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Calcium in PDB 1fih: N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine

Protein crystallography data

The structure of N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine, PDB code: 1fih was solved by H.Feinberg, D.Torgerson, K.Drickamer, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.66 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.490, 84.552, 98.542, 90.00, 105.43, 90.00
R / Rfree (%) 23.7 / 26.9

Other elements in 1fih:

The structure of N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 9 in 1fih

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Calcium binding site 1 out of 9 in the N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:25.6
occ:1.00
 OD1 A:ASP199 2.2 22.4 1.0
O A:HOH484 2.3 23.8 1.0
OD2 A:ASP161 2.3 29.4 1.0
O A:GLU198 2.4 27.6 1.0
OD1 A:ASP188 2.5 29.5 1.0
OE1 A:GLU165 2.6 27.6 1.0
OE2 A:GLU165 2.6 30.5 1.0
OD1 A:ASP161 2.8 25.7 1.0
CG A:ASP161 2.9 28.2 1.0
CD A:GLU165 2.9 28.7 1.0
CG A:ASP188 3.3 29.9 1.0
C A:GLU198 3.4 28.0 1.0
CG A:ASP199 3.4 22.8 1.0
CA A:ASP199 3.7 24.5 1.0
CB A:ASP188 3.9 30.1 1.0
O A:HOH485 3.9 37.8 1.0
N A:ASP199 4.0 25.3 1.0
CB A:ASP199 4.1 23.4 1.0
OD2 A:ASP188 4.2 28.5 1.0
OD2 A:ASP199 4.4 25.7 1.0
N A:GLU198 4.4 28.9 1.0
CA A:ASP188 4.4 32.2 1.0
CB A:ASP161 4.4 28.7 1.0
CG A:GLU165 4.4 29.5 1.0
CA A:GLU198 4.5 28.9 1.0
CZ A:PHE168 4.7 30.4 1.0
N A:GLY166 4.7 31.1 1.0
O A:HOH419 4.7 27.3 1.0
O A:ASP161 4.7 28.3 1.0
OD2 A:ASP211 4.8 27.7 1.0
C A:ASP199 5.0 24.8 1.0

Calcium binding site 2 out of 9 in 1fih

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Calcium binding site 2 out of 9 in the N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:28.1
occ:1.00
 OD1 A:ASP211 2.2 26.3 1.0
OE1 A:GLU198 2.3 25.7 1.0
OE1 A:GLN185 2.5 32.4 1.0
OD1 A:ASN210 2.5 29.9 1.0
O A:ASP211 2.5 27.1 1.0
OD1 A:ASP187 2.5 32.4 1.0
O3 A:NGA227 2.5 32.5 1.0
O4 A:NGA227 2.7 31.7 1.0
CG A:ASP211 3.3 29.0 1.0
CD A:GLU198 3.3 27.9 1.0
CD A:GLN185 3.4 35.1 1.0
CG A:ASN210 3.4 29.2 1.0
C4 A:NGA227 3.5 34.6 1.0
C3 A:NGA227 3.5 34.0 1.0
CG A:ASP187 3.5 32.6 1.0
C A:ASP211 3.6 27.5 1.0
OE2 A:GLU198 3.6 28.5 1.0
ND2 A:ASN210 3.7 26.9 1.0
N A:ASP211 3.8 26.6 1.0
NE2 A:GLN185 3.9 31.1 1.0
OD2 A:ASP211 4.0 27.7 1.0
OD2 A:ASP187 4.0 33.3 1.0
CA A:ASP211 4.1 25.9 1.0
N A:ASP187 4.2 33.0 1.0
C2 A:NGA227 4.2 36.0 1.0
CB A:ASP211 4.3 27.7 1.0
CG A:GLU198 4.6 28.0 1.0
CG A:GLN185 4.6 33.6 1.0
N A:ASP212 4.7 24.6 1.0
CB A:ASP187 4.7 34.1 1.0
C A:ASN210 4.7 28.0 1.0
CB A:GLU198 4.8 28.6 1.0
CB A:ASN210 4.8 28.3 1.0
CB A:TRP189 4.8 38.1 1.0
N A:ASP188 4.9 31.0 1.0
CA A:ASP187 4.9 32.7 1.0
C5 A:NGA227 4.9 36.6 1.0
N A:TRP189 4.9 32.8 1.0
CA A:ASN210 5.0 28.1 1.0

Calcium binding site 3 out of 9 in 1fih

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Calcium binding site 3 out of 9 in the N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:28.2
occ:1.00
 O A:HOH488 2.3 22.2 1.0
OE2 A:GLU84 2.4 28.4 1.0
CD A:GLU84 3.6 30.3 1.0
OE1 A:GLU84 4.1 29.3 1.0
OD1 A:ASN80 4.5 28.8 1.0
ND2 A:ASN80 4.7 26.6 1.0
O B:HOH456 4.8 35.8 1.0
CG A:GLU84 4.8 26.3 1.0

Calcium binding site 4 out of 9 in 1fih

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Calcium binding site 4 out of 9 in the N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:43.0
occ:1.00
 OD1 B:ASP199 2.2 51.5 1.0
OD2 B:ASP161 2.3 45.3 1.0
O B:HOH425 2.4 37.0 1.0
OE1 B:GLU165 2.4 40.5 1.0
OE2 B:GLU165 2.5 35.9 1.0
O B:GLU198 2.6 45.9 1.0
OD1 B:ASP188 2.6 45.2 1.0
CD B:GLU165 2.8 40.0 1.0
OD1 B:ASP161 2.8 43.9 1.0
CG B:ASP161 2.9 44.7 1.0
CG B:ASP188 3.3 50.6 1.0
C B:GLU198 3.4 48.2 1.0
CG B:ASP199 3.4 50.9 1.0
CA B:ASP199 3.6 47.0 1.0
O B:HOH417 3.7 38.4 1.0
CA B:CA3 3.8 49.7 1.0
CB B:ASP188 3.8 50.0 1.0
N B:ASP199 3.9 48.1 1.0
CB B:ASP199 4.0 48.9 1.0
OD2 B:ASP188 4.1 47.3 1.0
CG B:GLU165 4.3 43.0 1.0
CB B:ASP161 4.4 45.0 1.0
N B:GLU198 4.4 50.1 1.0
OD2 B:ASP199 4.4 52.7 1.0
CA B:GLU198 4.5 48.8 1.0
CA B:ASP188 4.5 52.5 1.0
O B:ASP161 4.6 47.9 1.0
OD2 B:ASP211 4.6 36.6 1.0
CZ B:PHE168 4.7 42.9 1.0
N B:GLY166 4.8 43.6 1.0
CA B:GLU165 4.8 45.8 1.0
C B:ASP199 4.9 47.0 1.0
CB B:GLU165 5.0 45.3 1.0

Calcium binding site 5 out of 9 in 1fih

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Calcium binding site 5 out of 9 in the N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:42.2
occ:1.00
 OD1 B:ASP211 2.3 39.6 1.0
OD1 B:ASP187 2.3 55.0 1.0
O B:ASP211 2.4 44.2 1.0
OE1 B:GLN185 2.4 50.1 1.0
OE1 B:GLU198 2.4 49.2 1.0
O4 B:NGA227 2.5 57.8 1.0
O3 B:NGA227 2.6 55.8 1.0
OD1 B:ASN210 2.7 45.0 1.0
CG B:ASP211 3.3 41.8 1.0
C4 B:NGA227 3.4 59.3 1.0
CD B:GLU198 3.4 49.8 1.0
CG B:ASP187 3.4 54.4 1.0
CD B:GLN185 3.4 49.2 1.0
C3 B:NGA227 3.5 58.6 1.0
C B:ASP211 3.5 44.0 1.0
CG B:ASN210 3.6 45.5 1.0
N B:ASP211 3.7 43.7 1.0
OE2 B:GLU198 3.8 50.2 1.0
ND2 B:ASN210 3.9 45.2 1.0
OD2 B:ASP187 3.9 52.6 1.0
NE2 B:GLN185 4.0 48.2 1.0
CA B:ASP211 4.0 42.9 1.0
OD2 B:ASP211 4.1 36.6 1.0
C2 B:NGA227 4.1 58.5 1.0
N B:ASP187 4.2 52.4 1.0
CB B:ASP211 4.3 41.4 1.0
CG B:GLN185 4.6 50.4 1.0
C B:ASN210 4.6 46.3 1.0
N B:ASP212 4.6 43.2 1.0
CG B:GLU198 4.7 49.0 1.0
CB B:ASP187 4.7 52.6 1.0
N B:ASP188 4.7 51.6 1.0
CB B:TRP189 4.7 58.9 1.0
C5 B:NGA227 4.8 60.1 1.0
N B:TRP189 4.8 56.0 1.0
CB B:GLU198 4.8 49.0 1.0
CB B:ASN210 4.8 46.0 1.0
N2 B:NGA227 4.9 58.4 1.0
CA B:ASP187 4.9 52.1 1.0
CA B:ASP212 4.9 43.2 1.0
CA B:ASN210 4.9 46.6 1.0

Calcium binding site 6 out of 9 in 1fih

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Calcium binding site 6 out of 9 in the N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:49.7
occ:1.00
 OE1 B:GLU165 2.3 40.5 1.0
O B:HOH417 2.3 38.4 1.0
OD1 B:ASP199 2.4 51.5 1.0
O B:HOH455 2.4 52.7 1.0
OD2 B:ASP199 2.5 52.7 1.0
CG B:ASP199 2.8 50.9 1.0
CD B:GLU165 3.5 40.0 1.0
CA B:CA1 3.8 43.0 1.0
CB B:GLU165 4.1 45.3 1.0
CG B:GLU165 4.1 43.0 1.0
OD1 B:ASP188 4.2 45.2 1.0
O B:ASP161 4.2 47.9 1.0
CB B:ASP199 4.2 48.9 1.0
OE2 B:GLU165 4.5 35.9 1.0
CA B:GLU165 4.5 45.8 1.0
OD2 B:ASP161 4.7 45.3 1.0
OD2 B:ASP188 4.8 47.3 1.0
OH B:TYR190 4.8 54.5 1.0
CG B:ASP188 4.8 50.6 1.0
O B:GLU162 4.9 56.1 1.0
N B:GLU165 5.0 47.3 1.0

Calcium binding site 7 out of 9 in 1fih

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Calcium binding site 7 out of 9 in the N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:32.1
occ:1.00
 OD1 C:ASP199 2.2 26.9 1.0
OD2 C:ASP161 2.3 33.2 1.0
O C:GLU198 2.3 29.8 1.0
O C:HOH470 2.4 33.5 1.0
OD1 C:ASP188 2.6 37.8 1.0
OE1 C:GLU165 2.6 27.1 1.0
OE2 C:GLU165 2.7 30.6 1.0
OD1 C:ASP161 2.8 31.6 1.0
CG C:ASP161 2.9 34.6 1.0
CD C:GLU165 3.0 30.8 1.0
C C:GLU198 3.3 31.4 1.0
CG C:ASP188 3.3 39.2 1.0
CG C:ASP199 3.4 27.2 1.0
CA C:ASP199 3.7 29.1 1.0
CB C:ASP188 3.8 37.9 1.0
N C:ASP199 3.8 28.5 1.0
CB C:ASP199 4.1 27.4 1.0
OD2 C:ASP188 4.2 36.0 1.0
N C:GLU198 4.3 34.3 1.0
OD2 C:ASP199 4.4 27.4 1.0
CA C:GLU198 4.4 32.9 1.0
CB C:ASP161 4.4 34.1 1.0
CA C:ASP188 4.5 38.7 1.0
CG C:GLU165 4.5 31.6 1.0
CZ C:PHE168 4.6 35.9 1.0
O C:HOH472 4.6 34.7 1.0
O C:ASP161 4.7 35.6 1.0
N C:GLY166 4.7 37.4 1.0
OD2 C:ASP211 4.8 34.6 1.0
O C:HOH458 4.9 38.8 1.0
C C:ASP199 4.9 30.4 1.0

Calcium binding site 8 out of 9 in 1fih

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Calcium binding site 8 out of 9 in the N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2

b:36.2
occ:1.00
 OD1 C:ASP211 2.1 30.6 1.0
OE1 C:GLU198 2.4 34.6 1.0
O C:ASP211 2.4 32.6 1.0
OE1 C:GLN185 2.4 39.4 1.0
OD1 C:ASP187 2.5 36.6 1.0
OD1 C:ASN210 2.7 34.6 1.0
O4 C:NGA227 2.7 40.5 1.0
O3 C:NGA227 2.7 41.9 1.0
CG C:ASP211 3.2 34.5 1.0
CD C:GLU198 3.3 35.7 1.0
CD C:GLN185 3.3 38.4 1.0
CG C:ASP187 3.4 40.4 1.0
C C:ASP211 3.5 33.8 1.0
C4 C:NGA227 3.5 44.0 1.0
CG C:ASN210 3.6 34.8 1.0
C3 C:NGA227 3.6 43.5 1.0
OE2 C:GLU198 3.7 35.7 1.0
NE2 C:GLN185 3.7 34.7 1.0
N C:ASP211 3.8 34.9 1.0
ND2 C:ASN210 3.9 33.4 1.0
OD2 C:ASP211 3.9 34.6 1.0
OD2 C:ASP187 3.9 38.8 1.0
CA C:ASP211 4.0 33.0 1.0
N C:ASP187 4.1 40.7 1.0
CB C:ASP211 4.2 34.9 1.0
C2 C:NGA227 4.3 45.3 1.0
CG C:GLU198 4.6 33.7 1.0
CG C:GLN185 4.6 37.4 1.0
CB C:ASP187 4.6 38.1 1.0
N C:ASP212 4.6 30.9 1.0
C C:ASN210 4.7 35.9 1.0
CB C:GLU198 4.7 35.2 1.0
CB C:TRP189 4.8 44.1 1.0
CA C:ASP187 4.8 40.0 1.0
N C:ASP188 4.8 37.6 1.0
CB C:ASN210 4.9 33.1 1.0
C5 C:NGA227 4.9 43.9 1.0
CA C:PRO186 4.9 40.0 1.0
N C:TRP189 5.0 41.0 1.0
CA C:ASP212 5.0 32.0 1.0

Calcium binding site 9 out of 9 in 1fih

Go back to Calcium Binding Sites List in 1fih
Calcium binding site 9 out of 9 in the N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of N-Acetylgalactosamine Binding Mutant of Mannose-Binding Protein A (Qpdwg-Hdrpy), Complex with N-Acetylgalactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca3

b:30.8
occ:1.00
 O A:HOH487 2.2 31.2 1.0
O C:HOH471 2.3 31.3 1.0
OE2 C:GLU84 2.5 31.6 1.0
O C:HOH473 2.5 36.9 1.0
CD C:GLU84 3.6 30.6 1.0
OE1 C:GLU84 4.1 32.6 1.0
NZ A:LYS89 4.4 39.4 1.0
ND2 C:ASN80 4.6 30.1 1.0
OD1 C:ASN80 4.6 30.5 1.0
O A:HOH469 4.7 49.5 1.0
CG C:GLU84 4.8 26.4 1.0
O C:HOH474 4.9 44.1 1.0

Reference:

H.Feinberg, D.Torgersen, K.Drickamer, W.I.Weis. Mechanism of pH-Dependent N-Acetylgalactosamine Binding By A Functional Mimic of the Hepatocyte Asialoglycoprotein Receptor. J.Biol.Chem. V. 275 35176 2000.
ISSN: ISSN 0021-9258
PubMed: 10931846
DOI: 10.1074/JBC.M005557200
Page generated: Sat Dec 12 02:55:39 2020

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