Calcium in PDB 6lzs: W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose.

Protein crystallography data

The structure of W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose., PDB code: 6lzs was solved by Y.Kitaoku, P.Ubonbal, L.T.Tran, R.C.Robinson, W.Suginta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.651, 80.379, 112.777, 90.19, 89.89, 79.08
R / Rfree (%) 21.4 / 28.2

Other elements in 6lzs:

The structure of W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose. also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms
Magnesium (Mg) 1 atom

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose. (pdb code 6lzs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose., PDB code: 6lzs:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 6lzs

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Calcium binding site 1 out of 11 in the W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:27.6
occ:1.00
 O A:LEU524 2.2 24.2 1.0
O A:ASN190 2.3 23.3 1.0
O A:HOH800 2.3 21.5 1.0
OD1 A:ASN190 2.4 33.0 1.0
O A:HOH900 2.4 32.7 1.0
CG A:ASN190 3.3 39.0 1.0
C A:ASN190 3.4 30.7 1.0
C A:LEU524 3.4 21.4 1.0
CA A:ASN190 3.9 27.1 1.0
CB A:ASN190 3.9 30.8 1.0
O A:HOH887 4.0 34.8 1.0
CA A:ASP525 4.2 22.4 1.0
ND2 A:ASN190 4.2 49.6 1.0
N A:ASP525 4.3 24.6 1.0
OD2 A:ASP192 4.4 37.9 1.0
CA A:LEU524 4.4 17.1 1.0
OD1 A:ASP525 4.5 25.7 1.0
N A:LEU191 4.5 24.9 1.0
O A:HOH728 4.6 26.5 1.0
CB A:LEU524 4.7 17.9 1.0
O A:HOH873 4.7 26.1 1.0
C A:ASP525 4.8 22.4 1.0
NZ A:LYS527 4.9 31.7 1.0
CA A:LEU191 4.9 32.1 1.0

Calcium binding site 2 out of 11 in 6lzs

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Calcium binding site 2 out of 11 in the W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca605

b:19.6
occ:1.00
 OD1 A:ASN340 2.3 22.7 1.0
O A:PHE344 2.3 15.6 1.0
OD1 A:ASP342 2.4 24.6 1.0
O A:HOH712 2.4 19.0 1.0
OD1 A:ASP338 2.5 18.7 1.0
OD2 A:ASP346 2.8 15.1 1.0
OD1 A:ASP346 2.9 20.9 1.0
CG A:ASP346 3.1 15.8 1.0
CG A:ASP342 3.3 23.2 1.0
CG A:ASN340 3.3 27.6 1.0
CG A:ASP338 3.4 22.6 1.0
C A:PHE344 3.5 15.6 1.0
OD2 A:ASP342 3.6 26.1 1.0
ND2 A:ASN340 3.9 38.0 1.0
N A:PHE344 4.1 25.3 1.0
CB A:ASP338 4.1 21.5 1.0
CA A:ASP338 4.1 20.2 1.0
CA A:PHE344 4.2 21.6 1.0
OD2 A:ASP338 4.3 16.4 1.0
N A:ASN340 4.3 20.5 1.0
O A:HOH763 4.3 12.7 1.0
CB A:PHE344 4.4 22.1 1.0
C A:VAL345 4.4 13.9 1.0
CB A:ASN340 4.4 16.7 1.0
N A:VAL339 4.4 19.1 1.0
N A:ASP346 4.5 15.9 1.0
CB A:ASP346 4.5 12.2 1.0
O A:VAL345 4.5 14.1 1.0
N A:VAL345 4.5 12.6 1.0
N A:ASP342 4.5 21.6 1.0
CB A:ASP342 4.6 25.8 1.0
C A:ASP338 4.6 18.8 1.0
OG A:SER352 4.6 37.6 1.0
CA A:ASN340 4.7 26.9 1.0
CA A:VAL345 4.7 12.9 1.0
C A:ASN340 4.8 19.4 1.0
CA A:ASP346 4.9 13.0 1.0
N A:LYS341 4.9 19.3 1.0
CA A:ASP342 5.0 22.5 1.0
N A:GLY343 5.0 23.9 1.0

Calcium binding site 3 out of 11 in 6lzs

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Calcium binding site 3 out of 11 in the W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:58.2
occ:1.00
 O A:ALA188 2.5 31.6 1.0
O A:LEU191 2.5 30.0 1.0
C A:ALA188 3.7 27.4 1.0
C A:LEU191 3.7 27.5 1.0
O A:HOH733 4.3 38.2 1.0
O A:ALA189 4.4 29.0 1.0
N A:LEU191 4.4 24.9 1.0
CA A:LEU191 4.4 32.1 1.0
CB A:LEU191 4.5 24.1 1.0
OE2 A:GLU181 4.5 30.2 1.0
CA A:ALA189 4.5 29.7 1.0
C A:ALA189 4.5 28.9 1.0
N A:ALA189 4.5 32.3 1.0
OD1 A:ASP192 4.6 34.0 1.0
CA A:ALA188 4.6 29.2 1.0
N A:ASP192 4.8 28.9 1.0
CB A:ALA188 4.8 33.8 1.0
OE1 A:GLU181 4.9 28.5 1.0
CA A:ASP192 5.0 25.5 1.0

Calcium binding site 4 out of 11 in 6lzs

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Calcium binding site 4 out of 11 in the W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:41.1
occ:1.00
 OD1 B:ASN190 2.1 46.6 1.0
O B:LEU524 2.4 31.0 1.0
O B:ASN190 2.4 40.2 1.0
CG B:ASN190 3.3 40.1 1.0
C B:LEU524 3.4 36.9 1.0
C B:ASN190 3.5 35.1 1.0
CA B:ASN190 3.9 32.4 1.0
CA B:ASP525 4.1 31.9 1.0
CB B:ASN190 4.1 39.3 1.0
N B:ASP525 4.2 37.7 1.0
ND2 B:ASN190 4.3 54.0 1.0
OD1 B:ASP525 4.4 26.9 1.0
OD2 B:ASP192 4.4 45.7 1.0
CA B:LEU524 4.4 30.7 1.0
CB B:LEU524 4.6 30.8 1.0
CE B:LYS527 4.7 64.8 1.0
N B:LEU191 4.7 30.8 1.0
O B:HOH701 4.7 25.4 1.0
C B:ASP525 4.8 37.4 1.0
CG B:ASP192 5.0 43.0 1.0

Calcium binding site 5 out of 11 in 6lzs

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Calcium binding site 5 out of 11 in the W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:19.4
occ:1.00
 OD1 B:ASN340 2.1 24.0 1.0
OD1 B:ASP338 2.3 16.9 1.0
O B:HOH712 2.4 20.2 1.0
O B:PHE344 2.4 21.3 1.0
OD1 B:ASP346 2.5 15.2 1.0
OD1 B:ASP342 2.7 21.5 1.0
OD2 B:ASP346 2.8 17.5 1.0
CG B:ASP346 3.0 17.4 1.0
CG B:ASN340 3.1 23.6 1.0
CG B:ASP342 3.3 25.2 1.0
OD2 B:ASP342 3.3 22.8 1.0
CG B:ASP338 3.4 13.1 1.0
C B:PHE344 3.5 21.6 1.0
ND2 B:ASN340 3.6 25.5 1.0
N B:PHE344 4.0 17.4 1.0
CA B:ASP338 4.1 17.7 1.0
CB B:ASP338 4.1 18.9 1.0
CA B:PHE344 4.2 14.9 1.0
N B:ASN340 4.2 20.6 1.0
O B:HOH832 4.2 17.1 1.0
OD2 B:ASP338 4.3 17.4 1.0
CB B:PHE344 4.3 17.0 1.0
N B:VAL339 4.4 12.4 1.0
CB B:ASP346 4.4 16.1 1.0
CB B:ASN340 4.4 15.4 1.0
C B:VAL345 4.5 14.9 1.0
N B:ASP346 4.5 16.9 1.0
OG B:SER352 4.5 22.8 1.0
N B:ASP342 4.5 29.0 1.0
CB B:ASP342 4.6 26.9 1.0
N B:VAL345 4.6 12.2 1.0
C B:ASP338 4.6 13.7 1.0
CA B:ASN340 4.6 19.6 1.0
O B:VAL345 4.7 17.6 1.0
C B:ASN340 4.7 21.5 1.0
N B:LYS341 4.8 18.4 1.0
CA B:VAL345 4.8 15.2 1.0
N B:GLY343 4.8 21.6 1.0
CA B:ASP346 4.9 14.2 1.0

Calcium binding site 6 out of 11 in 6lzs

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Calcium binding site 6 out of 11 in the W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:57.1
occ:1.00
 O B:LEU191 2.7 45.2 1.0
O B:ALA188 3.0 25.9 1.0
C B:LEU191 3.9 40.6 1.0
C B:ALA188 4.2 35.1 1.0
OD1 B:ASP192 4.4 46.0 1.0
CA B:ASP192 4.7 28.8 1.0
N B:ASP192 4.8 34.7 1.0
CA B:LEU191 4.8 36.2 1.0
N B:LEU191 4.9 30.8 1.0
OE2 B:GLU181 4.9 38.0 1.0
O B:ALA189 5.0 31.5 1.0

Calcium binding site 7 out of 11 in 6lzs

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Calcium binding site 7 out of 11 in the W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:30.4
occ:1.00
 O C:HOH776 2.3 18.3 1.0
O C:LEU524 2.3 22.8 1.0
O C:ASN190 2.4 23.9 1.0
OD1 C:ASN190 2.8 38.9 1.0
O C:HOH880 2.9 28.2 1.0
CG C:ASN190 2.9 34.9 1.0
ND2 C:ASN190 2.9 46.3 1.0
C C:LEU524 3.5 19.4 1.0
C C:ASN190 3.5 27.7 1.0
CA C:ASN190 4.0 22.1 1.0
CB C:ASN190 4.0 27.0 1.0
CA C:ASP525 4.3 19.3 1.0
N C:ASP525 4.3 21.9 1.0
CA C:LEU524 4.4 21.6 1.0
NZ C:LYS527 4.4 34.5 1.0
OD2 C:ASP192 4.5 40.1 1.0
CB C:LEU524 4.6 21.7 1.0
OD1 C:ASP525 4.6 21.2 1.0
N C:LEU191 4.7 18.2 1.0
C C:ASP525 4.8 23.8 1.0
O C:HOH816 4.8 29.1 1.0
O C:HOH770 5.0 30.6 1.0

Calcium binding site 8 out of 11 in 6lzs

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Calcium binding site 8 out of 11 in the W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca604

b:18.6
occ:1.00
 O C:HOH725 2.2 23.4 1.0
OD1 C:ASP346 2.3 18.9 1.0
OD1 C:ASN340 2.3 29.4 1.0
O C:PHE344 2.4 22.9 1.0
OD1 C:ASP338 2.5 24.7 1.0
OD1 C:ASP342 2.6 26.4 1.0
OD2 C:ASP346 2.6 15.2 1.0
ND2 C:ASN340 2.8 30.0 1.0
CG C:ASP346 2.8 17.8 1.0
CG C:ASN340 2.8 28.2 1.0
CG C:ASP342 3.4 29.5 1.0
CG C:ASP338 3.5 20.2 1.0
C C:PHE344 3.5 19.7 1.0
OD2 C:ASP342 3.7 25.7 1.0
OG C:SER352 4.0 34.9 1.0
N C:PHE344 4.1 16.9 1.0
O C:HOH821 4.2 16.1 1.0
CA C:ASP338 4.2 19.4 1.0
CA C:PHE344 4.2 18.4 1.0
N C:ASN340 4.2 21.4 1.0
CB C:ASN340 4.2 24.7 1.0
CB C:ASP338 4.2 18.1 1.0
CB C:PHE344 4.3 22.4 1.0
CB C:ASP346 4.3 20.6 1.0
OD2 C:ASP338 4.3 20.0 1.0
N C:VAL339 4.4 20.7 1.0
C C:VAL345 4.4 19.3 1.0
O C:VAL345 4.5 23.3 1.0
N C:VAL345 4.6 15.8 1.0
N C:ASP346 4.6 19.4 1.0
N C:ASP342 4.6 26.2 1.0
CA C:ASN340 4.6 23.8 1.0
C C:ASP338 4.7 25.7 1.0
CB C:ASP342 4.7 27.1 1.0
C C:ASN340 4.8 29.7 1.0
CA C:VAL345 4.8 11.3 1.0
N C:LYS341 4.9 23.8 1.0
CA C:ASP346 4.9 19.2 1.0
CB C:SER352 4.9 27.9 1.0

Calcium binding site 9 out of 11 in 6lzs

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Calcium binding site 9 out of 11 in the W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca605

b:28.5
occ:1.00
 O D:ASN190 2.3 34.7 1.0
O D:LEU524 2.3 26.1 1.0
O D:HOH835 2.3 26.0 1.0
O D:HOH910 2.3 25.5 1.0
OD1 D:ASN190 2.4 31.9 1.0
O D:HOH705 2.4 27.0 1.0
CG D:ASN190 3.3 35.6 1.0
C D:ASN190 3.3 26.4 1.0
C D:LEU524 3.5 23.9 1.0
CA D:ASN190 3.7 28.9 1.0
CB D:ASN190 3.9 27.4 1.0
ND2 D:ASN190 4.2 48.8 1.0
OD2 D:ASP192 4.2 30.7 1.0
CA D:ASP525 4.4 26.1 1.0
N D:ASP525 4.4 22.4 1.0
CA D:LEU524 4.5 22.9 1.0
N D:LEU191 4.5 22.7 1.0
CB D:LEU524 4.7 21.3 1.0
OD1 D:ASP525 4.8 31.0 1.0
CA D:LEU191 4.9 23.8 1.0
C D:ASP525 4.9 22.4 1.0

Calcium binding site 10 out of 11 in 6lzs

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Calcium binding site 10 out of 11 in the W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of W363A Mutant of Chitin-Specific Solute Binding Protein From Vibrio Harveyi in Complex with Chitobiose. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca606

b:26.0
occ:1.00
 OD1 D:ASN340 2.3 31.2 1.0
O D:PHE344 2.4 22.8 1.0
O D:HOH747 2.4 15.1 1.0
OD1 D:ASP338 2.4 24.9 1.0
OD1 D:ASP342 2.4 30.5 1.0
OD1 D:ASP346 2.5 23.8 1.0
OD2 D:ASP346 2.6 24.1 1.0
CG D:ASP346 2.9 25.8 1.0
CG D:ASP342 3.3 33.6 1.0
CG D:ASN340 3.3 33.2 1.0
CG D:ASP338 3.5 20.1 1.0
C D:PHE344 3.5 21.1 1.0
OD2 D:ASP342 3.7 32.4 1.0
ND2 D:ASN340 3.9 36.9 1.0
N D:PHE344 4.1 22.2 1.0
CA D:ASP338 4.1 26.9 1.0
CB D:ASP338 4.2 23.9 1.0
CA D:PHE344 4.2 21.5 1.0
N D:ASN340 4.3 28.5 1.0
OD2 D:ASP338 4.3 22.8 1.0
CB D:ASP346 4.3 16.3 1.0
C D:VAL345 4.4 17.9 1.0
N D:ASP342 4.4 27.5 1.0
N D:VAL339 4.4 22.2 1.0
CB D:ASN340 4.4 29.2 1.0
N D:ASP346 4.4 16.7 1.0
CB D:PHE344 4.4 16.5 1.0
CB D:ASP342 4.5 30.9 1.0
O D:HOH763 4.5 14.0 1.0
O D:VAL345 4.5 18.7 1.0
N D:VAL345 4.5 17.1 1.0
C D:ASP338 4.7 17.6 1.0
CA D:ASN340 4.7 33.0 1.0
CA D:VAL345 4.7 16.6 1.0
N D:LYS341 4.7 26.8 1.0
C D:ASN340 4.8 23.4 1.0
CA D:ASP346 4.8 19.0 1.0
N D:GLY343 4.8 25.9 1.0
OG D:SER352 4.8 40.3 1.0
CA D:ASP342 4.9 26.6 1.0

Reference:

Y.Kitaoku, P.Ubonbal, L.T.Tran, R.C.Robinson, W.Suginta. Structural Insight Into Chitin-Specific Solute-Binding Protein From Vibrio Harveyi To Be Published.
Page generated: Sat Apr 17 13:52:10 2021

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