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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Sat Dec 12 02:49:35 2020

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