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Calcium in PDB 1fif: N-Acetylgalactosamine-Selective Mutant of Mannose-Binding Protein-A (Qpdwg-Hdrpy)

Protein crystallography data

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

Resolution Low / High (Å) 28.68 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.340, 84.833, 97.142, 90.00, 107.88, 90.00
R / Rfree (%) 19.3 / 22.9

Other elements in 1fif:

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

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the N-Acetylgalactosamine-Selective Mutant of Mannose-Binding Protein-A (Qpdwg-Hdrpy) (pdb code 1fif). 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-Selective Mutant of Mannose-Binding Protein-A (Qpdwg-Hdrpy), PDB code: 1fif:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1fif

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


Mono view


Stereo pair view

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

b:14.7
occ:1.00
 O A:HOH554 2.3 12.1 1.0
OD2 A:ASP161 2.4 14.5 1.0
OD1 A:ASP199 2.4 13.0 1.0
O A:GLU198 2.4 15.8 1.0
OE2 A:GLU165 2.5 14.3 1.0
OD1 A:ASP188 2.6 16.2 1.0
OE1 A:GLU165 2.6 13.6 1.0
OD1 A:ASP161 2.7 15.6 1.0
CG A:ASP161 2.9 14.3 1.0
CD A:GLU165 2.9 13.0 1.0
CG A:ASP188 3.4 16.5 1.0
C A:GLU198 3.4 14.3 1.0
CG A:ASP199 3.5 14.4 1.0
CA A:ASP199 3.8 12.6 1.0
O A:HOH555 3.8 35.3 1.0
CB A:ASP188 3.9 15.0 1.0
N A:ASP199 4.0 11.8 1.0
CB A:ASP199 4.2 13.3 1.0
OD2 A:ASP188 4.3 16.8 1.0
N A:GLU198 4.4 15.3 1.0
CB A:ASP161 4.4 15.3 1.0
CG A:GLU165 4.4 15.2 1.0
CA A:ASP188 4.4 16.9 1.0
OD2 A:ASP199 4.5 16.9 1.0
CA A:GLU198 4.5 13.9 1.0
N A:GLY166 4.5 15.8 1.0
OD2 A:ASP211 4.7 15.5 1.0
O A:HOH498 4.7 14.3 1.0
CZ A:PHE168 4.7 15.9 1.0
O A:HOH433 4.7 18.4 1.0
O A:ASP161 4.9 16.4 1.0
CA A:GLU165 4.9 15.5 1.0
C A:ASP199 5.0 12.4 1.0

Calcium binding site 2 out of 9 in 1fif

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


Mono view


Stereo pair view

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

b:16.6
occ:1.00
 OD1 A:ASP211 2.3 12.6 1.0
OE1 A:GLU198 2.3 12.8 1.0
OD1 A:ASP187 2.4 17.7 1.0
O A:ASP211 2.5 16.5 1.0
OD1 A:ASN210 2.5 24.2 1.0
OE1 A:GLN185 2.5 18.9 1.0
O A:HOH439 2.6 28.4 1.0
O A:HOH444 2.7 25.4 1.0
CD A:GLU198 3.2 14.6 1.0
CG A:ASP211 3.3 15.6 1.0
CD A:GLN185 3.5 21.2 1.0
CG A:ASP187 3.5 18.1 1.0
CG A:ASN210 3.5 21.6 1.0
C A:ASP211 3.5 16.5 1.0
OE2 A:GLU198 3.6 16.6 1.0
N A:ASP211 3.7 15.1 1.0
NE2 A:GLN185 3.9 18.3 1.0
ND2 A:ASN210 3.9 23.6 1.0
OD2 A:ASP187 4.0 15.3 1.0
OD2 A:ASP211 4.0 15.5 1.0
CA A:ASP211 4.1 14.9 1.0
N A:ASP187 4.2 16.0 1.0
CB A:ASP211 4.3 15.3 1.0
CG A:GLU198 4.6 14.0 1.0
O A:HOH545 4.6 48.9 1.0
CB A:TRP189 4.6 23.1 1.0
N A:ASP212 4.6 16.5 1.0
CB A:ASP187 4.7 16.8 1.0
C A:ASN210 4.7 15.3 1.0
CG A:GLN185 4.7 16.6 1.0
N A:ASP188 4.7 15.9 1.0
N A:TRP189 4.8 19.4 1.0
CB A:GLU198 4.8 13.1 1.0
CB A:ASN210 4.8 17.4 1.0
CA A:ASP187 4.8 16.3 1.0
CA A:ASP212 5.0 16.2 1.0

Calcium binding site 3 out of 9 in 1fif

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


Mono view


Stereo pair view

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

b:14.0
occ:1.00
 O A:HOH416 2.3 12.9 1.0
OE2 A:GLU84 2.4 17.0 1.0
O A:HOH558 2.4 20.4 1.0
CD A:GLU84 3.5 18.7 1.0
OE1 A:GLU84 4.0 18.3 1.0
OD1 A:ASN80 4.4 16.4 1.0
O A:HOH560 4.7 27.8 1.0
ND2 A:ASN80 4.7 13.0 1.0
CG A:GLU84 4.7 13.9 1.0

Calcium binding site 4 out of 9 in 1fif

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


Mono view


Stereo pair view

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

b:16.4
occ:1.00
 O B:HOH364 2.3 12.7 1.0
OD2 B:ASP161 2.3 14.4 1.0
OD1 B:ASP199 2.4 11.5 1.0
O B:GLU198 2.5 17.4 1.0
OE2 B:GLU165 2.5 16.2 1.0
OE1 B:GLU165 2.5 16.1 1.0
OD1 B:ASP161 2.7 13.3 1.0
OD2 B:ASP188 2.7 18.9 1.0
CD B:GLU165 2.8 17.9 1.0
CG B:ASP161 2.9 15.7 1.0
C B:GLU198 3.4 18.5 1.0
CG B:ASP199 3.5 15.3 1.0
CG B:ASP188 3.6 21.6 1.0
CA B:ASP199 3.7 17.0 1.0
CB B:ASP188 3.8 21.0 1.0
CA B:CA3 3.8 17.4 1.0
N B:ASP199 4.0 18.6 1.0
O B:HOH231 4.0 18.2 1.0
CB B:ASP199 4.2 16.1 1.0
O B:HOH227 4.3 15.9 1.0
CG B:GLU165 4.3 17.1 1.0
CB B:ASP161 4.4 14.1 1.0
OD2 B:ASP199 4.5 12.6 1.0
CA B:GLU198 4.5 21.2 1.0
O B:ASP161 4.6 16.5 1.0
OD2 B:ASP211 4.6 19.7 1.0
CZ B:PHE168 4.6 19.6 1.0
N B:GLY166 4.7 17.1 1.0
N B:GLU198 4.7 20.4 1.0
OD1 B:ASP188 4.7 19.4 1.0
C B:ASP199 4.9 17.4 1.0
CA B:GLU165 4.9 17.0 1.0
O B:HOH365 4.9 15.8 1.0
CB B:GLU198 5.0 21.0 1.0

Calcium binding site 5 out of 9 in 1fif

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


Mono view


Stereo pair view

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

b:20.3
occ:1.00
 OD1 B:ASP211 2.3 17.0 1.0
OE1 B:GLU198 2.3 24.5 1.0
O B:ASP211 2.3 17.2 1.0
OD1 B:ASP187 2.4 21.3 1.0
O B:HOH363 2.4 18.2 1.0
OE1 B:GLN185 2.5 20.7 1.0
O B:HOH275 2.5 23.3 1.0
CG B:ASP211 3.3 18.4 1.0
C B:ASP211 3.3 17.8 1.0
CD B:GLU198 3.4 22.5 1.0
CG B:ASP187 3.4 23.3 1.0
CD B:GLN185 3.5 19.5 1.0
N B:ASP211 3.6 18.7 1.0
OE2 B:GLU198 3.8 24.4 1.0
OD2 B:ASP187 3.9 24.0 1.0
CA B:ASP211 3.9 17.4 1.0
NE2 B:GLN185 4.0 20.0 1.0
OD2 B:ASP211 4.0 19.7 1.0
CB B:ASP211 4.2 18.9 1.0
N B:ASP187 4.2 19.5 1.0
O B:HOH368 4.2 48.0 1.0
N B:ASP212 4.3 17.4 1.0
O B:HOH324 4.5 30.5 1.0
C B:ASN210 4.6 19.3 1.0
CA B:ASP212 4.6 18.2 1.0
CB B:ASP187 4.6 21.3 1.0
CG B:GLU198 4.6 21.5 1.0
CB B:ASN210 4.7 20.3 1.0
O B:HOH367 4.7 51.3 1.0
CA B:ASP187 4.8 20.7 1.0
CG B:GLN185 4.9 16.8 1.0
C B:ASP187 4.9 21.5 1.0
CA B:ASN210 4.9 19.2 1.0
ND2 B:ASN210 4.9 22.7 1.0
CB B:GLU198 4.9 21.0 1.0
N B:ASP188 5.0 21.0 1.0

Calcium binding site 6 out of 9 in 1fif

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


Mono view


Stereo pair view

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

b:17.4
occ:1.00
 O B:HOH365 2.2 15.8 1.0
OE1 B:GLU165 2.3 16.1 1.0
O B:HOH362 2.3 27.6 1.0
O B:HOH231 2.4 18.2 1.0
O B:HOH366 2.4 15.1 1.0
OD1 B:ASP199 2.5 11.5 1.0
OD2 B:ASP199 2.6 12.6 1.0
CG B:ASP199 2.9 15.3 1.0
CD B:GLU165 3.5 17.9 1.0
CA B:CA1 3.8 16.4 1.0
O B:HOH249 3.9 22.6 1.0
OD2 B:ASP188 4.1 18.9 1.0
O B:ASP161 4.1 16.5 1.0
CB B:GLU165 4.2 17.9 1.0
O B:GLY196 4.2 25.1 1.0
CG B:GLU165 4.3 17.1 1.0
CB B:ASP199 4.4 16.1 1.0
O B:HOH271 4.4 26.1 1.0
O B:HOH270 4.4 27.1 1.0
OE2 B:GLU165 4.5 16.2 1.0
CA B:GLU165 4.5 17.0 1.0
O B:HIS192 4.6 26.8 1.0
OD2 B:ASP161 4.6 14.4 1.0
O B:HOH370 4.7 46.9 1.0
CB B:HIS192 4.9 24.9 1.0
OD1 B:ASP161 4.9 13.3 1.0
CG B:ASP161 5.0 15.7 1.0

Calcium binding site 7 out of 9 in 1fif

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


Mono view


Stereo pair view

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

b:16.1
occ:1.00
 O C:HOH534 2.3 12.2 1.0
OD1 C:ASP199 2.3 13.5 1.0
OD2 C:ASP161 2.4 18.3 1.0
OD1 C:ASP188 2.4 19.8 1.0
O C:GLU198 2.5 14.4 1.0
OE2 C:GLU165 2.5 15.1 1.0
OE1 C:GLU165 2.6 15.6 1.0
OD1 C:ASP161 2.9 18.7 1.0
CD C:GLU165 2.9 16.9 1.0
CG C:ASP161 3.0 19.9 1.0
CG C:ASP188 3.3 20.1 1.0
C C:GLU198 3.4 15.5 1.0
CG C:ASP199 3.5 15.2 1.0
CA C:ASP199 3.8 15.7 1.0
CB C:ASP188 3.8 18.9 1.0
N C:ASP199 4.0 15.0 1.0
CB C:ASP199 4.2 15.3 1.0
OD2 C:ASP188 4.3 17.0 1.0
CG C:GLU165 4.4 15.7 1.0
CA C:ASP188 4.4 20.5 1.0
N C:GLU198 4.4 16.9 1.0
OD2 C:ASP199 4.4 15.3 1.0
CB C:ASP161 4.5 17.4 1.0
CA C:GLU198 4.5 15.2 1.0
CZ C:PHE168 4.6 16.6 1.0
N C:GLY166 4.6 21.9 1.0
OD2 C:ASP211 4.6 21.8 1.0
O C:HOH421 4.7 20.0 1.0
O C:HOH477 4.7 24.2 1.0
O C:ASP161 4.8 18.6 1.0
CA C:GLU165 4.9 20.9 1.0
C C:ASP199 5.0 17.3 1.0

Calcium binding site 8 out of 9 in 1fif

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


Mono view


Stereo pair view

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

b:18.9
occ:1.00
 OD1 C:ASP211 2.2 17.6 1.0
O C:HOH459 2.3 29.6 1.0
OE1 C:GLU198 2.3 17.8 1.0
OE1 C:GLN185 2.4 37.1 1.0
OD1 C:ASP187 2.4 19.8 1.0
O C:ASP211 2.5 19.7 1.0
OD1 C:ASN210 2.8 26.4 0.5
O C:HOH428 2.9 32.0 1.0
CD C:GLU198 3.1 17.9 1.0
CG C:ASP211 3.2 20.9 1.0
OE2 C:GLU198 3.4 20.8 1.0
CD C:GLN185 3.5 35.7 1.0
C C:ASP211 3.5 19.3 1.0
CG C:ASP187 3.6 21.8 1.0
CG C:ASN210 3.7 24.6 0.5
N C:ASP211 3.8 21.1 1.0
OD2 C:ASP211 3.9 21.8 1.0
NE2 C:GLN185 4.0 33.8 1.0
OD2 C:ASP187 4.0 20.8 1.0
ND2 C:ASN210 4.1 25.1 0.5
CA C:ASP211 4.1 20.6 1.0
CB C:ASP211 4.3 19.1 1.0
N C:ASP187 4.3 23.1 1.0
CG C:GLU198 4.5 16.6 1.0
CB C:TRP189 4.5 23.8 1.0
N C:ASP212 4.7 17.3 1.0
CB C:GLU198 4.7 17.2 1.0
N C:TRP189 4.7 23.1 1.0
N C:ASP188 4.7 20.1 1.0
CG C:GLN185 4.8 33.2 1.0
C C:ASN210 4.8 22.8 0.5
C C:ASN210 4.8 22.3 0.5
CB C:ASP187 4.8 21.7 1.0
CB C:ASN210 4.9 25.6 0.5
CA C:ASP187 4.9 22.0 1.0
CA C:ASP212 5.0 18.5 1.0
CB C:ASN210 5.0 23.8 0.5

Calcium binding site 9 out of 9 in 1fif

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


Mono view


Stereo pair view

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

b:15.6
occ:1.00
 O C:HOH535 2.3 16.0 1.0
O A:HOH557 2.3 17.8 1.0
OE2 C:GLU84 2.3 12.9 1.0
O C:HOH536 2.4 16.5 1.0
CD C:GLU84 3.4 16.2 1.0
OE1 C:GLU84 3.9 15.7 1.0
OD1 C:ASN80 4.5 15.2 1.0
NZ A:LYS89 4.5 18.1 1.0
ND2 C:ASN80 4.6 11.7 1.0
CG C:GLU84 4.7 14.7 1.0
O A:HOH521 4.7 28.1 1.0
O C:HOH537 4.8 33.0 1.0
CG C:ASN80 5.0 15.7 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 08:09:17 2024

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