Calcium in PDB 8wkb: Durio Zibethinus Trypsin Inhibitor Dzti-7

Protein crystallography data

The structure of Durio Zibethinus Trypsin Inhibitor Dzti-7, PDB code: 8wkb was solved by P.Deentanya, K.Wangkanont, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.68 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.242, 102.68, 116.922, 90, 90, 90
R / Rfree (%) 19.2 / 24.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Durio Zibethinus Trypsin Inhibitor Dzti-7 (pdb code 8wkb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Durio Zibethinus Trypsin Inhibitor Dzti-7, PDB code: 8wkb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8wkb

Go back to Calcium Binding Sites List in 8wkb
Calcium binding site 1 out of 6 in the Durio Zibethinus Trypsin Inhibitor Dzti-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Durio Zibethinus Trypsin Inhibitor Dzti-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:93.6
occ:0.98
 O1 D:GOL304 3.3 55.2 0.7
O D:ASN160 3.6 45.5 1.0
C1 D:GOL304 3.9 59.1 0.7
CZ3 B:TRP200 3.9 39.1 1.0
O D:HOH492 4.0 44.8 1.0
O D:GLY159 4.3 42.4 1.0
CH2 B:TRP200 4.3 43.6 1.0
NH2 B:ARG184 4.3 49.5 1.0
C D:ASN160 4.3 49.4 1.0
CG A:LEU80 4.4 51.7 1.0
OG A:SER78 4.5 55.4 1.0
CA D:ASN160 4.5 46.8 1.0
CD1 A:LEU80 4.7 48.3 1.0
CD2 A:LEU80 4.8 49.8 1.0

Calcium binding site 2 out of 6 in 8wkb

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Calcium binding site 2 out of 6 in the Durio Zibethinus Trypsin Inhibitor Dzti-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Durio Zibethinus Trypsin Inhibitor Dzti-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:87.5
occ:1.00
 O D:HOH492 3.5 44.8 1.0
OD2 A:ASP79 3.8 54.8 1.0
O B:ARG184 3.9 50.5 1.0
O B:HOH409 3.9 51.0 1.0
N A:GLY54 4.1 49.4 1.0
SD B:MET191 4.1 44.9 1.0
CE B:MET191 4.2 42.7 1.0
C B:ARG184 4.4 47.6 1.0
CA B:TYR185 4.5 48.7 1.0
O A:HOH401 4.6 54.3 1.0
CA A:GLY54 4.6 52.2 1.0
N B:GLY186 4.7 46.0 1.0
N B:TYR185 4.7 46.0 1.0
CG A:ASP79 4.8 56.7 1.0
NH2 B:ARG184 4.8 49.5 1.0
CB B:ARG184 4.9 47.0 1.0
C B:TYR185 5.0 47.8 1.0

Calcium binding site 3 out of 6 in 8wkb

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Calcium binding site 3 out of 6 in the Durio Zibethinus Trypsin Inhibitor Dzti-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Durio Zibethinus Trypsin Inhibitor Dzti-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca307

b:109.4
occ:1.00
 OD1 B:ASP96 2.7 81.2 1.0
CG B:ASP96 3.9 76.5 1.0
O B:SER93 4.0 84.4 1.0
OD2 B:ASP96 4.4 81.5 1.0
O B:ALA41 4.6 55.2 1.0
O B:HOH465 4.8 55.2 1.0
CB B:ALA41 5.0 55.1 1.0
C B:SER93 5.0 85.0 1.0

Calcium binding site 4 out of 6 in 8wkb

Go back to Calcium Binding Sites List in 8wkb
Calcium binding site 4 out of 6 in the Durio Zibethinus Trypsin Inhibitor Dzti-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Durio Zibethinus Trypsin Inhibitor Dzti-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:74.7
occ:1.00
 O D:ASN66 2.3 59.2 1.0
O D:HOH480 2.4 54.7 1.0
O D:HOH527 2.7 65.3 1.0
O D:HOH515 2.9 77.7 1.0
C D:ASN66 3.4 50.5 1.0
N D:GLN67 4.3 52.8 1.0
CA D:GLN67 4.3 49.5 1.0
CA D:ASN66 4.3 51.0 1.0
CB D:ASN66 4.4 50.3 1.0

Calcium binding site 5 out of 6 in 8wkb

Go back to Calcium Binding Sites List in 8wkb
Calcium binding site 5 out of 6 in the Durio Zibethinus Trypsin Inhibitor Dzti-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Durio Zibethinus Trypsin Inhibitor Dzti-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca305

b:68.3
occ:0.67
 OE2 D:GLU107 3.0 54.4 1.0
N D:THR120 3.5 45.7 1.0
OG1 D:THR120 3.7 41.8 1.0
CA D:SER119 3.8 50.6 1.0
CB D:SER119 3.8 45.8 1.0
CD D:GLU107 4.1 54.3 1.0
C D:SER119 4.2 46.1 1.0
CA D:THR120 4.5 42.7 1.0
CG D:GLU107 4.5 51.0 1.0
CB D:THR120 4.5 42.8 1.0
CG2 D:THR120 4.8 45.6 1.0
OG D:SER119 4.8 46.3 1.0
NH2 D:ARG112 4.8 39.2 1.0
CG2 D:VAL121 4.9 42.8 1.0

Calcium binding site 6 out of 6 in 8wkb

Go back to Calcium Binding Sites List in 8wkb
Calcium binding site 6 out of 6 in the Durio Zibethinus Trypsin Inhibitor Dzti-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Durio Zibethinus Trypsin Inhibitor Dzti-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca306

b:89.3
occ:0.86
 O D:HOH482 2.3 62.9 1.0
O D:SER93 2.6 78.2 1.0
OD1 D:ASP96 3.0 70.2 1.0
C D:SER93 3.6 79.8 1.0
CG D:ASP96 3.7 77.4 1.0
OD2 D:ASP96 4.0 78.5 1.0
CA D:SER93 4.2 81.9 1.0
CB D:SER93 4.3 81.8 1.0
N D:ASN94 4.7 83.6 1.0
O D:ASP95 4.8 74.2 1.0
CB D:ASP96 5.0 66.2 1.0

Reference:

P.Deentanya, K.Wangkanont. Durio Zibethinus Trypsin Inhibitor Dzti-7 To Be Published.
Page generated: Thu Oct 31 17:18:45 2024

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