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Calcium in PDB 4gky: Crystal Structure of A Carbohydrate-Binding Domain

Protein crystallography data

The structure of Crystal Structure of A Carbohydrate-Binding Domain, PDB code: 4gky was solved by R.C.Page, C.Zheng, J.C.Nix, S.Misra, B.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.33 / 2.42
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 110.263, 110.263, 38.332, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 21.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Carbohydrate-Binding Domain (pdb code 4gky). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A Carbohydrate-Binding Domain, PDB code: 4gky:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4gky

Go back to Calcium Binding Sites List in 4gky
Calcium binding site 1 out of 2 in the Crystal Structure of A Carbohydrate-Binding Domain


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 A Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:58.5
occ:1.00
OD1 A:ASP181 2.3 66.1 1.0
O A:PHE154 2.5 60.4 1.0
OD2 A:ASP152 2.6 60.5 1.0
O A:HOH443 2.6 63.0 1.0
O A:HOH442 2.6 56.5 1.0
OD1 A:ASP152 2.7 57.1 1.0
OD1 A:ASN156 2.9 68.0 1.0
CG A:ASP152 3.0 55.0 1.0
CG A:ASP181 3.3 61.0 1.0
C A:PHE154 3.7 60.0 1.0
CG A:ASN156 3.7 67.7 1.0
CB A:ASN156 3.9 61.3 1.0
OD2 A:ASP181 3.9 59.4 1.0
O A:HIS178 4.0 67.9 1.0
N A:ASN156 4.1 66.0 1.0
CB A:ASP181 4.2 62.2 1.0
CA A:PHE154 4.4 53.0 1.0
CA A:ASP181 4.4 62.5 1.0
CB A:PHE154 4.4 56.9 1.0
CE1 A:HIS178 4.5 73.2 1.0
N A:PHE154 4.5 51.1 1.0
CB A:ASP152 4.5 49.6 1.0
ND2 A:ASN162 4.5 57.1 1.0
ND1 A:HIS178 4.6 74.5 1.0
CD2 A:PHE154 4.6 59.7 1.0
CA A:ASN156 4.7 66.3 1.0
OD1 A:ASP121 4.7 59.8 1.0
N A:ASP155 4.7 62.3 1.0
OH A:TYR176 4.8 50.0 1.0
CZ A:PHE138 4.8 52.7 1.0
N A:ASP181 4.9 67.7 1.0
ND2 A:ASN156 5.0 73.7 1.0
CA A:ASP155 5.0 65.1 1.0
O A:HOH441 5.0 56.6 1.0
C A:ASP155 5.0 62.6 1.0

Calcium binding site 2 out of 2 in 4gky

Go back to Calcium Binding Sites List in 4gky
Calcium binding site 2 out of 2 in the Crystal Structure of A Carbohydrate-Binding Domain


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 A Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:68.0
occ:1.00
OD1 A:ASN161 2.3 63.5 1.0
OD2 A:ASP181 2.4 59.4 1.0
OD1 A:ASN162 2.5 67.5 1.0
OD1 A:ASP157 2.6 77.6 1.0
OD1 A:ASP155 2.6 69.0 1.0
O A:HOH444 2.7 71.6 1.0
OD2 A:ASP157 2.9 78.8 1.0
CG A:ASP157 3.0 75.4 1.0
CG A:ASN161 3.2 61.8 1.0
CG A:ASN162 3.4 61.5 1.0
CG A:ASP181 3.5 61.0 1.0
CG A:ASP155 3.5 69.7 1.0
ND2 A:ASN161 3.5 63.1 1.0
ND2 A:ASN162 3.7 57.1 1.0
CB A:ASP181 3.9 62.2 1.0
CA A:ASP155 4.1 65.1 1.0
CB A:ASP155 4.2 64.3 1.0
OD2 A:ASP155 4.4 72.6 1.0
CB A:ASP157 4.4 73.5 1.0
CB A:ASN161 4.5 58.9 1.0
N A:ASP157 4.5 72.3 1.0
CB A:LYS159 4.5 68.6 1.0
OD1 A:ASP181 4.6 66.1 1.0
N A:ASN161 4.6 65.3 1.0
N A:ASN156 4.6 66.0 1.0
C A:ASP155 4.7 62.6 1.0
C A:ASN161 4.7 65.5 1.0
N A:LYS159 4.7 71.8 1.0
CB A:ASN162 4.7 55.2 1.0
CA A:ASN161 4.8 62.7 1.0
CA A:ASP157 4.9 76.1 1.0
N A:ASN162 4.9 62.2 1.0
O A:ASN161 5.0 66.8 1.0
CG A:LYS159 5.0 76.9 1.0

Reference:

C.Zheng, R.C.Page, V.Das, J.C.Nix, E.Wigren, S.Misra, B.Zhang. Structural Characterization of Carbohydrate Binding By LMAN1 Protein Provides New Insight Into the Endoplasmic Reticulum Export of Factors V (Fv) and VIII (Fviii). J.Biol.Chem. V. 288 20499 2013.
ISSN: ISSN 0021-9258
PubMed: 23709226
DOI: 10.1074/JBC.M113.461434
Page generated: Sat Dec 12 04:48:16 2020

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