Atomistry » Calcium » PDB 5ckm-5cxl » 5cna
Atomistry »
  Calcium »
    PDB 5ckm-5cxl »
      5cna »

Calcium in PDB 5cna: Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure

Protein crystallography data

The structure of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure, PDB code: 5cna was solved by J.H.Naismith, C.Emmerich, J.Habash, S.J.Harrop, J.R.Helliwell, W.N.Hunter, J.Raftery, A.J.Kalb(Gilboa), J.Yariv, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.700, 128.600, 67.200, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / n/a

Other elements in 5cna:

The structure of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure 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 Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure (pdb code 5cna). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure, PDB code: 5cna:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5cna

Go back to Calcium Binding Sites List in 5cna
Calcium binding site 1 out of 4 in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca240

b:14.9
occ:1.00
O A:TYR12 2.3 22.2 1.0
OD2 A:ASP19 2.3 13.6 1.0
O A:HOH247 2.4 19.7 1.0
O A:HOH248 2.4 14.1 1.0
OD1 A:ASP10 2.4 8.9 1.0
OD1 A:ASN14 2.5 12.8 1.0
OD2 A:ASP10 2.8 11.2 1.0
CG A:ASP10 2.9 17.8 1.0
CG A:ASP19 3.5 9.2 1.0
C A:TYR12 3.5 18.9 1.0
CG A:ASN14 3.6 15.2 1.0
OD1 A:ASP19 3.9 12.9 1.0
N A:ASN14 4.1 25.5 1.0
CB A:ASN14 4.2 17.5 1.0
MN A:MN239 4.2 20.0 1.0
CA A:TYR12 4.3 18.9 1.0
N A:TYR12 4.4 18.0 1.0
N A:PRO13 4.4 23.1 1.0
CB A:ASP10 4.5 12.4 1.0
CA A:PRO13 4.5 24.8 1.0
O A:HOH246 4.5 14.2 1.0
CB A:TYR12 4.5 21.3 1.0
ND2 A:ASN14 4.6 16.8 1.0
C A:PRO13 4.6 26.4 1.0
CB A:ASP19 4.7 13.0 1.0
O A:ASP208 4.7 13.7 1.0
OD2 A:ASP208 4.7 12.5 1.0
CA A:ASN14 4.7 20.7 1.0
CE1 A:HIS24 4.8 20.8 1.0
CB A:ARG228 4.8 13.1 1.0
CA A:ARG228 4.9 13.3 1.0
O A:ARG228 4.9 17.8 1.0
CD1 A:TYR12 5.0 19.2 1.0

Calcium binding site 2 out of 4 in 5cna

Go back to Calcium Binding Sites List in 5cna
Calcium binding site 2 out of 4 in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca240

b:19.9
occ:1.00
O B:HOH253 2.2 18.2 1.0
O B:HOH256 2.2 14.8 1.0
O B:TYR12 2.3 24.1 1.0
OD1 B:ASP10 2.3 19.3 1.0
OD2 B:ASP19 2.5 17.5 1.0
OD1 B:ASN14 2.6 21.8 1.0
OD2 B:ASP10 2.7 16.1 1.0
CG B:ASP10 2.9 24.8 1.0
C B:TYR12 3.5 18.9 1.0
CG B:ASP19 3.6 16.4 1.0
CG B:ASN14 3.7 21.7 1.0
OD1 B:ASP19 4.0 20.6 1.0
N B:ASN14 4.2 23.2 1.0
MN B:MN239 4.3 18.3 1.0
CB B:ASN14 4.3 19.6 1.0
CA B:TYR12 4.3 19.7 1.0
N B:PRO13 4.4 21.4 1.0
CB B:ASP10 4.4 19.2 1.0
N B:TYR12 4.4 22.6 1.0
CA B:PRO13 4.5 24.0 1.0
CB B:TYR12 4.5 23.7 1.0
O B:ASP208 4.5 17.7 1.0
OD2 B:ASP208 4.5 18.7 1.0
O B:HOH254 4.6 21.8 1.0
C B:PRO13 4.6 26.5 1.0
CB B:ARG228 4.8 19.4 1.0
CA B:ARG228 4.8 18.3 1.0
ND2 B:ASN14 4.8 15.5 1.0
CB B:ASP19 4.8 19.8 1.0
O B:ARG228 4.8 17.0 1.0
CE1 B:HIS24 4.9 26.9 1.0
CA B:ASN14 4.9 24.6 1.0
CD2 B:TYR12 4.9 23.8 1.0

Calcium binding site 3 out of 4 in 5cna

Go back to Calcium Binding Sites List in 5cna
Calcium binding site 3 out of 4 in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca240

b:39.9
occ:1.00
OD2 C:ASP19 2.2 36.5 1.0
O C:HOH245 2.2 34.2 1.0
OD1 C:ASN14 2.2 48.9 1.0
O C:HOH246 2.4 56.1 1.0
O C:TYR12 2.4 46.5 1.0
OD1 C:ASP10 2.6 39.1 1.0
OD2 C:ASP10 2.9 37.0 1.0
CG C:ASP10 3.1 42.8 1.0
CG C:ASN14 3.3 51.3 1.0
CG C:ASP19 3.4 45.4 1.0
C C:TYR12 3.6 49.8 1.0
OD1 C:ASP19 3.9 50.1 1.0
CB C:ASN14 4.0 47.5 1.0
N C:ASN14 4.0 54.1 1.0
CB C:TYR12 4.2 54.9 1.0
ND2 C:ASN14 4.3 59.0 1.0
OD1 C:ASP208 4.3 44.5 1.0
CA C:TYR12 4.3 49.2 1.0
N C:TYR12 4.4 48.4 1.0
CB C:ASP19 4.5 47.5 1.0
N C:PRO13 4.6 52.5 1.0
O C:HOH244 4.6 46.7 1.0
MN C:MN239 4.6 41.4 1.0
CA C:ASN14 4.6 49.1 1.0
CB C:ASP10 4.6 34.8 1.0
O C:ASP208 4.6 34.1 1.0
CA C:PRO13 4.7 53.6 1.0
O C:ARG228 4.7 40.7 1.0
C C:PRO13 4.7 55.6 1.0
CD2 C:TYR12 4.7 55.0 1.0
CA C:ARG228 4.7 46.2 1.0

Calcium binding site 4 out of 4 in 5cna

Go back to Calcium Binding Sites List in 5cna
Calcium binding site 4 out of 4 in the Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Refined Structure of Concanavalin A Complexed with Alpha- Methyl-D-Mannopyranoside at 2.0 Angstroms Resolution and Comparison with the Saccharide-Free Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca240

b:23.9
occ:1.00
O D:HOH256 2.1 18.5 1.0
O D:HOH255 2.2 22.2 1.0
OD2 D:ASP19 2.3 34.1 1.0
O D:TYR12 2.3 29.7 1.0
OD1 D:ASP10 2.4 24.0 1.0
OD1 D:ASN14 2.5 29.6 1.0
OD2 D:ASP10 2.6 25.5 1.0
CG D:ASP10 2.8 30.7 1.0
CG D:ASP19 3.5 34.1 1.0
C D:TYR12 3.5 27.7 1.0
CG D:ASN14 3.6 27.0 1.0
OD1 D:ASP19 4.1 33.5 1.0
N D:ASN14 4.1 31.9 1.0
CB D:ASN14 4.1 24.2 1.0
MN D:MN239 4.3 26.5 1.0
CB D:ASP10 4.3 25.4 1.0
CA D:TYR12 4.4 28.4 1.0
N D:TYR12 4.4 29.1 1.0
N D:PRO13 4.5 29.5 1.0
CB D:TYR12 4.5 26.9 1.0
CA D:PRO13 4.6 28.5 1.0
O D:HOH252 4.6 22.1 1.0
ND2 D:ASN14 4.6 22.9 1.0
CB D:ASP19 4.7 33.1 1.0
OD1 D:ASP208 4.7 25.6 1.0
O D:ASP208 4.7 25.8 1.0
C D:PRO13 4.7 29.6 1.0
CA D:ASN14 4.8 27.0 1.0
CE1 D:HIS24 4.8 25.0 1.0
O D:ARG228 4.9 24.9 1.0
CA D:ARG228 4.9 25.8 1.0
CD2 D:TYR12 4.9 29.6 1.0
CB D:ARG228 4.9 27.1 1.0

Reference:

J.H.Naismith, C.Emmerich, J.Habash, S.J.Harrop, J.R.Helliwell, W.N.Hunter, J.Raftery, A.J.Kalb, J.Yariv. Refined Structure of Concanavalin A Complexed with Methyl Alpha-D-Mannopyranoside at 2.0 A Resolution and Comparison with the Saccharide-Free Structure. Acta Crystallogr.,Sect.D V. 50 847 1994.
ISSN: ISSN 0907-4449
PubMed: 15299352
DOI: 10.1107/S0907444994005287
Page generated: Sun Jul 14 17:11:32 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy