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

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

Go back to Calcium Binding Sites List in 1bch
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

Go back to Calcium Binding Sites List in 1bch
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

Go back to Calcium Binding Sites List in 1bch
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

Go back to Calcium Binding Sites List in 1bch
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

Go back to Calcium Binding Sites List in 1bch
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

Go back to Calcium Binding Sites List in 1bch
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

Go back to Calcium Binding Sites List in 1bch
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

Go back to Calcium Binding Sites List in 1bch
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

Go back to Calcium Binding Sites List in 1bch
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: Sat Dec 12 02:49:34 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy