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Calcium in PDB 1afd: Structural Basis of Galactose Recognition in C-Type Animal Lectins

Protein crystallography data

The structure of Structural Basis of Galactose Recognition in C-Type Animal Lectins, PDB code: 1afd was solved by A.R.Kolatkar, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.400, 84.700, 98.000, 90.00, 105.40, 90.00
R / Rfree (%) 23.4 / 28.2

Other elements in 1afd:

The structure of Structural Basis of Galactose Recognition in C-Type Animal Lectins also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural Basis of Galactose Recognition in C-Type Animal Lectins (pdb code 1afd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structural Basis of Galactose Recognition in C-Type Animal Lectins, PDB code: 1afd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1afd

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Calcium binding site 1 out of 8 in the Structural Basis of Galactose Recognition in C-Type Animal Lectins


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Basis of Galactose Recognition in C-Type Animal Lectins within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca1

b:20.5
occ:1.00
 O 1:HOH237 2.3 18.5 1.0
OD2 1:ASP161 2.4 19.2 1.0
OD1 1:ASP199 2.4 18.7 1.0
O 1:GLU198 2.5 17.2 1.0
OD1 1:ASP188 2.5 24.5 1.0
OE2 1:GLU165 2.6 24.6 1.0
OD1 1:ASP161 2.6 16.2 1.0
OE1 1:GLU165 2.7 25.2 1.0
CG 1:ASP161 2.9 15.6 1.0
CD 1:GLU165 3.0 22.5 1.0
CG 1:ASP188 3.3 22.8 1.0
C 1:GLU198 3.4 18.6 1.0
CG 1:ASP199 3.6 16.0 1.0
CA 1:ASP199 3.8 18.0 1.0
CB 1:ASP188 3.8 23.3 1.0
N 1:ASP199 3.9 19.1 1.0
OD2 1:ASP188 4.2 24.6 1.0
CB 1:ASP199 4.3 17.4 1.0
N 1:GLU198 4.3 21.4 1.0
CB 1:ASP161 4.4 17.4 1.0
CA 1:ASP188 4.4 26.0 1.0
CG 1:GLU165 4.5 20.6 1.0
CA 1:GLU198 4.5 19.1 1.0
OD2 1:ASP199 4.6 18.5 1.0
O 1:HOH256 4.6 25.1 1.0
OD2 1:ASP211 4.6 20.7 1.0
CZ 1:PHE168 4.7 21.0 1.0
O 1:ASP161 4.7 21.1 1.0
N 1:GLY166 4.7 19.4 1.0
O 1:HOH236 4.7 19.6 1.0
C 1:ASP199 5.0 18.3 1.0

Calcium binding site 2 out of 8 in 1afd

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Calcium binding site 2 out of 8 in the Structural Basis of Galactose Recognition in C-Type Animal Lectins


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Basis of Galactose Recognition in C-Type Animal Lectins within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca2

b:24.5
occ:1.00
 OE1 1:GLU198 2.2 24.7 1.0
OD1 1:ASP211 2.3 27.5 1.0
OD1 1:ASP187 2.4 28.5 1.0
OE1 1:GLN185 2.4 31.1 1.0
O 1:ASP211 2.6 19.9 1.0
OD1 1:ASN210 2.9 46.3 1.0
O 1:HOH355 2.9 37.5 1.0
CD 1:GLU198 3.3 14.3 1.0
CG 1:ASP211 3.3 23.1 1.0
CG 1:ASP187 3.4 26.2 1.0
CD 1:GLN185 3.5 27.6 1.0
C 1:ASP211 3.6 21.1 1.0
OE2 1:GLU198 3.6 21.1 1.0
O 1:HOH354 3.7 38.8 1.0
N 1:ASP211 3.8 18.9 1.0
CG 1:ASN210 3.9 39.3 1.0
OD2 1:ASP187 3.9 26.4 1.0
NE2 1:GLN185 3.9 23.0 1.0
OD2 1:ASP211 4.0 20.7 1.0
CA 1:ASP211 4.1 17.4 1.0
N 1:ASP187 4.2 24.0 1.0
CB 1:ASP211 4.3 20.4 1.0
ND2 1:ASN210 4.4 46.6 1.0
CB 1:TRP189 4.5 30.6 1.0
CG 1:GLU198 4.5 15.9 1.0
C 1:ASN210 4.6 20.3 1.0
CB 1:ASP187 4.7 25.4 1.0
CB 1:GLU198 4.7 19.4 1.0
CG 1:GLN185 4.7 21.8 1.0
N 1:ILE212 4.7 20.6 1.0
N 1:TRP189 4.8 25.0 1.0
N 1:ASP188 4.8 24.6 1.0
CA 1:ASP187 4.9 24.9 1.0

Calcium binding site 3 out of 8 in 1afd

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Calcium binding site 3 out of 8 in the Structural Basis of Galactose Recognition in C-Type Animal Lectins


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Basis of Galactose Recognition in C-Type Animal Lectins within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca3

b:23.0
occ:1.00
 O 1:HOH350 2.3 17.7 1.0
O 1:HOH288 2.3 31.9 1.0
OE2 1:GLU84 2.5 28.5 1.0
CD 1:GLU84 3.6 26.8 1.0
OE1 1:GLU84 4.0 23.5 1.0
OD1 1:ASN80 4.4 22.1 1.0
ND2 1:ASN80 4.6 16.5 1.0
O 1:HOH291 4.6 27.6 1.0
CG 1:GLU84 4.8 25.8 1.0
CG 1:ASN80 4.9 19.0 1.0
O 1:HOH371 5.0 33.0 1.0

Calcium binding site 4 out of 8 in 1afd

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Calcium binding site 4 out of 8 in the Structural Basis of Galactose Recognition in C-Type Animal Lectins


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Basis of Galactose Recognition in C-Type Animal Lectins within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca1

b:46.4
occ:1.00
 OE1 2:GLU165 2.4 48.1 1.0
OD2 2:ASP161 2.4 46.5 1.0
OD1 2:ASP188 2.6 44.9 1.0
O 2:GLU198 2.6 52.7 1.0
OD1 2:ASP199 2.7 43.6 1.0
O 2:HOH245 2.8 40.1 1.0
OD1 2:ASP161 2.9 39.9 1.0
CG 2:ASP161 3.0 43.7 1.0
CG 2:ASP188 3.2 53.5 1.0
CD 2:GLU165 3.4 51.9 1.0
C 2:GLU198 3.5 53.3 1.0
CG 2:ASP199 3.7 44.4 1.0
CA 2:ASP199 3.8 47.7 1.0
CB 2:ASP188 3.8 58.0 1.0
OE2 2:GLU165 3.8 44.1 1.0
OD2 2:ASP188 4.0 52.4 1.0
N 2:ASP199 4.0 50.0 1.0
O 2:HOH254 4.2 26.4 1.0
CB 2:ASP199 4.3 46.5 1.0
OD2 2:ASP211 4.4 27.3 1.0
CZ 2:PHE168 4.5 50.9 1.0
CB 2:ASP161 4.5 42.5 1.0
N 2:GLU198 4.6 59.2 1.0
CA 2:GLU198 4.6 55.4 1.0
OD2 2:ASP199 4.6 49.0 1.0
CA 2:ASP188 4.6 65.9 1.0
CG 2:GLU165 4.7 53.0 1.0
CB 2:GLU165 4.8 55.1 1.0
CA 2:GLU165 4.8 52.6 1.0
N 2:GLY166 4.8 53.7 1.0
C 2:ASP199 4.8 47.3 1.0
O 2:ASP161 4.9 45.5 1.0
CE2 2:PHE168 4.9 51.4 1.0

Calcium binding site 5 out of 8 in 1afd

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Calcium binding site 5 out of 8 in the Structural Basis of Galactose Recognition in C-Type Animal Lectins


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural Basis of Galactose Recognition in C-Type Animal Lectins within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca2

b:45.8
occ:1.00
 OE1 2:GLU198 2.1 51.8 1.0
O 2:ASP211 2.4 40.7 1.0
OD1 2:ASP211 2.4 36.0 1.0
OD1 2:ASP187 2.5 49.9 1.0
OD1 2:ASN210 2.7 60.8 1.0
OE1 2:GLN185 2.9 38.1 1.0
CD 2:GLU198 3.1 53.1 1.0
CG 2:ASP187 3.4 48.8 1.0
OE2 2:GLU198 3.4 52.9 1.0
CG 2:ASP211 3.4 39.6 1.0
C 2:ASP211 3.5 42.6 1.0
CG 2:ASN210 3.6 55.1 1.0
OD2 2:ASP187 3.7 46.5 1.0
N 2:ASP211 3.7 41.8 1.0
CD 2:GLN185 3.8 39.9 1.0
NE2 2:GLN185 3.9 42.6 1.0
CA 2:ASP211 4.0 41.6 1.0
ND2 2:ASN210 4.1 58.4 1.0
OD2 2:ASP211 4.2 27.3 1.0
CB 2:ASP211 4.3 40.0 1.0
CG 2:GLU198 4.4 54.0 1.0
N 2:ASP187 4.5 52.4 1.0
C 2:ASN210 4.6 43.3 1.0
CB 2:GLU198 4.6 55.7 1.0
N 2:ILE212 4.6 42.4 1.0
N 2:ASP188 4.6 61.8 1.0
CB 2:ASP187 4.7 52.3 1.0
N 2:TRP189 4.7 76.4 1.0
CB 2:ASN210 4.8 48.6 1.0
CB 2:TRP189 4.9 85.9 1.0
CA 2:ILE212 4.9 44.3 1.0
CA 2:ASN210 5.0 44.0 1.0

Calcium binding site 6 out of 8 in 1afd

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Calcium binding site 6 out of 8 in the Structural Basis of Galactose Recognition in C-Type Animal Lectins


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structural Basis of Galactose Recognition in C-Type Animal Lectins within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca1

b:29.8
occ:1.00
 O 3:GLU198 2.3 23.0 1.0
OD2 3:ASP161 2.4 27.4 1.0
OD1 3:ASP199 2.4 24.6 1.0
OD1 3:ASP188 2.5 26.1 1.0
O 3:HOH231 2.5 26.5 1.0
OE1 3:GLU165 2.7 24.2 1.0
OE2 3:GLU165 2.7 20.4 1.0
OD1 3:ASP161 2.7 27.1 1.0
CG 3:ASP161 2.9 24.4 1.0
CD 3:GLU165 3.0 20.9 1.0
C 3:GLU198 3.3 21.9 1.0
CG 3:ASP188 3.4 23.6 1.0
CG 3:ASP199 3.6 19.1 1.0
CA 3:ASP199 3.7 21.2 1.0
CB 3:ASP188 3.9 28.1 1.0
N 3:ASP199 3.9 21.2 1.0
CB 3:ASP199 4.2 19.9 1.0
N 3:GLU198 4.3 25.9 1.0
CB 3:ASP161 4.4 24.7 1.0
OD2 3:ASP188 4.4 23.0 1.0
CA 3:GLU198 4.4 23.2 1.0
CA 3:ASP188 4.4 32.6 1.0
OD2 3:ASP199 4.5 21.3 1.0
CG 3:GLU165 4.5 19.3 1.0
OD2 3:ASP211 4.6 25.9 1.0
CZ 3:PHE168 4.6 23.0 1.0
O 3:ASP161 4.7 26.1 1.0
O 3:HOH239 4.7 35.7 1.0
N 3:GLY166 4.7 31.0 1.0
O 3:HOH238 4.8 24.8 1.0
C 3:ASP199 4.9 21.7 1.0

Calcium binding site 7 out of 8 in 1afd

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Calcium binding site 7 out of 8 in the Structural Basis of Galactose Recognition in C-Type Animal Lectins


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structural Basis of Galactose Recognition in C-Type Animal Lectins within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca2

b:30.8
occ:1.00
 OD1 3:ASP211 2.2 24.4 1.0
OE1 3:GLU198 2.3 23.6 1.0
O 3:ASP211 2.5 27.9 1.0
OD1 3:ASP187 2.5 39.8 1.0
OE1 3:GLN185 2.6 39.8 1.0
OD1 3:ASN210 2.9 48.5 1.0
CG 3:ASP211 3.3 23.0 1.0
CD 3:GLU198 3.3 25.1 1.0
O 3:HOH323 3.4 48.2 1.0
CD 3:GLN185 3.5 39.4 1.0
C 3:ASP211 3.6 27.8 1.0
CG 3:ASP187 3.6 39.1 1.0
OE2 3:GLU198 3.8 25.6 1.0
NE2 3:GLN185 3.8 40.0 1.0
N 3:ASP211 3.9 30.4 1.0
CG 3:ASN210 3.9 46.3 1.0
OD2 3:ASP211 3.9 25.9 1.0
OD2 3:ASP187 4.0 38.3 1.0
CA 3:ASP211 4.1 27.0 1.0
CB 3:ASP211 4.3 24.2 1.0
N 3:ASP187 4.3 36.5 1.0
ND2 3:ASN210 4.4 51.9 1.0
CB 3:TRP189 4.5 35.0 1.0
CG 3:GLU198 4.5 24.2 1.0
CB 3:GLU198 4.6 24.1 1.0
N 3:ILE212 4.7 24.8 1.0
C 3:ASN210 4.7 31.7 1.0
N 3:TRP189 4.7 32.7 1.0
N 3:ASP188 4.7 34.4 1.0
CB 3:ASP187 4.8 37.6 1.0
CG 3:GLN185 4.9 33.7 1.0
CA 3:ASP187 4.9 37.5 1.0

Calcium binding site 8 out of 8 in 1afd

Go back to Calcium Binding Sites List in 1afd
Calcium binding site 8 out of 8 in the Structural Basis of Galactose Recognition in C-Type Animal Lectins


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structural Basis of Galactose Recognition in C-Type Animal Lectins within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca3

b:23.2
occ:1.00
 O 3:HOH266 2.3 21.0 1.0
O 1:HOH248 2.3 21.7 1.0
OE2 3:GLU84 2.3 24.3 1.0
O 3:HOH257 2.6 30.8 1.0
CD 3:GLU84 3.5 23.9 1.0
OE1 3:GLU84 4.0 27.8 1.0
NZ 1:LYS89 4.4 29.0 1.0
ND2 3:ASN80 4.4 21.9 1.0
OD1 3:ASN80 4.5 25.2 1.0
O 1:HOH283 4.5 38.6 1.0
CG 3:GLU84 4.6 16.1 1.0
O 1:HOH249 4.7 27.1 1.0
O 3:HOH267 4.9 35.9 1.0
CG 3:ASN80 4.9 23.9 1.0

Reference:

A.R.Kolatkar, W.I.Weis. Structural Basis of Galactose Recognition By C-Type Animal Lectins. J.Biol.Chem. V. 271 6679 1996.
ISSN: ISSN 0021-9258
PubMed: 8636086
DOI: 10.1074/JBC.271.12.6679
Page generated: Thu Jul 11 05:49:45 2024

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