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

Calcium in PDB 1afa: 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: 1afa 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 (°) 80.700, 84.400, 97.500, 90.00, 104.00, 90.00
R / Rfree (%) 22.1 / 26.8

Other elements in 1afa:

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 1afa). 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: 1afa:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1afa

Go back to Calcium Binding Sites List in 1afa
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:21.0
occ:1.00
 OD2 1:ASP161 2.3 16.6 1.0
OD1 1:ASP199 2.5 19.2 1.0
O 1:GLU198 2.5 17.8 1.0
OD1 1:ASP188 2.5 20.9 1.0
OE1 1:GLU165 2.5 16.6 1.0
OE2 1:GLU165 2.6 18.5 1.0
O 1:HOH262 2.6 17.4 1.0
OD1 1:ASP161 2.7 14.5 1.0
CG 1:ASP161 2.9 18.1 1.0
CD 1:GLU165 2.9 19.5 1.0
CG 1:ASP188 3.3 23.7 1.0
C 1:GLU198 3.5 18.1 1.0
CG 1:ASP199 3.6 21.1 1.0
CA 1:ASP199 3.8 19.0 1.0
CB 1:ASP188 3.8 21.9 1.0
O 1:HOH300 4.0 29.5 1.0
N 1:ASP199 4.0 17.8 1.0
OD2 1:ASP188 4.2 23.5 1.0
CB 1:ASP199 4.3 18.8 1.0
CB 1:ASP161 4.4 20.4 1.0
CG 1:GLU165 4.4 19.2 1.0
CZ 1:PHE168 4.4 18.8 1.0
N 1:GLU198 4.4 22.2 1.0
CA 1:ASP188 4.5 23.4 1.0
N 1:GLY166 4.5 21.5 1.0
OD2 1:ASP199 4.5 18.6 1.0
O 1:HOH263 4.6 19.1 1.0
CA 1:GLU198 4.6 20.5 1.0
O 1:HOH278 4.7 24.6 1.0
OD2 1:ASP211 4.7 19.3 1.0
O 1:ASP161 4.7 21.0 1.0
CA 1:GLU165 4.9 19.7 1.0
C 1:ASP199 5.0 20.4 1.0

Calcium binding site 2 out of 9 in 1afa

Go back to Calcium Binding Sites List in 1afa
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:22.1
occ:1.00
 OD1 1:ASP211 2.2 20.1 1.0
OE1 1:GLU198 2.4 20.0 1.0
OD1 1:ASP187 2.4 15.6 1.0
OD1 1:ASN210 2.4 21.8 1.0
OE1 1:GLN185 2.5 23.9 1.0
O 1:ASP211 2.5 17.2 1.0
O3 1:MBG1 2.6 23.4 1.0
O4 1:MBG1 2.8 26.0 1.0
CG 1:ASP211 3.4 19.8 1.0
CD 1:GLN185 3.4 25.1 1.0
CG 1:ASN210 3.4 19.3 1.0
CG 1:ASP187 3.4 19.0 1.0
CD 1:GLU198 3.5 16.9 1.0
C4 1:MBG1 3.6 27.3 1.0
C 1:ASP211 3.6 18.7 1.0
C3 1:MBG1 3.6 25.3 1.0
N 1:ASP211 3.7 20.2 1.0
ND2 1:ASN210 3.8 11.1 1.0
NE2 1:GLN185 3.9 23.3 1.0
OD2 1:ASP187 3.9 19.6 1.0
OE2 1:GLU198 3.9 19.4 1.0
CA 1:ASP211 4.0 18.6 1.0
OD2 1:ASP211 4.1 19.3 1.0
N 1:ASP187 4.2 21.2 1.0
C2 1:MBG1 4.3 27.0 1.0
CB 1:ASP211 4.3 17.6 1.0
CG 1:GLN185 4.5 23.2 1.0
C 1:ASN210 4.5 21.3 1.0
CB 1:ASP187 4.6 20.7 1.0
CB 1:ASN210 4.7 15.2 1.0
CG 1:GLU198 4.7 17.8 1.0
N 1:ILE212 4.7 18.5 1.0
CB 1:TRP189 4.8 28.2 1.0
CA 1:ASP187 4.8 22.8 1.0
CA 1:ASN210 4.8 19.4 1.0
CB 1:GLU198 4.8 18.6 1.0
N 1:ASP188 4.9 23.1 1.0
CB 1:GLN185 4.9 22.0 1.0
C5 1:MBG1 5.0 28.5 1.0
CA 1:PRO186 5.0 20.5 1.0

Calcium binding site 3 out of 9 in 1afa

Go back to Calcium Binding Sites List in 1afa
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:21.1
occ:1.00
 O 1:HOH229 2.2 16.7 1.0
OE2 1:GLU84 2.4 23.9 1.0
CD 1:GLU84 3.6 23.1 1.0
OE1 1:GLU84 4.1 19.9 1.0
OD1 1:ASN80 4.4 21.3 1.0
ND2 1:ASN80 4.7 14.4 1.0
O 1:HOH314 4.7 27.2 1.0
CG 1:GLU84 4.7 21.1 1.0

Calcium binding site 4 out of 9 in 1afa

Go back to Calcium Binding Sites List in 1afa
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:36.4
occ:1.00
 OD2 2:ASP161 2.3 27.5 1.0
O 2:GLU198 2.4 46.4 1.0
OE1 2:GLU165 2.5 29.1 1.0
OD1 2:ASP199 2.6 46.1 1.0
OD1 2:ASP161 2.7 35.8 1.0
OE2 2:GLU165 2.8 28.3 1.0
OD1 2:ASP188 2.8 39.6 1.0
CG 2:ASP161 2.9 33.6 1.0
CD 2:GLU165 3.0 29.6 1.0
CG 2:ASP188 3.4 40.1 1.0
C 2:GLU198 3.4 47.2 1.0
CG 2:ASP199 3.7 46.0 1.0
CA 2:ASP199 3.8 45.9 1.0
CA 2:CA227 3.8 31.1 1.0
N 2:ASP199 4.0 46.3 1.0
CB 2:ASP188 4.0 42.4 1.0
OD2 2:ASP188 4.0 40.8 1.0
CB 2:ASP199 4.3 46.1 1.0
CB 2:ASP161 4.4 30.2 1.0
N 2:GLU198 4.4 52.8 1.0
CG 2:GLU165 4.4 28.8 1.0
CZ 2:PHE168 4.5 29.5 1.0
O 2:ASP161 4.5 37.3 1.0
CA 2:GLU198 4.5 48.0 1.0
OD2 2:ASP211 4.6 34.9 1.0
CA 2:ASP188 4.6 45.6 1.0
OD2 2:ASP199 4.7 45.5 1.0
N 2:GLY166 4.8 33.5 1.0
C 2:ASP199 4.9 45.0 1.0
O 2:HOH304 4.9 23.0 1.0
CA 2:GLU165 4.9 32.1 1.0
CE1 2:PHE168 4.9 27.2 1.0

Calcium binding site 5 out of 9 in 1afa

Go back to Calcium Binding Sites List in 1afa
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:Ca2

b:56.6
occ:1.00
 OE1 2:GLN185 2.1 46.4 1.0
OD1 2:ASP211 2.2 32.3 1.0
OE1 2:GLU198 2.5 43.3 1.0
O4 2:MBG3 2.6 75.8 1.0
OD1 2:ASP187 2.7 52.9 1.0
OD1 2:ASN210 2.7 45.1 1.0
O3 2:MBG3 2.9 72.4 1.0
O 2:ASP211 3.0 42.1 1.0
CD 2:GLN185 3.1 46.7 1.0
CG 2:ASP211 3.4 34.9 1.0
CG 2:ASP187 3.4 53.1 1.0
CG 2:ASN210 3.5 45.9 1.0
C4 2:MBG3 3.5 75.0 1.0
NE2 2:GLN185 3.6 48.8 1.0
C3 2:MBG3 3.7 73.7 1.0
N 2:ASP211 3.7 40.9 1.0
CD 2:GLU198 3.7 44.9 1.0
OD2 2:ASP187 3.8 55.4 1.0
ND2 2:ASN210 3.8 45.9 1.0
C 2:ASP211 3.9 41.3 1.0
N 2:ASP187 4.0 44.9 1.0
CA 2:ASP211 4.2 40.2 1.0
OD2 2:ASP211 4.2 34.9 1.0
CG 2:GLN185 4.3 45.5 1.0
C2 2:MBG3 4.3 73.3 1.0
OE2 2:GLU198 4.3 44.5 1.0
CB 2:ASP211 4.4 38.0 1.0
C 2:ASN210 4.5 43.2 1.0
CB 2:ASP187 4.6 49.4 1.0
CB 2:ASN210 4.7 45.5 1.0
CA 2:ASN210 4.7 45.0 1.0
CB 2:GLN185 4.8 45.2 1.0
CA 2:ASP187 4.8 46.6 1.0
N 2:ASP188 4.8 46.4 1.0
CA 2:PRO186 4.9 40.1 1.0
C5 2:MBG3 4.9 75.4 1.0
CG 2:GLU198 4.9 44.4 1.0
C 2:PRO186 5.0 42.3 1.0

Calcium binding site 6 out of 9 in 1afa

Go back to Calcium Binding Sites List in 1afa
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:Ca227

b:31.1
occ:1.00
 O 2:HOH304 2.3 23.0 1.0
OE1 2:GLU165 2.4 29.1 1.0
OD1 2:ASP199 2.4 46.1 1.0
OD2 2:ASP199 2.7 45.5 1.0
CG 2:ASP199 2.9 46.0 1.0
CD 2:GLU165 3.6 29.6 1.0
CA 2:CA1 3.8 36.4 1.0
O 2:HOH309 3.9 55.6 1.0
CB 2:GLU165 4.0 31.9 1.0
O 2:ASP161 4.0 37.3 1.0
CG 2:GLU165 4.2 28.8 1.0
OD1 2:ASP188 4.3 39.6 1.0
CB 2:ASP199 4.4 46.1 1.0
CA 2:GLU165 4.4 32.1 1.0
OD2 2:ASP161 4.5 27.5 1.0
OE2 2:GLU165 4.5 28.3 1.0
OD2 2:ASP188 4.6 40.8 1.0
CG 2:ASP188 4.8 40.1 1.0
CG 2:ASP161 4.9 33.6 1.0
OH 2:TYR190 4.9 53.4 1.0
N 2:GLU165 4.9 30.9 1.0
O 2:GLU162 5.0 41.2 1.0
OD1 2:ASP161 5.0 35.8 1.0

Calcium binding site 7 out of 9 in 1afa

Go back to Calcium Binding Sites List in 1afa
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:17.8
occ:1.00
 OD2 3:ASP161 2.3 14.7 1.0
O 3:GLU198 2.4 18.4 1.0
OD1 3:ASP199 2.5 20.7 1.0
O 3:HOH260 2.5 18.3 1.0
OD1 3:ASP188 2.5 22.8 1.0
OE1 3:GLU165 2.6 16.6 1.0
OD1 3:ASP161 2.6 17.6 1.0
OE2 3:GLU165 2.7 14.9 1.0
CG 3:ASP161 2.8 16.6 1.0
CD 3:GLU165 3.0 16.9 1.0
C 3:GLU198 3.4 17.8 1.0
CG 3:ASP188 3.4 21.9 1.0
CG 3:ASP199 3.6 21.4 1.0
CA 3:ASP199 3.8 16.9 1.0
CB 3:ASP188 3.9 22.2 1.0
N 3:ASP199 3.9 16.3 1.0
CB 3:ASP199 4.2 18.8 1.0
OD2 3:ASP188 4.3 20.4 1.0
N 3:GLU198 4.3 18.2 1.0
CB 3:ASP161 4.3 17.0 1.0
CZ 3:PHE168 4.4 15.4 1.0
CA 3:ASP188 4.4 21.6 1.0
CA 3:GLU198 4.4 18.0 1.0
CG 3:GLU165 4.5 19.3 1.0
OD2 3:ASP199 4.5 21.4 1.0
O 3:HOH231 4.5 29.4 1.0
N 3:GLY166 4.7 21.6 1.0
O 3:HOH264 4.7 19.6 1.0
OD2 3:ASP211 4.7 16.1 1.0
O 3:ASP161 4.8 19.2 1.0
CE2 3:PHE168 4.9 16.6 1.0
C 3:ASP199 4.9 18.5 1.0
CA 3:GLU165 5.0 21.5 1.0

Calcium binding site 8 out of 9 in 1afa

Go back to Calcium Binding Sites List in 1afa
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:Ca227

b:21.8
occ:1.00
 OD1 3:ASP211 2.3 14.9 1.0
OE1 3:GLU198 2.3 19.3 1.0
O3 3:MBG2 2.4 25.3 1.0
OD1 3:ASP187 2.4 24.1 1.0
OD1 3:ASN210 2.5 21.7 1.0
OE1 3:GLN185 2.5 28.6 1.0
O 3:ASP211 2.5 22.1 1.0
O4 3:MBG2 2.7 28.5 1.0
CD 3:GLU198 3.3 16.0 1.0
CG 3:ASP211 3.3 17.8 1.0
C4 3:MBG2 3.3 27.2 1.0
CD 3:GLN185 3.4 28.3 1.0
C3 3:MBG2 3.4 28.3 1.0
CG 3:ASP187 3.5 22.4 1.0
CG 3:ASN210 3.6 22.3 1.0
C 3:ASP211 3.6 20.7 1.0
OE2 3:GLU198 3.7 19.8 1.0
NE2 3:GLN185 3.7 27.2 1.0
N 3:ASP211 3.8 20.3 1.0
OD2 3:ASP187 3.9 22.7 1.0
OD2 3:ASP211 4.1 16.1 1.0
CA 3:ASP211 4.1 17.1 1.0
ND2 3:ASN210 4.1 17.9 1.0
C2 3:MBG2 4.2 30.8 1.0
N 3:ASP187 4.2 22.5 1.0
CB 3:ASP211 4.3 17.3 1.0
CG 3:GLU198 4.6 18.6 1.0
CG 3:GLN185 4.6 24.7 1.0
C 3:ASN210 4.6 20.5 1.0
CB 3:TRP189 4.7 25.2 1.0
CB 3:ASP187 4.7 21.5 1.0
N 3:ILE212 4.7 18.6 1.0
C5 3:MBG2 4.8 28.8 1.0
CB 3:ASN210 4.8 22.4 1.0
CB 3:GLU198 4.8 18.2 1.0
CA 3:ASP187 4.8 22.9 1.0
N 3:ASP188 4.9 20.6 1.0
O2 3:MBG2 4.9 28.5 1.0
N 3:TRP189 4.9 22.0 1.0
CA 3:ASN210 5.0 22.5 1.0

Calcium binding site 9 out of 9 in 1afa

Go back to Calcium Binding Sites List in 1afa
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:Ca3

b:17.9
occ:1.00
 OE2 3:GLU84 2.3 19.8 1.0
O 1:HOH251 2.4 25.9 1.0
O 3:HOH228 2.4 13.2 1.0
O 3:HOH352 2.7 31.6 1.0
CD 3:GLU84 3.4 19.7 1.0
OE1 3:GLU84 3.9 20.1 1.0
NZ 1:LYS89 4.3 29.3 1.0
OD1 3:ASN80 4.5 23.4 1.0
O 1:HOH250 4.6 38.3 1.0
O 3:HOH240 4.6 22.6 1.0
CG 3:GLU84 4.6 15.9 1.0
ND2 3:ASN80 4.6 19.6 1.0
O 3:HOH321 4.8 29.2 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 05:48:36 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy