Atomistry » Calcium » PDB 1qd6-1qlk » 1qdc
Atomistry »
  Calcium »
    PDB 1qd6-1qlk »
      1qdc »

Calcium in PDB 1qdc: Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex

Protein crystallography data

The structure of Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex, PDB code: 1qdc was solved by J.Bouckaert, R.Loris, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.510, 117.030, 120.920, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.1

Other elements in 1qdc:

The structure of Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex (pdb code 1qdc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex, PDB code: 1qdc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1qdc

Go back to Calcium Binding Sites List in 1qdc
Calcium binding site 1 out of 4 in the Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca241

b:12.5
occ:1.00
O A:TYR12 2.3 14.6 1.0
OD1 A:ASN14 2.4 15.1 1.0
OD2 A:ASP19 2.4 13.0 1.0
OD1 A:ASP10 2.5 17.6 1.0
OD2 A:ASP10 2.5 11.9 1.0
O A:HOH246 2.5 13.4 1.0
O A:HOH244 2.5 11.9 1.0
CG A:ASP10 2.8 13.7 1.0
CG A:ASP19 3.5 13.5 1.0
CG A:ASN14 3.5 15.8 1.0
C A:TYR12 3.6 16.3 1.0
OD1 A:ASP19 3.9 14.3 1.0
N A:ASN14 3.9 18.9 1.0
CB A:ASN14 4.1 17.1 1.0
CB A:ASP10 4.3 12.5 1.0
MN A:MN240 4.3 33.8 1.0
CA A:TYR12 4.4 15.0 1.0
N A:TYR12 4.5 14.7 1.0
CB A:TYR12 4.5 12.8 1.0
N A:PRO13 4.5 19.7 1.0
CA A:PRO13 4.5 19.4 1.0
O A:HOH251 4.6 16.4 1.0
ND2 A:ASN14 4.6 16.5 1.0
C A:PRO13 4.6 18.7 1.0
OD1 A:ASP208 4.7 8.7 1.0
CA A:ASN14 4.7 17.6 1.0
CB A:ASP19 4.7 14.2 1.0
O A:ASP208 4.7 11.3 1.0
CE1 A:HIS24 4.8 13.0 1.0
CA A:ARG228 4.9 14.1 1.0
CB A:ARG228 4.9 18.6 1.0
O A:ARG228 4.9 11.9 1.0
CD2 A:TYR12 5.0 13.0 1.0

Calcium binding site 2 out of 4 in 1qdc

Go back to Calcium Binding Sites List in 1qdc
Calcium binding site 2 out of 4 in the Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca244

b:17.3
occ:1.00
O B:TYR12 2.4 19.3 1.0
OD2 B:ASP19 2.5 15.4 1.0
OD2 B:ASP10 2.5 16.4 1.0
OD1 B:ASN14 2.5 19.0 1.0
OD1 B:ASP10 2.5 17.0 1.0
O B:HOH1250 2.6 18.2 1.0
O B:HOH1241 2.6 14.2 1.0
CG B:ASP10 2.8 17.8 1.0
C B:TYR12 3.6 21.3 1.0
CG B:ASP19 3.6 16.5 1.0
CG B:ASN14 3.6 18.6 1.0
N B:ASN14 4.0 21.7 1.0
OD1 B:ASP19 4.1 15.4 1.0
CB B:ASN14 4.2 17.9 1.0
CB B:ASP10 4.3 13.3 1.0
MN B:MN243 4.3 37.0 1.0
CA B:TYR12 4.4 20.9 1.0
CB B:TYR12 4.5 20.0 1.0
N B:PRO13 4.5 23.5 1.0
N B:TYR12 4.5 21.8 1.0
CA B:PRO13 4.6 22.6 1.0
O B:ASP208 4.6 16.1 1.0
C B:PRO13 4.7 23.6 1.0
O B:HOH1248 4.7 17.2 1.0
OD1 B:ASP208 4.7 16.9 1.0
ND2 B:ASN14 4.7 14.1 1.0
CA B:ASN14 4.7 20.8 1.0
CB B:ASP19 4.8 16.6 1.0
CA B:ARG228 4.8 16.4 1.0
O B:ARG228 4.8 15.6 1.0
CE1 B:HIS24 4.9 13.2 1.0
CB B:ARG228 4.9 17.4 1.0
CD2 B:TYR12 5.0 23.8 1.0

Calcium binding site 3 out of 4 in 1qdc

Go back to Calcium Binding Sites List in 1qdc
Calcium binding site 3 out of 4 in the Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca246

b:21.6
occ:1.00
O C:TYR12 2.3 22.9 1.0
OD2 C:ASP10 2.4 20.4 1.0
OD1 C:ASN14 2.4 30.2 1.0
OD2 C:ASP19 2.5 22.6 1.0
OD1 C:ASP10 2.6 24.9 1.0
O C:HOH2244 2.6 18.9 1.0
O C:HOH2243 2.6 18.2 1.0
CG C:ASP10 2.8 23.1 1.0
C C:TYR12 3.6 26.9 1.0
CG C:ASN14 3.6 32.4 1.0
CG C:ASP19 3.7 25.9 1.0
N C:ASN14 4.0 28.7 1.0
CB C:ASN14 4.1 28.5 1.0
OD1 C:ASP19 4.1 21.0 1.0
CB C:ASP10 4.3 24.1 1.0
CA C:TYR12 4.4 25.5 1.0
MN C:MN245 4.4 41.5 1.0
O C:HOH2254 4.4 23.9 1.0
N C:TYR12 4.5 23.2 1.0
CB C:TYR12 4.5 27.6 1.0
N C:PRO13 4.5 27.7 1.0
CA C:PRO13 4.6 28.5 1.0
O C:ASP208 4.6 16.7 1.0
C C:PRO13 4.6 27.9 1.0
CA C:ASN14 4.7 29.6 1.0
ND2 C:ASN14 4.7 25.0 1.0
OD1 C:ASP208 4.7 26.4 1.0
CE1 C:HIS24 4.8 17.3 1.0
O C:ARG228 4.8 20.6 1.0
CB C:ASP19 4.9 25.1 1.0
CA C:ARG228 4.9 22.3 1.0
CD2 C:TYR12 5.0 28.3 1.0

Calcium binding site 4 out of 4 in 1qdc

Go back to Calcium Binding Sites List in 1qdc
Calcium binding site 4 out of 4 in the Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Man(APLHA1-6)Man(ALPHA1-O)Methyl Concanavalin A Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca248

b:17.6
occ:1.00
O D:TYR12 2.4 21.3 1.0
OD2 D:ASP10 2.4 14.4 1.0
O D:HOH3245 2.5 18.2 1.0
OD1 D:ASN14 2.5 21.1 1.0
OD2 D:ASP19 2.5 18.9 1.0
O D:HOH3242 2.5 15.9 1.0
OD1 D:ASP10 2.6 19.1 1.0
CG D:ASP10 2.9 18.9 1.0
CG D:ASN14 3.6 22.6 1.0
C D:TYR12 3.6 20.0 1.0
CG D:ASP19 3.6 20.7 1.0
N D:ASN14 4.0 20.7 1.0
OD1 D:ASP19 4.1 17.6 1.0
CB D:ASN14 4.1 19.6 1.0
MN D:MN247 4.3 38.4 1.0
CB D:ASP10 4.3 14.4 1.0
CA D:TYR12 4.5 19.1 1.0
CB D:TYR12 4.6 16.5 1.0
N D:PRO13 4.6 22.4 1.0
CA D:PRO13 4.6 22.4 1.0
N D:TYR12 4.6 19.4 1.0
O D:ASP208 4.6 11.7 1.0
OD1 D:ASP208 4.7 12.0 1.0
C D:PRO13 4.7 23.5 1.0
CA D:ARG228 4.7 17.3 1.0
O D:HOH3252 4.7 23.6 1.0
CA D:ASN14 4.7 22.2 1.0
ND2 D:ASN14 4.7 18.9 1.0
O D:ARG228 4.8 16.1 1.0
CB D:ARG228 4.8 22.0 1.0
CB D:ASP19 4.8 21.2 1.0
CE1 D:HIS24 4.9 10.9 1.0
CD2 D:TYR12 5.0 19.5 1.0

Reference:

J.Bouckaert, T.W.Hamelryck, L.Wyns, R.Loris. The Crystal Structures of Man(ALPHA1-3)Man(ALPHA1-O)Me and Man(ALPHA1-6)Man(ALPHA1-O)Me in Complex with Concanavalin A. J.Biol.Chem. V. 274 29188 1999.
ISSN: ISSN 0021-9258
PubMed: 10506175
DOI: 10.1074/JBC.274.41.29188
Page generated: Sat Dec 12 03:16:15 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy