Atomistry » Calcium » PDB 158d-1ai6 » 1afd
Atomistry »
  Calcium »
    PDB 158d-1ai6 »
      1afd »

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

Go back to Calcium Binding Sites List in 1afd
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

Go back to Calcium Binding Sites List in 1afd
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

Go back to Calcium Binding Sites List in 1afd
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

Go back to Calcium Binding Sites List in 1afd
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

Go back to Calcium Binding Sites List in 1afd
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

Go back to Calcium Binding Sites List in 1afd
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

Go back to Calcium Binding Sites List in 1afd
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy