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Calcium in PDB 1afb: 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: 1afb 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 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.800, 84.500, 97.100, 90.00, 104.30, 90.00
R / Rfree (%) 21.7 / 26.1

Other elements in 1afb:

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 1afb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Structural Basis of Galactose Recognition in C-Type Animal Lectins, PDB code: 1afb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1afb

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Calcium binding site 1 out of 9 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:Ca227

b:23.7
occ:1.00
 OD2 1:ASP161 2.3 21.0 1.0
OD1 1:ASP199 2.4 19.9 1.0
O 1:GLU198 2.4 19.4 1.0
O 1:HOH261 2.5 25.2 1.0
OE1 1:GLU165 2.6 23.0 1.0
OD1 1:ASP161 2.6 19.9 1.0
OE2 1:GLU165 2.7 21.4 1.0
OD1 1:ASP188 2.7 24.5 1.0
CG 1:ASP161 2.8 22.6 1.0
CD 1:GLU165 3.0 24.2 1.0
CG 1:ASP188 3.4 28.1 1.0
C 1:GLU198 3.4 19.7 1.0
CG 1:ASP199 3.5 20.6 1.0
CA 1:ASP199 3.8 20.5 1.0
CB 1:ASP188 3.8 26.6 1.0
N 1:ASP199 4.0 17.9 1.0
O 1:HOH297 4.0 35.6 1.0
CB 1:ASP199 4.2 19.7 1.0
OD2 1:ASP188 4.3 25.8 1.0
CB 1:ASP161 4.3 24.8 1.0
CA 1:ASP188 4.4 27.0 1.0
N 1:GLU198 4.4 24.1 1.0
CZ 1:PHE168 4.4 26.2 1.0
CG 1:GLU165 4.5 21.9 1.0
OD2 1:ASP199 4.5 22.7 1.0
CA 1:GLU198 4.6 21.9 1.0
N 1:GLY166 4.6 25.2 1.0
O 1:HOH276 4.6 34.4 1.0
O 1:ASP161 4.8 24.3 1.0
OD2 1:ASP211 4.8 22.5 1.0
O 1:HOH262 4.8 29.0 1.0
C 1:ASP199 4.9 21.4 1.0
CA 1:GLU165 5.0 24.0 1.0
CE1 1:PHE168 5.0 24.2 1.0

Calcium binding site 2 out of 9 in 1afb

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Calcium binding site 2 out of 9 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:24.2
occ:1.00
 OD1 1:ASP211 2.2 23.4 1.0
OE1 1:GLU198 2.3 23.9 1.0
OD1 1:ASN210 2.4 27.1 1.0
OD1 1:ASP187 2.4 24.2 1.0
O 1:ASP211 2.5 21.6 1.0
OE1 1:GLN185 2.6 27.6 1.0
O3 1:NGA1 2.6 30.3 1.0
O4 1:NGA1 2.7 27.8 1.0
CG 1:ASP211 3.3 22.1 1.0
CD 1:GLU198 3.4 19.6 1.0
CD 1:GLN185 3.4 27.8 1.0
CG 1:ASN210 3.4 23.4 1.0
CG 1:ASP187 3.5 24.5 1.0
C4 1:NGA1 3.5 31.6 1.0
C3 1:NGA1 3.6 32.2 1.0
C 1:ASP211 3.6 22.1 1.0
N 1:ASP211 3.7 22.2 1.0
ND2 1:ASN210 3.8 16.4 1.0
OE2 1:GLU198 3.8 22.0 1.0
NE2 1:GLN185 3.8 23.9 1.0
OD2 1:ASP187 3.9 23.4 1.0
OD2 1:ASP211 4.0 22.5 1.0
CA 1:ASP211 4.1 22.3 1.0
N 1:ASP187 4.2 26.9 1.0
CB 1:ASP211 4.3 19.2 1.0
C2 1:NGA1 4.4 35.5 1.0
CG 1:GLN185 4.5 25.9 1.0
C 1:ASN210 4.6 22.3 1.0
CG 1:GLU198 4.6 19.4 1.0
CB 1:ASP187 4.6 26.0 1.0
N 1:ILE212 4.7 21.6 1.0
CB 1:TRP189 4.7 27.8 1.0
CB 1:ASN210 4.7 20.0 1.0
CB 1:GLU198 4.7 19.4 1.0
CA 1:ASP187 4.8 26.6 1.0
N 1:ASP188 4.9 26.7 1.0
C5 1:NGA1 4.9 33.5 1.0
CA 1:ASN210 4.9 22.0 1.0
CB 1:GLN185 4.9 25.5 1.0
N 1:TRP189 5.0 26.2 1.0

Calcium binding site 3 out of 9 in 1afb

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Calcium binding site 3 out of 9 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:23.6
occ:1.00
 O 1:HOH229 2.3 20.5 1.0
OE2 1:GLU84 2.4 23.2 1.0
CD 1:GLU84 3.6 23.6 1.0
OE1 1:GLU84 4.1 26.5 1.0
OD1 1:ASN80 4.5 23.9 1.0
O 1:HOH311 4.6 28.1 1.0
CG 1:GLU84 4.8 19.7 1.0
ND2 1:ASN80 4.8 17.9 1.0

Calcium binding site 4 out of 9 in 1afb

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Calcium binding site 4 out of 9 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:33.7
occ:1.00
 OD2 2:ASP161 2.3 31.9 1.0
O 2:GLU198 2.5 34.9 1.0
OD1 2:ASP199 2.5 34.7 1.0
OE2 2:GLU165 2.6 33.8 1.0
OE1 2:GLU165 2.7 35.7 1.0
OD1 2:ASP161 2.7 40.2 1.0
OD1 2:ASP188 2.7 39.4 1.0
CG 2:ASP161 2.9 37.7 1.0
CD 2:GLU165 3.0 35.5 1.0
CG 2:ASP188 3.4 35.8 1.0
C 2:GLU198 3.5 34.4 1.0
CG 2:ASP199 3.7 35.0 1.0
CA 2:ASP199 3.7 33.0 1.0
CA 2:CA3 3.9 39.1 1.0
CB 2:ASP188 4.0 35.7 1.0
N 2:ASP199 4.0 33.8 1.0
OD2 2:ASP188 4.1 34.3 1.0
CB 2:ASP199 4.2 33.4 1.0
CB 2:ASP161 4.4 34.9 1.0
CZ 2:PHE168 4.4 31.9 1.0
CG 2:GLU165 4.5 35.3 1.0
N 2:GLU198 4.5 38.9 1.0
CA 2:ASP188 4.5 39.0 1.0
CA 2:GLU198 4.6 35.4 1.0
O 2:HOH305 4.6 41.0 1.0
N 2:GLY166 4.6 35.4 1.0
OD2 2:ASP211 4.7 29.4 1.0
OD2 2:ASP199 4.7 37.4 1.0
O 2:ASP161 4.8 39.7 1.0
C 2:ASP199 4.9 32.6 1.0
O 2:HOH303 4.9 22.7 1.0
CA 2:GLU165 4.9 35.8 1.0
CE1 2:PHE168 5.0 31.3 1.0
CE2 2:PHE168 5.0 33.4 1.0

Calcium binding site 5 out of 9 in 1afb

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Calcium binding site 5 out of 9 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:Ca227

b:42.1
occ:1.00
 OD1 2:ASP211 2.2 27.8 1.0
OE1 2:GLU198 2.3 36.7 1.0
OD1 2:ASP187 2.5 44.9 1.0
O 2:ASP211 2.6 35.1 1.0
OE1 2:GLN185 2.6 38.5 1.0
OD1 2:ASN210 2.7 43.1 1.0
O4 2:NGA2 2.8 52.1 1.0
O3 2:NGA2 2.8 48.8 1.0
CG 2:ASP211 3.2 32.8 1.0
CD 2:GLU198 3.3 35.6 1.0
CD 2:GLN185 3.4 40.7 1.0
CG 2:ASP187 3.5 45.5 1.0
C4 2:NGA2 3.5 53.0 1.0
C 2:ASP211 3.6 36.0 1.0
CG 2:ASN210 3.6 41.1 1.0
C3 2:NGA2 3.7 52.6 1.0
NE2 2:GLN185 3.7 39.1 1.0
N 2:ASP211 3.8 38.0 1.0
OE2 2:GLU198 3.8 37.0 1.0
OD2 2:ASP211 3.9 29.4 1.0
ND2 2:ASN210 3.9 39.1 1.0
OD2 2:ASP187 4.0 47.7 1.0
CA 2:ASP211 4.0 35.8 1.0
CB 2:ASP211 4.2 36.6 1.0
N 2:ASP187 4.3 41.9 1.0
C2 2:NGA2 4.4 55.7 1.0
CG 2:GLU198 4.6 33.0 1.0
C 2:ASN210 4.6 39.3 1.0
CG 2:GLN185 4.6 39.4 1.0
CB 2:ASP187 4.7 42.5 1.0
CB 2:GLU198 4.7 32.2 1.0
N 2:ILE212 4.7 36.0 1.0
N 2:ASP188 4.8 40.4 1.0
CB 2:TRP189 4.8 46.6 1.0
CB 2:ASN210 4.9 39.5 1.0
N 2:TRP189 4.9 41.4 1.0
CA 2:ASP187 4.9 41.8 1.0
C5 2:NGA2 5.0 55.0 1.0
CA 2:ASN210 5.0 40.5 1.0

Calcium binding site 6 out of 9 in 1afb

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Calcium binding site 6 out of 9 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
2:Ca3

b:39.1
occ:1.00
 O 2:HOH303 2.2 22.7 1.0
OE1 2:GLU165 2.3 35.7 1.0
OD1 2:ASP199 2.4 34.7 1.0
OD2 2:ASP199 2.6 37.4 1.0
CG 2:ASP199 2.8 35.0 1.0
O 2:HOH304 2.9 38.8 1.0
CD 2:GLU165 3.5 35.5 1.0
CA 2:CA1 3.9 33.7 1.0
CB 2:GLU165 4.2 34.5 1.0
OD1 2:ASP188 4.2 39.4 1.0
CG 2:GLU165 4.3 35.3 1.0
O 2:ASP161 4.3 39.7 1.0
O 2:HOH315 4.3 44.6 1.0
CB 2:ASP199 4.3 33.4 1.0
OE2 2:GLU165 4.4 33.8 1.0
CA 2:GLU165 4.5 35.8 1.0
OD2 2:ASP188 4.5 34.3 1.0
OD2 2:ASP161 4.7 31.9 1.0
CG 2:ASP188 4.8 35.8 1.0
OH 2:TYR190 4.8 49.7 1.0
O 2:GLU162 4.9 39.0 1.0
N 2:GLU165 5.0 35.3 1.0
OD1 2:ASP161 5.0 40.2 1.0

Calcium binding site 7 out of 9 in 1afb

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Calcium binding site 7 out of 9 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:Ca1

b:25.4
occ:1.00
 OD2 3:ASP161 2.3 24.1 1.0
OD1 3:ASP199 2.4 27.3 1.0
O 3:HOH259 2.4 26.2 1.0
O 3:GLU198 2.5 23.2 1.0
OE1 3:GLU165 2.5 21.6 1.0
OD1 3:ASP188 2.6 24.1 1.0
OE2 3:GLU165 2.6 21.4 1.0
OD1 3:ASP161 2.6 23.8 1.0
CG 3:ASP161 2.8 23.4 1.0
CD 3:GLU165 2.9 20.9 1.0
CG 3:ASP188 3.4 23.2 1.0
C 3:GLU198 3.4 22.3 1.0
CG 3:ASP199 3.5 25.3 1.0
CA 3:ASP199 3.8 21.4 1.0
CB 3:ASP188 3.9 25.2 1.0
N 3:ASP199 4.0 21.1 1.0
CB 3:ASP199 4.2 22.3 1.0
OD2 3:ASP188 4.2 20.1 1.0
CB 3:ASP161 4.3 22.1 1.0
N 3:GLU198 4.4 23.4 1.0
OD2 3:ASP199 4.4 22.4 1.0
CZ 3:PHE168 4.4 21.2 1.0
CG 3:GLU165 4.5 23.1 1.0
CA 3:ASP188 4.5 26.0 1.0
CA 3:GLU198 4.5 23.9 1.0
N 3:GLY166 4.6 28.6 1.0
O 3:HOH231 4.6 32.0 1.0
O 3:ASP161 4.7 22.7 1.0
OD2 3:ASP211 4.8 22.8 1.0
O 3:HOH263 4.8 25.6 1.0
CA 3:GLU165 4.9 26.8 1.0
CE1 3:PHE168 4.9 20.9 1.0
C 3:ASP199 4.9 20.9 1.0

Calcium binding site 8 out of 9 in 1afb

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Calcium binding site 8 out of 9 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:Ca2

b:25.3
occ:1.00
 OD1 3:ASP211 2.3 23.6 1.0
OE1 3:GLU198 2.4 23.2 1.0
OD1 3:ASP187 2.4 24.8 1.0
OD1 3:ASN210 2.5 24.1 1.0
O 3:ASP211 2.5 23.2 1.0
O3 3:NGA3 2.5 26.3 1.0
OE1 3:GLN185 2.5 31.9 1.0
O4 3:NGA3 2.6 29.9 1.0
C4 3:NGA3 3.3 31.6 1.0
CG 3:ASP211 3.3 24.0 1.0
CG 3:ASP187 3.4 28.0 1.0
CD 3:GLU198 3.4 20.5 1.0
CD 3:GLN185 3.4 31.2 1.0
C3 3:NGA3 3.4 32.1 1.0
CG 3:ASN210 3.5 24.6 1.0
C 3:ASP211 3.6 24.1 1.0
OE2 3:GLU198 3.7 21.3 1.0
N 3:ASP211 3.8 26.4 1.0
OD2 3:ASP187 3.8 30.0 1.0
NE2 3:GLN185 3.8 28.0 1.0
ND2 3:ASN210 3.9 22.3 1.0
OD2 3:ASP211 4.1 22.8 1.0
CA 3:ASP211 4.1 23.0 1.0
C2 3:NGA3 4.2 36.2 1.0
N 3:ASP187 4.2 29.7 1.0
CB 3:ASP211 4.3 24.3 1.0
CB 3:ASP187 4.6 28.4 1.0
CG 3:GLN185 4.6 26.5 1.0
CG 3:GLU198 4.7 21.8 1.0
C 3:ASN210 4.7 25.1 1.0
N 3:ILE212 4.7 19.8 1.0
CB 3:TRP189 4.7 28.7 1.0
C5 3:NGA3 4.7 34.7 1.0
CA 3:ASP187 4.8 29.5 1.0
CB 3:ASN210 4.8 22.8 1.0
CB 3:GLU198 4.8 22.5 1.0
N 3:ASP188 4.8 27.6 1.0
N 3:TRP189 4.9 28.6 1.0
N2 3:NGA3 5.0 35.5 1.0
CA 3:ASN210 5.0 25.2 1.0

Calcium binding site 9 out of 9 in 1afb

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Calcium binding site 9 out of 9 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 9 of Structural Basis of Galactose Recognition in C-Type Animal Lectins within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca227

b:21.3
occ:1.00
 O 1:HOH250 2.2 25.2 1.0
O 3:HOH228 2.3 20.9 1.0
OE2 3:GLU84 2.4 23.2 1.0
O 3:HOH335 2.5 26.3 1.0
CD 3:GLU84 3.5 24.3 1.0
OE1 3:GLU84 4.0 26.3 1.0
NZ 1:LYS89 4.3 28.9 1.0
O 3:HOH240 4.5 28.6 1.0
OD1 3:ASN80 4.5 24.5 1.0
ND2 3:ASN80 4.6 23.6 1.0
O 1:HOH249 4.6 39.9 1.0
O 3:HOH311 4.7 29.7 1.0
CG 3:GLU84 4.8 19.8 1.0
CG 3:ASN80 5.0 23.1 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 05:49:17 2024

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