Atomistry » Calcium » PDB 1b85-1bjj » 1bcj
Atomistry »
  Calcium »
    PDB 1b85-1bjj »
      1bcj »

Calcium in PDB 1bcj: Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine

Protein crystallography data

The structure of Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine, PDB code: 1bcj 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) 30.00 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.920, 84.530, 97.860, 90.00, 104.49, 90.00
R / Rfree (%) 22 / 26.1

Other elements in 1bcj:

The structure of Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine (pdb code 1bcj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine, PDB code: 1bcj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1bcj

Go back to Calcium Binding Sites List in 1bcj
Calcium binding site 1 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca227

b:27.9
occ:1.00
 OD1 1:ASP199 2.4 26.0 1.0
OD2 1:ASP161 2.4 22.8 1.0
O 1:GLU198 2.4 25.4 1.0
O 1:HOH237 2.5 23.0 1.0
OE2 1:GLU165 2.6 27.5 1.0
OD1 1:ASP188 2.6 23.1 1.0
OE1 1:GLU165 2.6 26.6 1.0
OD1 1:ASP161 2.7 28.9 1.0
CD 1:GLU165 2.9 27.9 1.0
CG 1:ASP161 2.9 27.0 1.0
CG 1:ASP188 3.3 26.0 1.0
C 1:GLU198 3.4 26.1 1.0
CG 1:ASP199 3.5 22.5 1.0
CB 1:ASP188 3.7 26.5 1.0
CA 1:ASP199 3.8 22.7 1.0
N 1:ASP199 4.0 23.1 1.0
CA 1:CA3 4.0 28.1 1.0
O 1:HOH236 4.1 25.4 1.0
OD2 1:ASP188 4.2 27.9 1.0
CB 1:ASP199 4.2 23.4 1.0
CA 1:ASP188 4.3 29.8 1.0
N 1:GLU198 4.4 30.3 1.0
CG 1:GLU165 4.4 27.2 1.0
CB 1:ASP161 4.4 26.6 1.0
OD2 1:ASP199 4.5 27.0 1.0
CA 1:GLU198 4.5 28.2 1.0
N 1:GLY166 4.6 28.2 1.0
O 1:ASP161 4.7 26.1 1.0
O 1:HOH249 4.7 29.0 1.0
CZ 1:PHE168 4.7 28.2 1.0
O 1:HOH246 4.7 30.0 1.0
OD2 1:ASP211 4.9 26.1 1.0
CA 1:GLU165 4.9 28.7 1.0

Calcium binding site 2 out of 9 in 1bcj

Go back to Calcium Binding Sites List in 1bcj
Calcium binding site 2 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca2

b:28.6
occ:1.00
 OD1 1:ASP211 2.1 27.3 1.0
OE1 1:GLN185 2.4 27.9 1.0
OE1 1:GLU198 2.5 30.9 1.0
OD1 1:ASN210 2.5 26.4 1.0
O 1:ASP211 2.5 24.2 1.0
OD1 1:ASP187 2.5 29.3 1.0
O4 1:NGA1 2.7 31.6 1.0
O3 1:NGA1 2.7 32.7 1.0
CG 1:ASP211 3.2 26.5 1.0
CG 1:ASN210 3.4 25.0 1.0
CD 1:GLU198 3.4 29.6 1.0
CD 1:GLN185 3.4 32.2 1.0
CG 1:ASP187 3.5 30.6 1.0
C4 1:NGA1 3.5 33.4 1.0
C 1:ASP211 3.5 24.5 1.0
C3 1:NGA1 3.6 34.5 1.0
ND2 1:ASN210 3.6 20.5 1.0
N 1:ASP211 3.7 24.8 1.0
OE2 1:GLU198 3.8 28.3 1.0
OD2 1:ASP211 3.9 26.1 1.0
NE2 1:GLN185 3.9 29.1 1.0
OD2 1:ASP187 4.0 34.4 1.0
CA 1:ASP211 4.0 23.9 1.0
N 1:ASP187 4.2 30.2 1.0
CB 1:ASP211 4.2 23.9 1.0
C2 1:NGA1 4.3 35.8 1.0
C 1:ASN210 4.5 26.6 1.0
CG 1:GLN185 4.6 28.7 1.0
CB 1:TRP189 4.7 34.1 1.0
CB 1:ASN210 4.7 24.5 1.0
CB 1:ASP187 4.7 30.1 1.0
N 1:ILE212 4.7 25.5 1.0
CG 1:GLU198 4.7 25.3 1.0
CA 1:ASP187 4.9 30.2 1.0
CB 1:GLU198 4.9 25.1 1.0
N 1:TRP189 4.9 32.1 1.0
CA 1:ASN210 4.9 26.1 1.0
N 1:ASP188 4.9 28.6 1.0
C5 1:NGA1 4.9 35.9 1.0
CA 1:PRO186 4.9 29.1 1.0
CB 1:GLN185 5.0 26.8 1.0

Calcium binding site 3 out of 9 in 1bcj

Go back to Calcium Binding Sites List in 1bcj
Calcium binding site 3 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca3

b:28.1
occ:1.00
 OE1 1:GLU165 2.3 26.6 1.0
O 1:HOH236 2.4 25.4 1.0
OD2 1:ASP199 2.5 27.0 1.0
O 1:HOH231 2.7 27.3 1.0
OD1 1:ASP199 2.8 26.0 1.0
CG 1:ASP199 3.0 22.5 1.0
CD 1:GLU165 3.5 27.9 1.0
CA 1:CA227 4.0 27.9 1.0
CB 1:GLU165 4.1 26.4 1.0
OD1 1:ASP188 4.1 23.1 1.0
CG 1:GLU165 4.2 27.2 1.0
O 1:ASP161 4.3 26.1 1.0
OE2 1:GLU165 4.5 27.5 1.0
CB 1:ASP199 4.5 23.4 1.0
CA 1:GLU165 4.5 28.7 1.0
O 1:HOH311 4.6 41.2 1.0
O 1:HOH283 4.6 36.3 1.0
O 1:HOH267 4.7 34.6 1.0
OD2 1:ASP161 4.8 22.8 1.0
OD2 1:ASP188 4.8 27.9 1.0
CG 1:ASP188 4.8 26.0 1.0
OD1 1:ASP161 4.9 28.9 1.0
O 1:HOH317 4.9 49.8 1.0
N 1:GLU165 5.0 26.7 1.0

Calcium binding site 4 out of 9 in 1bcj

Go back to Calcium Binding Sites List in 1bcj
Calcium binding site 4 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca227

b:41.6
occ:1.00
 O 2:GLU198 2.4 50.8 1.0
OD2 2:ASP161 2.4 51.8 1.0
O 2:HOH303 2.5 36.0 1.0
OD1 2:ASP199 2.6 42.6 1.0
OE1 2:GLU165 2.7 50.1 1.0
OE2 2:GLU165 2.8 50.0 1.0
OD1 2:ASP161 2.9 55.0 1.0
CG 2:ASP161 3.0 53.1 1.0
CD 2:GLU165 3.1 51.5 1.0
OD1 2:ASP188 3.1 54.6 1.0
C 2:GLU198 3.3 49.7 1.0
CG 2:ASP188 3.4 53.4 1.0
CG 2:ASP199 3.6 43.8 1.0
CA 2:ASP199 3.7 45.4 1.0
N 2:ASP199 3.8 47.5 1.0
CA 2:CA3 3.9 44.9 1.0
OD2 2:ASP188 3.9 52.0 1.0
CB 2:ASP188 4.0 52.3 1.0
O 2:HOH302 4.1 42.6 1.0
CB 2:ASP199 4.2 44.8 1.0
N 2:GLU198 4.4 53.4 1.0
CA 2:GLU198 4.4 51.3 1.0
CA 2:ASP188 4.5 53.1 1.0
CB 2:ASP161 4.5 50.2 1.0
CG 2:GLU165 4.6 50.2 1.0
OD2 2:ASP199 4.6 45.8 1.0
CZ 2:PHE168 4.6 44.5 1.0
OD2 2:ASP211 4.6 47.5 1.0
O 2:HOH253 4.7 43.4 1.0
N 2:GLY166 4.7 48.4 1.0
C 2:ASP199 4.8 43.8 1.0
CA 2:GLU165 4.9 49.7 1.0
O 2:HOH228 4.9 28.3 1.0

Calcium binding site 5 out of 9 in 1bcj

Go back to Calcium Binding Sites List in 1bcj
Calcium binding site 5 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca2

b:53.7
occ:1.00
 OD1 2:ASP211 2.3 43.4 1.0
OE1 2:GLU198 2.3 53.2 1.0
OD1 2:ASP187 2.4 50.2 1.0
OE1 2:GLN185 2.5 47.8 1.0
O4 2:NGA1 2.6 68.5 1.0
O3 2:NGA1 2.6 65.2 1.0
O 2:ASP211 2.6 43.3 1.0
OD1 2:ASN210 2.9 40.9 1.0
CD 2:GLU198 3.4 52.1 1.0
C4 2:NGA1 3.4 68.7 1.0
CG 2:ASP211 3.4 44.9 1.0
CG 2:ASP187 3.4 52.0 1.0
CD 2:GLN185 3.5 47.6 1.0
C3 2:NGA1 3.5 68.3 1.0
CG 2:ASN210 3.6 44.8 1.0
C 2:ASP211 3.7 44.1 1.0
ND2 2:ASN210 3.7 42.0 1.0
OE2 2:GLU198 3.7 51.3 1.0
OD2 2:ASP187 3.8 53.4 1.0
N 2:ASP211 3.9 44.5 1.0
NE2 2:GLN185 4.0 46.6 1.0
C2 2:NGA1 4.1 69.1 1.0
OD2 2:ASP211 4.1 47.5 1.0
CA 2:ASP211 4.2 44.0 1.0
CB 2:ASP211 4.4 45.2 1.0
CG 2:GLN185 4.6 47.8 1.0
N 2:ASP187 4.6 52.5 1.0
CG 2:GLU198 4.6 49.5 1.0
CB 2:TRP189 4.7 60.8 1.0
CB 2:ASP187 4.7 51.4 1.0
C 2:ASN210 4.7 45.3 1.0
C5 2:NGA1 4.8 69.6 1.0
CB 2:GLU198 4.8 49.6 1.0
N 2:ILE212 4.8 44.9 1.0
N 2:TRP189 4.8 56.3 1.0
N2 2:NGA1 4.9 69.9 1.0
CB 2:ASN210 4.9 43.4 1.0
N 2:ASP188 5.0 52.1 1.0

Calcium binding site 6 out of 9 in 1bcj

Go back to Calcium Binding Sites List in 1bcj
Calcium binding site 6 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca3

b:44.9
occ:1.00
 O 2:HOH228 2.4 28.3 1.0
O 2:HOH249 2.4 34.9 1.0
OE1 2:GLU165 2.5 50.1 1.0
OD1 2:ASP199 2.5 42.6 1.0
O 2:HOH302 2.6 42.6 1.0
OD2 2:ASP199 2.7 45.8 1.0
CG 2:ASP199 3.0 43.8 1.0
CD 2:GLU165 3.6 51.5 1.0
CA 2:CA227 3.9 41.6 1.0
CB 2:GLU165 4.0 49.8 1.0
OD2 2:ASP161 4.3 51.8 1.0
CG 2:GLU165 4.3 50.2 1.0
CA 2:GLU165 4.3 49.7 1.0
OD2 2:ASP188 4.4 52.0 1.0
OD1 2:ASP188 4.4 54.6 1.0
CB 2:ASP199 4.5 44.8 1.0
OH 2:TYR190 4.5 64.8 1.0
O 2:ASP161 4.6 51.8 1.0
O 2:GLU162 4.6 54.4 1.0
OE2 2:GLU165 4.6 50.0 1.0
N 2:GLU165 4.7 49.8 1.0
CG 2:ASP188 4.8 53.4 1.0
CG 2:ASP161 5.0 53.1 1.0

Calcium binding site 7 out of 9 in 1bcj

Go back to Calcium Binding Sites List in 1bcj
Calcium binding site 7 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca227

b:28.2
occ:1.00
 O 3:GLU198 2.3 24.9 1.0
O 3:HOH236 2.4 24.4 1.0
OD1 3:ASP199 2.4 24.5 1.0
OD2 3:ASP161 2.4 27.4 1.0
OD1 3:ASP188 2.6 30.6 1.0
OE1 3:GLU165 2.6 26.1 1.0
OE2 3:GLU165 2.8 26.4 1.0
OD1 3:ASP161 2.8 25.9 1.0
CG 3:ASP161 3.0 29.7 1.0
CD 3:GLU165 3.1 26.8 1.0
C 3:GLU198 3.2 25.7 1.0
CG 3:ASP188 3.4 31.9 1.0
CG 3:ASP199 3.5 26.2 1.0
CA 3:ASP199 3.6 25.2 1.0
N 3:ASP199 3.8 25.3 1.0
CB 3:ASP188 3.9 31.6 1.0
CA 3:CA3 4.0 27.3 1.0
OD2 3:ASP188 4.1 29.1 1.0
CB 3:ASP199 4.1 25.1 1.0
N 3:GLU198 4.2 27.4 1.0
CA 3:GLU198 4.3 27.7 1.0
CA 3:ASP188 4.4 32.4 1.0
CB 3:ASP161 4.5 28.3 1.0
OD2 3:ASP199 4.5 24.7 1.0
CZ 3:PHE168 4.5 31.2 1.0
CG 3:GLU165 4.6 27.7 1.0
OD2 3:ASP211 4.7 23.9 1.0
N 3:GLY166 4.7 31.7 1.0
O 3:HOH231 4.8 27.7 1.0
O 3:ASP161 4.8 30.0 1.0
C 3:ASP199 4.9 26.2 1.0

Calcium binding site 8 out of 9 in 1bcj

Go back to Calcium Binding Sites List in 1bcj
Calcium binding site 8 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca2

b:31.3
occ:1.00
 OD1 3:ASP211 2.2 26.8 1.0
OE1 3:GLN185 2.4 37.6 1.0
OE1 3:GLU198 2.5 29.8 1.0
OD1 3:ASP187 2.5 35.1 1.0
OD1 3:ASN210 2.5 30.7 1.0
O3 3:NGA1 2.5 35.3 1.0
O 3:ASP211 2.6 26.1 1.0
O4 3:NGA1 2.6 36.8 1.0
CG 3:ASP211 3.3 27.1 1.0
CD 3:GLN185 3.4 37.0 1.0
C4 3:NGA1 3.4 39.9 1.0
CG 3:ASP187 3.4 34.9 1.0
CD 3:GLU198 3.4 29.9 1.0
C3 3:NGA1 3.5 39.7 1.0
CG 3:ASN210 3.5 31.9 1.0
C 3:ASP211 3.7 25.7 1.0
OE2 3:GLU198 3.8 28.1 1.0
OD2 3:ASP187 3.8 36.3 1.0
N 3:ASP211 3.8 27.3 1.0
ND2 3:ASN210 3.8 27.6 1.0
NE2 3:GLN185 4.0 39.2 1.0
OD2 3:ASP211 4.0 23.9 1.0
C2 3:NGA1 4.1 40.9 1.0
CA 3:ASP211 4.2 24.9 1.0
N 3:ASP187 4.2 34.0 1.0
CB 3:ASP211 4.3 27.4 1.0
CG 3:GLN185 4.5 36.7 1.0
CB 3:ASP187 4.6 33.6 1.0
C 3:ASN210 4.7 28.0 1.0
CG 3:GLU198 4.7 27.3 1.0
CB 3:TRP189 4.7 35.1 1.0
CB 3:ASN210 4.8 28.9 1.0
N 3:ILE212 4.8 25.7 1.0
N 3:ASP188 4.8 31.5 1.0
C5 3:NGA1 4.8 41.4 1.0
CB 3:GLU198 4.9 27.0 1.0
N 3:TRP189 4.9 33.9 1.0
CA 3:ASP187 4.9 34.5 1.0
CB 3:GLN185 5.0 35.7 1.0
CA 3:ASN210 5.0 30.5 1.0
N2 3:NGA1 5.0 39.9 1.0

Calcium binding site 9 out of 9 in 1bcj

Go back to Calcium Binding Sites List in 1bcj
Calcium binding site 9 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Mannose-Binding Protein-A Mutant (Qpdwghv) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca3

b:27.3
occ:1.00
 OE1 3:GLU165 2.4 26.1 1.0
OD2 3:ASP199 2.5 24.7 1.0
OD1 3:ASP199 2.6 24.5 1.0
CG 3:ASP199 2.9 26.2 1.0
CD 3:GLU165 3.6 26.8 1.0
CA 3:CA227 4.0 28.2 1.0
CB 3:GLU165 4.2 28.5 1.0
CG 3:GLU165 4.2 27.7 1.0
O 3:HOH265 4.3 33.3 1.0
O 3:ASP161 4.3 30.0 1.0
CB 3:ASP199 4.4 25.1 1.0
OD1 3:ASP188 4.4 30.6 1.0
O 3:HOH264 4.5 34.7 1.0
O 3:HOH242 4.5 29.3 1.0
OE2 3:GLU165 4.6 26.4 1.0
CA 3:GLU165 4.6 29.8 1.0
OD2 3:ASP161 4.8 27.4 1.0
OD2 3:ASP188 4.9 29.1 1.0
OD1 3:ASP161 4.9 25.9 1.0

Reference:

A.R.Kolatkar, A.K.Leung, R.Isecke, R.Brossmer, K.Drickamer, W.I.Weis. Mechanism of N-Acetylgalactosamine Binding to A C-Type Animal Lectin Carbohydrate-Recognition Domain. J.Biol.Chem. V. 273 19502 1998.
ISSN: ISSN 0021-9258
PubMed: 9677372
DOI: 10.1074/JBC.273.31.19502
Page generated: Thu Jul 11 06:20:48 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