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

Protein crystallography data

The structure of Mannose-Binding Protein-A Mutant (Qpdwgh) Complexed with N- Acetyl-D-Galactosamine, PDB code: 1bch 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 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.490, 85.010, 98.710, 90.00, 104.82, 90.00
R / Rfree (%) 21.9 / 25.2

Other elements in 1bch:

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

Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Mannose-Binding Protein-A Mutant (Qpdwgh) Complexed with N- Acetyl-D-Galactosamine (pdb code 1bch). 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 (Qpdwgh) Complexed with N- Acetyl-D-Galactosamine, PDB code: 1bch:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1bch

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Calcium binding site 1 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwgh) 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 (Qpdwgh) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca227

b:26.5
occ:1.00
 O 1:HOH241 2.4 22.8 1.0
O 1:GLU198 2.4 22.2 1.0
OD1 1:ASP199 2.4 22.0 1.0
OD2 1:ASP161 2.4 23.6 1.0
OE1 1:GLU165 2.5 27.8 1.0
OD1 1:ASP188 2.5 27.8 1.0
OE2 1:GLU165 2.6 27.3 1.0
OD1 1:ASP161 2.7 22.0 1.0
CD 1:GLU165 2.9 27.2 1.0
CG 1:ASP161 2.9 24.7 1.0
CG 1:ASP188 3.3 29.7 1.0
C 1:GLU198 3.4 23.8 1.0
CG 1:ASP199 3.6 21.8 1.0
CA 1:ASP199 3.8 22.5 1.0
CB 1:ASP188 3.8 29.4 1.0
N 1:ASP199 3.9 21.2 1.0
O 1:HOH274 4.0 35.5 1.0
OD2 1:ASP188 4.1 27.6 1.0
CB 1:ASP199 4.2 21.8 1.0
N 1:GLU198 4.3 27.1 1.0
CA 1:ASP188 4.4 31.2 1.0
CG 1:GLU165 4.4 26.7 1.0
CB 1:ASP161 4.4 26.0 1.0
CA 1:GLU198 4.5 25.9 1.0
OD2 1:ASP199 4.5 23.2 1.0
O 1:HOH275 4.6 31.7 1.0
CZ 1:PHE168 4.6 26.8 1.0
N 1:GLY166 4.6 27.1 1.0
O 1:ASP161 4.7 27.4 1.0
OD2 1:ASP211 4.7 24.3 1.0
O 1:HOH242 4.7 26.3 1.0
CA 1:GLU165 4.9 26.0 1.0
C 1:ASP199 5.0 22.5 1.0

Calcium binding site 2 out of 9 in 1bch

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Calcium binding site 2 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwgh) 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 (Qpdwgh) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca2

b:28.9
occ:1.00
 OD1 1:ASP211 2.3 24.1 1.0
OE1 1:GLU198 2.4 26.4 1.0
OD1 1:ASP187 2.5 28.8 1.0
O3 1:A2G1 2.5 25.3 0.3
O 1:ASP211 2.5 24.6 1.0
OD1 1:ASN210 2.5 25.1 1.0
OE1 1:GLN185 2.6 28.8 1.0
O4 1:A2G1 2.6 23.5 0.3
O4 1:A2G1 2.6 20.1 0.3
O3 1:A2G1 2.6 22.5 0.3
CD 1:GLU198 3.3 24.9 1.0
C4 1:A2G1 3.3 24.5 0.3
CG 1:ASP211 3.3 26.2 1.0
CD 1:GLN185 3.4 30.0 1.0
C3 1:A2G1 3.4 25.1 0.3
CG 1:ASP187 3.4 30.0 1.0
CG 1:ASN210 3.4 25.6 1.0
C4 1:A2G1 3.5 21.6 0.3
C3 1:A2G1 3.6 21.8 0.3
OE2 1:GLU198 3.6 27.6 1.0
C 1:ASP211 3.6 24.3 1.0
ND2 1:ASN210 3.8 22.9 1.0
N 1:ASP211 3.8 25.2 1.0
OD2 1:ASP187 3.8 27.7 1.0
NE2 1:GLN185 3.8 29.0 1.0
OD2 1:ASP211 4.1 24.3 1.0
CA 1:ASP211 4.1 23.7 1.0
C2 1:A2G1 4.2 24.6 0.3
N 1:ASP187 4.2 32.0 1.0
C2 1:A2G1 4.3 21.2 0.3
CB 1:ASP211 4.3 24.4 1.0
CG 1:GLN185 4.5 27.7 1.0
CB 1:TRP189 4.6 37.6 1.0
CG 1:GLU198 4.6 25.6 1.0
C 1:ASN210 4.6 26.3 1.0
CB 1:ASP187 4.7 31.7 1.0
N 1:ILE212 4.7 24.9 1.0
C5 1:A2G1 4.8 26.1 0.3
CB 1:ASN210 4.8 24.6 1.0
CB 1:GLU198 4.8 24.7 1.0
N 1:TRP189 4.8 34.0 1.0
N 1:ASP188 4.9 29.9 1.0
C5 1:A2G1 4.9 22.6 0.3
CA 1:ASP187 4.9 30.8 1.0
CA 1:ASN210 5.0 26.6 1.0

Calcium binding site 3 out of 9 in 1bch

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Calcium binding site 3 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwgh) 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 (Qpdwgh) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Ca3

b:25.5
occ:1.00
 OE2 1:GLU84 2.4 25.5 1.0
O 1:HOH228 2.5 19.8 1.0
CD 1:GLU84 3.5 26.7 1.0
OE1 1:GLU84 4.0 27.3 1.0
OD1 1:ASN80 4.5 23.9 1.0
ND2 1:ASN80 4.6 23.6 1.0
O 2:HOH234 4.6 31.2 1.0
CG 1:GLU84 4.7 26.3 1.0
CG 1:ASN80 5.0 24.4 1.0

Calcium binding site 4 out of 9 in 1bch

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Calcium binding site 4 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwgh) 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 (Qpdwgh) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca227

b:34.1
occ:1.00
 O 2:HOH272 2.3 31.9 1.0
O 2:GLU198 2.4 38.2 1.0
OD1 2:ASP199 2.5 39.0 1.0
OD2 2:ASP161 2.5 32.7 1.0
OE1 2:GLU165 2.6 37.9 1.0
OE2 2:GLU165 2.6 30.7 1.0
OD1 2:ASP161 2.7 32.5 1.0
OD1 2:ASP188 2.7 41.0 1.0
CD 2:GLU165 2.9 34.7 1.0
CG 2:ASP161 2.9 34.4 1.0
C 2:GLU198 3.3 39.4 1.0
CG 2:ASP188 3.3 43.4 1.0
CG 2:ASP199 3.6 37.9 1.0
CA 2:ASP199 3.6 36.5 1.0
N 2:ASP199 3.8 37.8 1.0
CB 2:ASP188 3.8 42.7 1.0
O 2:HOH293 3.9 38.8 1.0
OD2 2:ASP188 4.0 43.3 1.0
CA 2:CA3 4.0 48.5 1.0
CB 2:ASP199 4.2 37.6 1.0
N 2:GLU198 4.3 43.0 1.0
CA 2:GLU198 4.4 40.1 1.0
CA 2:ASP188 4.4 43.1 1.0
CG 2:GLU165 4.4 37.7 1.0
CB 2:ASP161 4.4 33.9 1.0
O 2:HOH261 4.5 34.4 1.0
CZ 2:PHE168 4.5 31.9 1.0
OD2 2:ASP211 4.6 32.9 1.0
OD2 2:ASP199 4.6 39.6 1.0
O 2:ASP161 4.6 38.3 1.0
N 2:GLY166 4.8 37.8 1.0
C 2:ASP199 4.8 35.6 1.0
CA 2:GLU165 4.9 39.6 1.0

Calcium binding site 5 out of 9 in 1bch

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Calcium binding site 5 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwgh) 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 (Qpdwgh) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca2

b:35.7
occ:1.00
 OE1 2:GLU198 2.2 40.8 1.0
OD1 2:ASP211 2.4 30.9 1.0
OE1 2:GLN185 2.4 44.3 1.0
OD1 2:ASP187 2.4 41.2 1.0
O 2:ASP211 2.5 33.9 1.0
OD1 2:ASN210 2.5 41.9 1.0
O3 2:NGA1 2.6 39.7 1.0
O4 2:NGA1 2.7 40.6 1.0
CD 2:GLU198 3.3 40.4 1.0
CD 2:GLN185 3.3 42.8 1.0
CG 2:ASP211 3.4 35.1 1.0
C4 2:NGA1 3.5 43.7 1.0
CG 2:ASP187 3.5 42.7 1.0
CG 2:ASN210 3.5 41.5 1.0
C3 2:NGA1 3.5 42.4 1.0
C 2:ASP211 3.5 36.1 1.0
OE2 2:GLU198 3.7 41.0 1.0
N 2:ASP211 3.7 36.1 1.0
NE2 2:GLN185 3.8 43.2 1.0
ND2 2:ASN210 3.9 40.5 1.0
OD2 2:ASP187 3.9 41.8 1.0
CA 2:ASP211 4.1 35.3 1.0
OD2 2:ASP211 4.1 32.9 1.0
C2 2:NGA1 4.2 43.4 1.0
CB 2:ASP211 4.3 34.7 1.0
N 2:ASP187 4.3 41.6 1.0
CG 2:GLN185 4.5 42.6 1.0
CB 2:TRP189 4.5 51.2 1.0
CG 2:GLU198 4.6 39.9 1.0
C 2:ASN210 4.6 38.5 1.0
N 2:ILE212 4.7 35.5 1.0
CB 2:GLU198 4.7 40.3 1.0
CB 2:ASP187 4.7 41.4 1.0
N 2:TRP189 4.7 46.6 1.0
N 2:ASP188 4.8 41.6 1.0
CB 2:ASN210 4.8 39.8 1.0
C5 2:NGA1 4.9 45.7 1.0
CA 2:ASP187 4.9 41.3 1.0
CA 2:ASN210 5.0 39.3 1.0

Calcium binding site 6 out of 9 in 1bch

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Calcium binding site 6 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwgh) 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 (Qpdwgh) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca3

b:48.5
occ:1.00
 OE1 2:GLU165 2.3 37.9 1.0
O 2:HOH293 2.3 38.8 1.0
O 2:HOH312 2.4 45.4 1.0
OD1 2:ASP199 2.4 39.0 1.0
OD2 2:ASP199 2.5 39.6 1.0
O 2:HOH310 2.5 40.1 1.0
O 2:HOH311 2.6 41.4 1.0
CG 2:ASP199 2.8 37.9 1.0
CD 2:GLU165 3.4 34.7 1.0
CB 2:GLU165 3.9 39.9 1.0
CA 2:CA227 4.0 34.1 1.0
CG 2:GLU165 4.1 37.7 1.0
O 2:ASP161 4.2 38.3 1.0
CB 2:ASP199 4.3 37.6 1.0
OD1 2:ASP188 4.3 41.0 1.0
CA 2:GLU165 4.4 39.6 1.0
OE2 2:GLU165 4.4 30.7 1.0
OD2 2:ASP188 4.6 43.3 1.0
O 2:HOH271 4.7 50.8 1.0
OD2 2:ASP161 4.8 32.7 1.0
O 2:GLU162 4.8 43.8 1.0
CG 2:ASP188 4.9 43.4 1.0
N 2:GLU165 4.9 40.4 1.0
OD1 2:ASP161 5.0 32.5 1.0

Calcium binding site 7 out of 9 in 1bch

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Calcium binding site 7 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwgh) 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 (Qpdwgh) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca227

b:27.9
occ:1.00
 O 3:GLU198 2.3 28.0 1.0
O 3:HOH242 2.4 27.1 1.0
OD1 3:ASP199 2.4 23.9 1.0
OE1 3:GLU165 2.5 23.8 1.0
OD2 3:ASP161 2.5 33.1 1.0
OD1 3:ASP188 2.6 36.0 1.0
OE2 3:GLU165 2.7 25.5 1.0
OD1 3:ASP161 2.8 31.2 1.0
CD 3:GLU165 2.9 25.7 1.0
CG 3:ASP161 3.0 32.9 1.0
C 3:GLU198 3.2 27.4 1.0
CG 3:ASP188 3.3 36.0 1.0
CG 3:ASP199 3.5 25.3 1.0
CA 3:ASP199 3.7 27.7 1.0
CB 3:ASP188 3.7 36.6 1.0
N 3:ASP199 3.8 26.2 1.0
CB 3:ASP199 4.2 27.0 1.0
OD2 3:ASP188 4.2 34.6 1.0
N 3:GLU198 4.3 29.5 1.0
CA 3:GLU198 4.3 28.9 1.0
CA 3:ASP188 4.4 38.3 1.0
OD2 3:ASP199 4.4 24.6 1.0
CG 3:GLU165 4.4 28.4 1.0
CB 3:ASP161 4.5 32.2 1.0
N 3:GLY166 4.6 35.6 1.0
CZ 3:PHE168 4.7 36.1 1.0
O 3:HOH276 4.7 37.7 1.0
O 3:ASP161 4.8 33.5 1.0
O 3:HOH244 4.8 36.8 1.0
OD2 3:ASP211 4.8 32.3 1.0
CA 3:GLU165 4.9 32.2 1.0
C 3:ASP199 4.9 28.4 1.0

Calcium binding site 8 out of 9 in 1bch

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Calcium binding site 8 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwgh) 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 (Qpdwgh) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca2

b:35.1
occ:1.00
 OD1 3:ASP211 2.1 29.9 1.0
OE1 3:GLN185 2.4 43.7 1.0
OE1 3:GLU198 2.4 30.8 1.0
O3 3:NGA1 2.5 43.2 1.0
OD1 3:ASP187 2.5 38.5 1.0
O 3:ASP211 2.5 28.7 1.0
OD1 3:ASN210 2.6 31.7 1.0
O4 3:NGA1 2.6 44.2 1.0
CD 3:GLN185 3.2 43.7 1.0
CG 3:ASP211 3.3 32.4 1.0
C4 3:NGA1 3.4 44.6 1.0
CD 3:GLU198 3.4 29.8 1.0
C3 3:NGA1 3.4 45.7 1.0
CG 3:ASP187 3.5 40.7 1.0
CG 3:ASN210 3.5 33.1 1.0
C 3:ASP211 3.6 28.6 1.0
NE2 3:GLN185 3.6 43.1 1.0
OE2 3:GLU198 3.8 30.0 1.0
N 3:ASP211 3.8 30.9 1.0
ND2 3:ASN210 3.8 28.9 1.0
OD2 3:ASP187 3.9 39.9 1.0
OD2 3:ASP211 4.0 32.3 1.0
CA 3:ASP211 4.1 29.7 1.0
C2 3:NGA1 4.2 47.1 1.0
CB 3:ASP211 4.3 30.8 1.0
N 3:ASP187 4.3 40.6 1.0
CG 3:GLN185 4.5 43.4 1.0
CB 3:TRP189 4.7 39.1 1.0
CG 3:GLU198 4.7 29.2 1.0
C 3:ASN210 4.7 32.8 1.0
CB 3:ASP187 4.7 40.7 1.0
N 3:ILE212 4.8 27.4 1.0
C5 3:NGA1 4.8 47.2 1.0
CB 3:GLU198 4.8 27.6 1.0
CB 3:ASN210 4.8 31.9 1.0
N 3:TRP189 4.9 37.6 1.0
N 3:ASP188 4.9 38.9 1.0
CA 3:ASP187 5.0 41.4 1.0

Calcium binding site 9 out of 9 in 1bch

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Calcium binding site 9 out of 9 in the Mannose-Binding Protein-A Mutant (Qpdwgh) 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 (Qpdwgh) Complexed with N- Acetyl-D-Galactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca3

b:27.8
occ:1.00
 O 1:HOH239 2.3 31.6 1.0
O 3:HOH228 2.3 24.0 1.0
OE2 3:GLU84 2.4 25.2 1.0
O 3:HOH249 2.4 26.9 1.0
CD 3:GLU84 3.5 23.6 1.0
OE1 3:GLU84 4.0 28.0 1.0
NZ 1:LYS89 4.2 26.9 1.0
O 3:HOH236 4.4 32.9 1.0
O 3:HOH290 4.6 46.5 1.0
ND2 3:ASN80 4.6 27.8 1.0
OD1 3:ASN80 4.6 25.6 1.0
O 1:HOH271 4.7 34.9 1.0
O 3:HOH248 4.7 38.2 1.0
CG 3:GLU84 4.8 21.3 1.0
O 3:HOH296 4.9 54.5 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 06:20:26 2024

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