162 3.5 18.2 1.0
CG A:ASP157 3.5 22.5 1.0
CG A:ASP155 3.6 18.2 1.0
ND2 A:ASN161 3.8 22.1 1.0
OD2 A:ASP157 3.9 22.8 1.0
CB A:ASP181 3.9 16.7 1.0
ND2 A:ASN162 3.9 17.4 1.0
CA A:ASP155 4.0 17.4 1.0
CB A:ASP155 4.2 17.5 1.0
CB A:LYS159 4.3 25.6 1.0
O A:ASN161 4.3 19.9 1.0
O A:HOH23 4.4 20.0 1.0
C A:ASN161 4.4 20.2 1.0
N A:LYS159 4.4 24.9 1.0
C A:ASP155 4.5 18.0 1.0
OD1 A:ASP181 4.5 15.3 1.0
OD2 A:ASP155 4.5 20.1 1.0
N A:ASN161 4.6 22.2 1.0
N A:ASP157 4.6 21.0 1.0
N A:ASN156 4.6 18.4 1.0
CB A:ASN161 4.6 21.0 1.0
CA A:ASN161 4.8 21.1 1.0
CB A:ASN162 4.8 18.1 1.0
CA A:LYS159 4.8 25.4 1.0
N A:ASN162 4.8 19.1 1.0
CB A:ASP157 4.9 21.8 1.0
N A:GLY158 5.0 23.4 1.0

Calcium binding site 3 out of 4 in 3a4u

Go back to Calcium Binding Sites List in 3a4u
Calcium binding site 3 out of 4 in the Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53


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 MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca147

b:14.1
occ:1.00
O B:LEU87 2.3 15.7 1.0
OD1 B:ASP81 2.3 15.3 1.0
O B:HOH159 2.4 13.1 1.0
OD1 B:ASP83 2.4 14.6 1.0
OD1 B:ASN85 2.4 15.2 1.0
OE1 B:GLU92 2.5 13.6 1.0
OE2 B:GLU92 2.5 13.7 1.0
CD B:GLU92 2.8 13.2 1.0
CG B:ASP83 3.3 16.6 1.0
CG B:ASN85 3.4 15.7 1.0
C B:LEU87 3.5 16.0 1.0
CG B:ASP81 3.5 16.7 1.0
OD2 B:ASP83 3.7 16.9 1.0
ND2 B:ASN85 3.9 16.2 1.0
CA B:ASP81 4.1 16.9 1.0
N B:LEU87 4.2 16.4 1.0
CB B:ASP81 4.3 16.6 1.0
N B:ASN85 4.3 16.4 1.0
CA B:LEU87 4.3 16.1 1.0
CG B:GLU92 4.4 13.1 1.0
N B:LEU88 4.4 15.4 1.0
CA B:LEU88 4.4 14.9 1.0
OD2 B:ASP81 4.4 17.3 1.0
N B:ASP83 4.5 16.9 1.0
C B:ASP81 4.5 16.8 1.0
OD2 B:ASP89 4.5 16.2 1.0
CB B:ASN85 4.6 16.4 1.0
N B:GLY84 4.6 16.7 1.0
N B:TYR82 4.6 16.9 1.0
CB B:ASP83 4.7 16.8 1.0
CB B:LEU87 4.7 16.1 1.0
O B:HOH150 4.8 16.2 1.0
N B:ASP89 4.8 13.8 1.0
CA B:ASN85 4.8 16.5 1.0
N B:ASN86 4.9 16.9 1.0
CA B:ASP83 4.9 16.9 1.0
C B:LEU88 5.0 14.6 1.0
C B:ASP83 5.0 17.0 1.0

Calcium binding site 4 out of 4 in 3a4u

Go back to Calcium Binding Sites List in 3a4u
Calcium binding site 4 out of 4 in the Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53


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 MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca148

b:22.0
occ:1.00
OD1 B:ASP129 2.4 20.8 1.0
O B:HOH152 2.4 20.7 1.0
OD1 B:ASP133 2.4 18.8 1.0
OD1 B:ASN131 2.4 26.2 1.0
O B:TYR135 2.4 17.6 1.0
O B:HOH154 2.5 22.6 1.0
O B:HOH163 2.7 24.1 1.0
CG B:ASP133 3.3 20.4 1.0
CG B:ASP129 3.4 22.6 1.0
CG B:ASN131 3.5 26.1 1.0
C B:TYR135 3.5 17.8 1.0
OD2 B:ASP133 3.6 21.5 1.0
OE1 B:GLU140 4.1 22.7 1.0
OD2 B:ASP129 4.1 21.6 1.0
ND2 B:ASN131 4.2 26.9 1.0
N B:TYR135 4.2 17.4 1.0
N B:ASN131 4.2 25.5 1.0
N B:ASP133 4.2 22.0 1.0
CA B:TYR135 4.3 17.4 1.0
OE2 B:GLU140 4.3 22.6 1.0
CA B:ASP129 4.4 24.3 1.0
CB B:ASP129 4.4 23.9 1.0
CB B:ASP133 4.4 20.7 1.0
CB B:TYR135 4.5 17.6 1.0
N B:ILE136 4.5 18.1 1.0
N B:LYS130 4.5 25.3 1.0
O B:HOH174 4.5 30.9 1.0
CB B:ASN131 4.6 25.5 1.0
C B:ASP129 4.6 24.8 1.0
N B:ASN132 4.6 24.6 1.0
CD B:GLU140 4.6 22.4 1.0
CA B:ILE136 4.7 18.7 1.0
CA B:ASN131 4.7 25.4 1.0
CA B:ASP133 4.8 20.8 1.0
C B:ASN131 4.8 25.1 1.0
N B:GLY134 4.9 18.8 1.0

Reference:

M.Nishio, Y.Kamiya, T.Mizushima, S.Wakatsuki, H.Sasakawa, K.Yamamoto, S.Uchiyama, M.Noda, A.R.Mckay, K.Fukui, H.P.Hauri, K.Kato. Structural Basis For the Cooperative Interplay Between the Two Causative Gene Products of Combined Factor V and Factor VIII Deficiency. Proc.Natl.Acad.Sci.Usa V. 107 4034 2010.
ISSN: ISSN 0027-8424
PubMed: 20142513
DOI: 10.1073/PNAS.0908526107
Page generated: Tue Jul 8 10:23:37 2025

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