Atomistry » Calcium » PDB 1fak-1fn6 » 1fih
Atomistry »
  Calcium »
    PDB 1fak-1fn6 »
      1fih »

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

Go back to Calcium Binding Sites List in 1fih
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

Go back to Calcium Binding Sites List in 1fih
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

Go back to Calcium Binding Sites List in 1fih
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

Go back to Calcium Binding Sites List in 1fih
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

Go back to Calcium Binding Sites List in 1fih
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

Go back to Calcium Binding Sites List in 1fih
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

Go back to Calcium Binding Sites List in 1fih
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

Go back to Calcium Binding Sites List in 1fih
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: Thu Jul 11 08:09:19 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy