Calcium in PDB 6lzr: Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose.

Protein crystallography data

The structure of Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose., PDB code: 6lzr 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) 45.30 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.879, 57.108, 164.259, 90, 99.53, 90
R / Rfree (%) 23.8 / 27.1

Other elements in 6lzr:

The structure of Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose. also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Chlorine (Cl) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose. (pdb code 6lzr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose., PDB code: 6lzr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6lzr

Go back to Calcium Binding Sites List in 6lzr
Calcium binding site 1 out of 6 in the Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca619

b:32.8
occ:1.00
O A:HOH1036 2.2 27.3 1.0
O A:HOH723 2.2 24.3 1.0
O A:HOH1052 2.3 31.8 1.0
O A:HOH1059 2.3 27.2 1.0
O A:HOH904 2.3 27.6 1.0
O A:HOH721 2.5 22.0 1.0
O A:ALA81 4.1 22.6 1.0
OD1 A:ASP86 4.2 21.3 1.0
O A:HOH1050 4.3 29.8 1.0
OD2 A:ASP86 4.4 20.8 1.0
OG1 A:THR83 4.4 23.0 1.0
ND1 A:HIS144 4.5 25.1 1.0
CB A:ASP85 4.6 25.1 1.0
CG A:ASP86 4.7 20.7 1.0
OD2 A:ASP85 4.8 40.3 1.0
CB A:HIS144 4.8 25.7 1.0
O A:HOH957 5.0 31.6 1.0

Calcium binding site 2 out of 6 in 6lzr

Go back to Calcium Binding Sites List in 6lzr
Calcium binding site 2 out of 6 in the Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca620

b:11.7
occ:1.00
OD1 A:ASN340 2.2 14.4 1.0
O A:PHE344 2.4 11.1 1.0
OD1 A:ASP338 2.4 12.8 1.0
OD1 A:ASP342 2.4 13.6 1.0
O A:HOH736 2.4 15.4 1.0
OD2 A:ASP346 2.5 13.2 1.0
OD1 A:ASP346 2.6 17.2 1.0
CG A:ASP346 2.9 11.4 1.0
CG A:ASP342 3.3 16.0 1.0
CG A:ASP338 3.4 14.4 1.0
CG A:ASN340 3.4 18.0 1.0
C A:PHE344 3.5 12.7 1.0
OD2 A:ASP342 3.7 20.0 1.0
OG A:SER352 4.1 20.8 1.0
ND2 A:ASN340 4.1 27.3 1.0
N A:ASN340 4.1 16.4 1.0
N A:PHE344 4.1 10.8 1.0
CA A:ASP338 4.1 12.9 1.0
CB A:ASP338 4.1 12.8 1.0
CA A:PHE344 4.2 12.8 1.0
OD2 A:ASP338 4.2 16.1 1.0
N A:VAL339 4.3 11.9 1.0
CB A:ASP346 4.4 11.5 1.0
C A:VAL345 4.4 13.4 1.0
CB A:PHE344 4.4 10.5 1.0
O A:HOH905 4.5 11.9 1.0
N A:ASP342 4.5 14.6 1.0
N A:ASP346 4.5 11.5 1.0
O A:VAL345 4.5 12.2 1.0
CB A:ASN340 4.6 15.0 1.0
N A:VAL345 4.6 13.1 1.0
CB A:ASP342 4.6 17.0 1.0
C A:ASP338 4.6 12.2 1.0
CA A:ASN340 4.6 14.7 1.0
C A:ASN340 4.7 13.1 1.0
CA A:VAL345 4.8 14.0 1.0
N A:LYS341 4.8 14.6 1.0
CA A:ASP346 4.9 11.4 1.0
N A:GLY343 4.9 13.4 1.0
CA A:ASP342 5.0 16.5 1.0

Calcium binding site 3 out of 6 in 6lzr

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Calcium binding site 3 out of 6 in the Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca621

b:14.2
occ:1.00
O A:LEU524 2.3 13.3 1.0
OD1 A:ASN190 2.4 17.5 1.0
O A:HOH828 2.4 25.6 1.0
O A:HOH718 2.4 17.9 1.0
O A:ASN190 2.5 15.2 1.0
O A:HOH1040 2.5 22.3 1.0
O A:HOH753 2.5 23.0 1.0
O A:HOH960 2.6 26.1 1.0
CG A:ASN190 3.5 16.0 1.0
C A:ASN190 3.5 14.6 1.0
C A:LEU524 3.5 14.3 1.0
CA A:ASN190 3.9 12.0 1.0
CB A:ASN190 4.3 14.2 1.0
CA A:ASP525 4.4 8.6 1.0
OD2 A:ASP192 4.4 30.9 1.0
N A:ASP525 4.4 10.3 1.0
ND2 A:ASN190 4.4 15.2 1.0
CA A:LEU524 4.5 9.1 1.0
O A:HOH940 4.5 32.5 1.0
OD1 A:ASP525 4.6 13.7 1.0
CB A:LEU524 4.7 12.4 1.0
N A:LEU191 4.7 12.7 1.0
O A:HOH717 4.7 14.8 1.0
C A:ASP525 5.0 11.5 1.0

Calcium binding site 4 out of 6 in 6lzr

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Calcium binding site 4 out of 6 in the Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca612

b:46.7
occ:1.00
N B:ASP227 3.4 15.9 1.0
OD1 B:ASP225 3.4 41.6 1.0
N B:ILE226 3.5 16.0 1.0
C B:ASP225 3.7 17.9 1.0
OD2 B:ASP227 3.7 37.9 1.0
CA B:ASP225 3.8 17.2 1.0
CB B:ASP227 3.8 19.0 1.0
CG B:ASP227 4.0 22.7 1.0
CG2 B:ILE226 4.1 14.2 1.0
CA B:ASP227 4.2 15.0 1.0
O B:HOH876 4.2 17.2 1.0
O B:ASP225 4.3 17.4 1.0
C B:ILE226 4.4 17.3 1.0
CA B:ILE226 4.4 14.9 1.0
CG B:ASP225 4.5 30.5 1.0
N B:ASP225 4.8 16.3 1.0
CB B:ASP225 4.8 22.2 1.0
N B:ARG228 4.8 17.6 1.0
CB B:ILE226 4.9 12.6 1.0
OD1 B:ASP227 4.9 24.9 1.0
CB B:TYR288 5.0 15.0 1.0

Calcium binding site 5 out of 6 in 6lzr

Go back to Calcium Binding Sites List in 6lzr
Calcium binding site 5 out of 6 in the Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca613

b:15.2
occ:1.00
O B:LEU524 2.3 12.6 1.0
OD1 B:ASN190 2.3 18.5 1.0
O2 B:EDO607 2.4 29.0 1.0
O B:ASN190 2.4 14.8 1.0
O B:HOH759 2.5 20.5 1.0
O1 B:EDO607 2.5 23.4 1.0
O B:HOH892 2.6 23.4 1.0
O B:HOH735 2.6 16.4 1.0
C2 B:EDO607 3.0 32.0 1.0
C1 B:EDO607 3.2 25.5 1.0
C B:ASN190 3.4 14.3 1.0
CG B:ASN190 3.4 16.4 1.0
C B:LEU524 3.5 11.4 1.0
CA B:ASN190 3.8 15.0 1.0
OD2 B:ASP192 4.1 32.8 1.0
CB B:ASN190 4.2 17.1 1.0
ND2 B:ASN190 4.4 16.5 1.0
N B:ASP525 4.4 10.2 1.0
CA B:ASP525 4.5 10.8 1.0
CA B:LEU524 4.5 11.7 1.0
OD1 B:ASP525 4.6 15.6 1.0
N B:LEU191 4.6 13.7 1.0
CB B:LEU524 4.6 12.2 1.0
O B:HOH821 4.6 15.1 1.0

Calcium binding site 6 out of 6 in 6lzr

Go back to Calcium Binding Sites List in 6lzr
Calcium binding site 6 out of 6 in the Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Chitin-Specific Solute Binding Protein From Vibrio Harveyi Co- Crystalized with Chitotetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca614

b:11.7
occ:1.00
OD1 B:ASN340 2.3 15.7 1.0
O B:HOH740 2.3 17.5 1.0
O B:PHE344 2.4 11.1 1.0
OD1 B:ASP338 2.4 13.7 1.0
OD2 B:ASP346 2.4 12.4 1.0
OD1 B:ASP342 2.5 14.6 1.0
OD1 B:ASP346 2.5 16.6 1.0
CG B:ASP346 2.8 14.5 1.0
CG B:ASP342 3.4 18.1 1.0
CG B:ASP338 3.4 13.7 1.0
CG B:ASN340 3.4 19.7 1.0
C B:PHE344 3.5 10.7 1.0
OD2 B:ASP342 3.8 18.6 1.0
OG B:SER352 4.0 21.9 1.0
ND2 B:ASN340 4.1 24.4 1.0
CA B:ASP338 4.1 9.8 1.0
CB B:ASP338 4.2 13.0 1.0
N B:ASN340 4.2 16.3 1.0
N B:PHE344 4.2 13.4 1.0
O B:HOH904 4.2 13.0 1.0
CA B:PHE344 4.2 12.5 1.0
CB B:ASP346 4.3 11.6 1.0
N B:VAL339 4.3 12.6 1.0
OD2 B:ASP338 4.3 15.2 1.0
C B:VAL345 4.3 12.5 1.0
CB B:PHE344 4.4 11.7 1.0
O B:VAL345 4.4 12.4 1.0
N B:ASP346 4.5 11.3 1.0
N B:VAL345 4.6 9.4 1.0
N B:ASP342 4.6 15.8 1.0
CB B:ASN340 4.6 16.3 1.0
CB B:ASP342 4.6 18.6 1.0
C B:ASP338 4.6 11.8 1.0
CA B:VAL345 4.7 11.1 1.0
CA B:ASN340 4.7 14.4 1.0
C B:ASN340 4.8 12.9 1.0
CA B:ASP346 4.8 9.5 1.0
N B:LYS341 4.9 12.5 1.0
CB B:SER352 5.0 15.5 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 13:52:06 2021

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