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:
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
Go back to
Calcium Binding Sites List in 6lzr
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
Go back to
Calcium Binding Sites List in 6lzr
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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