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

Protein crystallography data

The structure of Crystal Structure of A Carbohydrate-Binding Domain, PDB code: 4gkx 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) 37.19 / 2.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.283, 111.498, 111.388, 60.09, 89.21, 86.25
R / Rfree (%) 24.6 / 28.6

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of A Carbohydrate-Binding Domain (pdb code 4gkx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of A Carbohydrate-Binding Domain, PDB code: 4gkx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 4gkx

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Calcium binding site 1 out of 12 in the Crystal Structure of A Carbohydrate-Binding Domain


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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:43.9
occ:1.00
O A:HOH448 2.5 33.3 1.0
OD1 A:ASP152 2.5 33.5 1.0
OD2 A:ASP152 2.5 44.0 1.0
OD1 A:ASP181 2.7 48.1 1.0
O A:PHE154 2.8 35.8 1.0
CG A:ASP152 2.8 34.1 1.0
OD1 A:ASN156 2.9 46.1 1.0
CG A:ASP181 3.6 46.4 1.0
CG A:ASN156 3.8 50.1 1.0
C A:PHE154 3.9 31.6 1.0
CB A:ASP181 4.2 33.3 1.0
CA A:ASP181 4.3 37.2 1.0
N A:ASN156 4.3 41.3 1.0
CB A:ASP152 4.3 31.4 1.0
CB A:ASN156 4.4 47.9 1.0
OD2 A:ASP181 4.4 48.5 1.0
N A:PHE154 4.4 35.1 1.0
CB A:PHE154 4.4 42.4 1.0
CA A:PHE154 4.5 34.2 1.0
NE2 A:HIS178 4.5 49.9 1.0
CE1 A:HIS178 4.5 48.7 1.0
ND2 A:ASN162 4.6 36.5 1.0
O A:HIS178 4.6 52.9 1.0
O A:HOH435 4.7 36.8 1.0
ND2 A:ASN156 4.7 57.7 1.0
OH A:TYR176 4.7 42.8 1.0
OD1 A:ASP121 4.8 42.5 1.0
N A:ASP181 4.8 38.3 1.0
HO7 A:2M4303 4.8 51.2 0.7
N A:ASP155 4.9 40.3 1.0
O A:ASP121 4.9 31.2 1.0
CD2 A:HIS178 5.0 40.5 1.0
ND1 A:HIS178 5.0 57.0 1.0

Calcium binding site 2 out of 12 in 4gkx

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Calcium binding site 2 out of 12 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:46.2
occ:1.00
OD2 A:ASP181 2.1 48.5 1.0
OD1 A:ASN162 2.2 37.9 1.0
OD1 A:ASN161 2.3 39.9 1.0
OD1 A:ASP157 2.3 47.5 1.0
OD1 A:ASP155 2.6 44.0 1.0
O A:HOH446 2.9 38.7 1.0
CG A:ASN161 2.9 36.6 1.0
ND2 A:ASN161 3.0 36.1 1.0
CG A:ASP157 3.3 47.9 1.0
CG A:ASP181 3.4 46.4 1.0
CG A:ASN162 3.4 39.2 1.0
OD2 A:ASP157 3.6 48.6 1.0
CG A:ASP155 3.7 42.4 1.0
CB A:ASP181 4.1 33.3 1.0
ND2 A:ASN162 4.1 36.5 1.0
O A:ASN161 4.1 35.5 1.0
CB A:ASN161 4.2 33.2 1.0
CA A:ASP155 4.2 43.6 1.0
C A:ASN161 4.3 38.0 1.0
N A:ASN161 4.3 41.1 1.0
CB A:LYS159 4.3 41.7 1.0
OD1 A:ASP181 4.3 48.1 1.0
CB A:ASP155 4.4 41.9 1.0
CA A:ASN161 4.5 35.6 1.0
N A:ASP157 4.5 44.3 1.0
N A:LYS159 4.5 40.8 1.0
CB A:ASN162 4.6 35.1 1.0
C A:ASP155 4.6 42.7 1.0
CG A:LYS159 4.6 44.1 1.0
OD2 A:ASP155 4.6 42.0 1.0
CB A:ASP157 4.7 47.0 1.0
N A:ASN156 4.7 41.3 1.0
N A:ASN162 4.8 35.0 1.0
N A:GLY158 4.8 50.8 1.0
CA A:LYS159 4.9 44.9 1.0
CA A:ASP157 5.0 44.8 1.0

Calcium binding site 3 out of 12 in 4gkx

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Calcium binding site 3 out of 12 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 3 of Crystal Structure of A Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:45.8
occ:1.00
OD1 B:ASP152 2.5 43.3 1.0
O B:PHE154 2.5 42.0 1.0
O B:HOH435 2.5 40.4 1.0
OD2 B:ASP152 2.5 35.2 1.0
OD1 B:ASN156 2.5 49.4 1.0
OD1 B:ASP181 2.5 39.5 1.0
CG B:ASP152 2.8 35.0 1.0
CG B:ASP181 3.4 43.4 1.0
CG B:ASN156 3.6 48.7 1.0
C B:PHE154 3.7 44.4 1.0
CB B:ASN156 4.1 50.3 1.0
N B:ASN156 4.1 52.8 1.0
CB B:ASP181 4.1 43.7 1.0
CA B:ASP181 4.2 45.9 1.0
OD2 B:ASP181 4.2 44.0 1.0
O B:HIS178 4.3 50.6 1.0
CB B:ASP152 4.3 31.0 1.0
N B:PHE154 4.4 32.3 1.0
CA B:PHE154 4.4 36.2 1.0
ND2 B:ASN162 4.6 40.5 1.0
CB B:PHE154 4.6 37.9 1.0
OH B:TYR176 4.6 39.7 1.0
ND2 B:ASN156 4.7 49.6 1.0
N B:ASP155 4.7 45.9 1.0
N B:ASP181 4.8 52.4 1.0
CA B:ASN156 4.8 49.4 1.0
CE1 B:HIS178 4.8 50.6 1.0
HO7 B:2M4303 4.9 51.3 0.7
O B:ASP121 4.9 34.8 1.0
CD2 B:PHE154 5.0 45.2 1.0
CZ B:PHE138 5.0 33.0 1.0
OD1 B:ASP121 5.0 36.6 1.0
CA B:ASP155 5.0 49.7 1.0

Calcium binding site 4 out of 12 in 4gkx

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Calcium binding site 4 out of 12 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 4 of Crystal Structure of A Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:54.1
occ:1.00
OD2 B:ASP181 2.2 44.0 1.0
OD1 B:ASN161 2.3 46.0 1.0
OD1 B:ASP157 2.3 52.0 1.0
OD1 B:ASN162 2.5 51.6 1.0
ND2 B:ASN161 2.7 52.4 1.0
CG B:ASN161 2.8 48.2 1.0
OD1 B:ASP155 3.0 50.3 1.0
CG B:ASP157 3.2 47.2 1.0
CG B:ASP181 3.3 43.4 1.0
OD2 B:ASP157 3.4 54.1 1.0
CG B:ASN162 3.7 43.7 1.0
CB B:ASP181 3.9 43.7 1.0
CG B:ASP155 4.1 53.2 1.0
CB B:ASN161 4.1 36.0 1.0
O B:ASN161 4.2 44.0 1.0
ND2 B:ASN162 4.2 40.5 1.0
C B:ASN161 4.3 48.9 1.0
OD1 B:ASP181 4.4 39.5 1.0
N B:ASN161 4.5 52.0 1.0
CA B:ASN161 4.6 45.2 1.0
CA B:ASP155 4.6 49.7 1.0
CB B:ASP157 4.6 51.1 1.0
CB B:LYS159 4.7 51.6 1.0
N B:ASP157 4.7 50.0 1.0
N B:LYS159 4.8 52.8 1.0
CB B:ASP155 4.8 52.4 1.0
CB B:ASN162 4.9 35.5 1.0
N B:ASN162 4.9 42.5 1.0
N B:ASN156 5.0 52.8 1.0
C B:ASP155 5.0 52.4 1.0

Calcium binding site 5 out of 12 in 4gkx

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Calcium binding site 5 out of 12 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 5 of Crystal Structure of A Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:56.0
occ:1.00
OD1 C:ASN156 2.2 49.6 1.0
OD2 C:ASP152 2.4 46.5 1.0
OD1 C:ASP152 2.4 47.1 1.0
O C:HOH435 2.5 44.7 1.0
O C:PHE154 2.7 48.4 1.0
CG C:ASP152 2.7 44.1 1.0
OD1 C:ASP181 2.8 55.5 1.0
CG C:ASN156 3.4 49.0 1.0
CG C:ASP181 3.6 51.7 1.0
C C:PHE154 3.9 50.2 1.0
CB C:ASP152 4.2 49.1 1.0
CB C:ASP181 4.2 46.6 1.0
CB C:ASN156 4.3 53.0 1.0
CA C:ASP181 4.3 50.4 1.0
ND2 C:ASN156 4.3 44.0 1.0
O C:HIS178 4.3 59.3 1.0
N C:ASN156 4.3 40.7 1.0
OH C:TYR176 4.4 56.0 1.0
OD2 C:ASP181 4.4 50.9 1.0
CE1 C:HIS178 4.5 55.1 1.0
N C:PHE154 4.5 43.8 1.0
CA C:PHE154 4.6 47.9 1.0
CZ C:PHE138 4.7 39.0 1.0
CB C:PHE154 4.7 49.5 1.0
ND2 C:ASN162 4.7 46.3 1.0
ND1 C:HIS178 4.8 52.7 1.0
N C:ASP181 4.8 53.3 1.0
O C:ASP121 4.8 38.5 1.0
HO7 C:2M4303 4.9 61.3 0.6
NE2 C:HIS178 4.9 49.5 1.0
N C:ASP155 4.9 50.8 1.0
CA C:ASN156 5.0 54.1 1.0
OD1 C:ASP121 5.0 51.2 1.0
CA C:ASP152 5.0 47.1 1.0

Calcium binding site 6 out of 12 in 4gkx

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Calcium binding site 6 out of 12 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 6 of Crystal Structure of A Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:63.4
occ:1.00
OD1 C:ASN161 2.2 55.7 1.0
OD2 C:ASP181 2.2 50.9 1.0
OD1 C:ASN162 2.4 49.9 1.0
OD1 C:ASP157 2.4 57.7 1.0
CG C:ASN161 2.7 57.7 1.0
ND2 C:ASN161 2.7 55.9 1.0
OD1 C:ASP155 3.0 53.3 1.0
CG C:ASP157 3.3 55.0 1.0
CG C:ASP181 3.4 51.7 1.0
OD2 C:ASP157 3.5 49.7 1.0
CG C:ASN162 3.5 44.7 1.0
CB C:ASP181 4.0 46.6 1.0
O C:ASN161 4.0 56.0 1.0
CB C:ASN161 4.0 44.5 1.0
CG C:ASP155 4.1 53.0 1.0
ND2 C:ASN162 4.1 46.3 1.0
C C:ASN161 4.2 50.4 1.0
N C:ASN161 4.3 49.3 1.0
CA C:ASN161 4.4 44.3 1.0
OD1 C:ASP181 4.4 55.5 1.0
CA C:ASP155 4.6 51.5 1.0
CB C:LYS159 4.6 55.6 1.0
CB C:ASP157 4.7 55.5 1.0
N C:ASP157 4.8 50.7 1.0
N C:LYS159 4.8 56.0 1.0
CB C:ASN162 4.8 47.1 1.0
CB C:ASP155 4.8 51.1 1.0
N C:ASN162 4.8 43.8 1.0
OD2 C:ASP155 5.0 57.7 1.0
C C:ASP155 5.0 45.1 1.0

Calcium binding site 7 out of 12 in 4gkx

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Calcium binding site 7 out of 12 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 7 of Crystal Structure of A Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:72.9
occ:1.00
OD1 D:ASN156 2.3 67.0 1.0
OD1 D:ASP152 2.4 57.6 1.0
OD2 D:ASP152 2.4 57.6 1.0
O D:HOH446 2.5 53.8 1.0
CG D:ASP152 2.7 55.3 1.0
O D:PHE154 2.8 60.7 1.0
OD1 D:ASP181 2.9 76.0 1.0
CG D:ASN156 3.5 72.8 1.0
CG D:ASP181 3.8 74.4 1.0
C D:PHE154 4.0 63.5 1.0
CB D:ASP152 4.2 51.2 1.0
CE1 D:HIS178 4.4 74.9 1.0
O D:HIS178 4.4 85.0 1.0
ND2 D:ASN156 4.4 75.8 1.0
CA D:ASP181 4.4 74.7 1.0
CB D:ASP181 4.4 77.1 1.0
CB D:ASN156 4.4 77.9 1.0
N D:PHE154 4.4 51.5 1.0
OH D:TYR176 4.4 77.9 1.0
CZ D:PHE138 4.5 44.2 1.0
N D:ASN156 4.5 72.6 1.0
CA D:PHE154 4.6 59.3 1.0
O D:ASP121 4.6 39.5 1.0
OD2 D:ASP181 4.6 77.9 1.0
ND1 D:HIS178 4.7 76.3 1.0
OD1 D:ASP121 4.8 56.1 1.0
ND2 D:ASN162 4.8 62.5 1.0
HO7 D:2M4303 4.9 74.3 0.6
NE2 D:HIS178 4.9 67.7 1.0
CE2 D:PHE138 4.9 43.5 1.0
CA D:ASP152 4.9 44.6 1.0
CB D:PHE154 4.9 60.8 1.0
N D:ASP181 5.0 71.3 1.0

Calcium binding site 8 out of 12 in 4gkx

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Calcium binding site 8 out of 12 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 8 of Crystal Structure of A Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:70.3
occ:1.00
OD2 D:ASP181 2.2 77.9 1.0
OD1 D:ASN161 2.3 79.7 1.0
OD1 D:ASN162 2.3 70.5 1.0
OD1 D:ASP157 2.5 86.7 1.0
CG D:ASN161 2.7 73.3 1.0
ND2 D:ASN161 2.8 76.7 1.0
OD1 D:ASP155 2.9 80.3 1.0
CG D:ASP181 3.3 74.4 1.0
CG D:ASP157 3.4 85.5 1.0
CG D:ASN162 3.4 62.2 1.0
OD2 D:ASP157 3.6 83.5 1.0
CB D:ASP181 3.9 77.1 1.0
O D:ASN161 4.0 67.3 1.0
CG D:ASP155 4.0 82.8 1.0
ND2 D:ASN162 4.0 62.5 1.0
CB D:ASN161 4.1 71.8 1.0
C D:ASN161 4.2 70.8 1.0
N D:ASN161 4.4 77.2 1.0
OD1 D:ASP181 4.4 76.0 1.0
CA D:ASN161 4.4 79.2 1.0
CA D:ASP155 4.5 74.8 1.0
CB D:ASP155 4.7 78.7 1.0
CB D:ASN162 4.7 61.9 1.0
N D:ASP157 4.7 85.1 1.0
CB D:LYS159 4.7 71.3 1.0
N D:ASN162 4.8 62.0 1.0
CB D:ASP157 4.8 79.0 1.0
N D:LYS159 4.8 84.2 1.0
OD2 D:ASP155 4.9 84.7 1.0
C D:ASP155 4.9 72.2 1.0
N D:ASN156 4.9 72.6 1.0

Calcium binding site 9 out of 12 in 4gkx

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Calcium binding site 9 out of 12 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 9 of Crystal Structure of A Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:57.4
occ:1.00
OD1 E:ASN156 2.2 72.9 1.0
OD1 E:ASP152 2.4 53.2 1.0
O E:HOH423 2.5 49.1 1.0
O E:PHE154 2.6 61.2 1.0
OD2 E:ASP152 2.6 55.4 1.0
CG E:ASP152 2.9 48.6 1.0
OD1 E:ASP181 2.9 72.4 1.0
CG E:ASN156 3.4 68.9 1.0
C E:PHE154 3.7 64.2 1.0
CG E:ASP181 3.8 68.1 1.0
ND2 E:ASN156 4.3 55.5 1.0
N E:PHE154 4.3 56.4 1.0
CB E:ASN156 4.3 75.3 1.0
CA E:PHE154 4.3 57.1 1.0
CB E:ASP152 4.3 40.0 1.0
N E:ASN156 4.3 68.4 1.0
CE1 E:HIS178 4.4 62.7 1.0
O E:HIS178 4.5 72.4 1.0
CB E:PHE154 4.5 58.6 1.0
CB E:ASP181 4.5 62.4 1.0
OD1 E:ASP121 4.5 50.7 1.0
CA E:ASP181 4.5 68.2 1.0
OD2 E:ASP181 4.6 74.2 1.0
O E:ASP121 4.6 46.2 1.0
OH E:TYR176 4.7 55.4 1.0
HO7 E:2M4303 4.7 74.9 0.7
ND2 E:ASN162 4.7 51.0 1.0
CZ E:PHE138 4.8 41.7 1.0
ND1 E:HIS178 4.8 69.3 1.0
N E:ASP155 4.8 64.9 1.0
NE2 E:HIS178 4.8 62.2 1.0
CD2 E:PHE154 4.8 63.3 1.0
CA E:ASN156 5.0 72.9 1.0

Calcium binding site 10 out of 12 in 4gkx

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Calcium binding site 10 out of 12 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 10 of Crystal Structure of A Carbohydrate-Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:63.7
occ:1.00
OD2 E:ASP181 2.2 74.2 1.0
OD1 E:ASP157 2.2 70.8 1.0
OD1 E:ASN161 2.3 66.0 1.0
OD1 E:ASN162 2.5 67.9 1.0
ND2 E:ASN161 2.8 80.1 1.0
CG E:ASN161 2.8 69.7 1.0
OD1 E:ASP155 2.9 67.5 1.0
CG E:ASP157 3.1 76.8 1.0
OD2 E:ASP157 3.3 73.1 1.0
CG E:ASP181 3.3 68.1 1.0
CG E:ASN162 3.7 57.8 1.0
CB E:ASP181 3.9 62.4 1.0
CG E:ASP155 4.1 69.6 1.0
CB E:ASN161 4.1 69.5 1.0
O E:ASN161 4.2 64.5 1.0
ND2 E:ASN162 4.2 51.0 1.0
C E:ASN161 4.4 72.5 1.0
OD1 E:ASP181 4.4 72.4 1.0
N E:ASN161 4.5 73.2 1.0
CB E:ASP157 4.5 78.5 1.0
CA E:ASP155 4.6 62.2 1.0
CA E:ASN161 4.6 70.8 1.0
N E:ASP157 4.6 75.3 1.0
CB E:LYS159 4.6 69.0 1.0
N E:LYS159 4.7 79.3 1.0
CB E:ASP155 4.8 63.9 1.0
N E:ASN156 4.9 68.4 1.0
CB E:ASN162 4.9 56.7 1.0
C E:ASP155 4.9 70.8 1.0
N E:ASN162 4.9 71.2 1.0
OD2 E:ASP155 4.9 70.6 1.0
N E:GLY158 5.0 80.0 1.0
CA E:ASP157 5.0 79.9 1.0
CG E:LYS159 5.0 72.5 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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