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Calcium in PDB 6utu: Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group

Protein crystallography data

The structure of Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group, PDB code: 6utu was solved by Y.Zhang, S.Wang, Z.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 2.85
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 158.100, 158.100, 64.700, 90.00, 90.00, 120.00
R / Rfree (%) 21.4 / 29.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group (pdb code 6utu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group, PDB code: 6utu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 6utu

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Calcium binding site 1 out of 9 in the Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:80.3
occ:1.00
 OD2 C:ASP65 2.2 79.2 1.0
OE1 C:GLU82 2.2 78.2 1.0
O C:VAL77 2.4 76.0 1.0
OE2 C:GLU82 2.6 73.9 1.0
CD C:GLU82 2.7 76.0 1.0
CG C:ASP65 2.8 77.6 1.0
OD1 C:ASP78 2.8 70.1 1.0
OD1 C:ASP65 2.9 64.9 1.0
C C:VAL77 3.5 75.6 1.0
O C:ASP65 3.7 86.0 1.0
CA C:ASP78 3.7 69.4 1.0
CG C:ASP78 3.8 70.9 1.0
N C:ASP78 4.0 74.5 1.0
CB C:ASP78 4.1 72.1 1.0
CG C:GLU82 4.1 71.4 1.0
CB C:ASP65 4.2 81.1 1.0
NH1 C:ARG300 4.5 77.9 1.0
C C:ASP65 4.6 79.3 1.0
CG2 C:VAL77 4.6 75.0 1.0
NE1 C:TRP84 4.7 64.0 1.0
CA C:ASP65 4.7 79.4 1.0
CA C:VAL77 4.8 79.7 1.0
OD2 C:ASP78 4.9 72.5 1.0
NH2 C:ARG300 5.0 69.5 1.0

Calcium binding site 2 out of 9 in 6utu

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Calcium binding site 2 out of 9 in the Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:73.4
occ:1.00
 OD1 C:ASP152 2.3 74.2 1.0
OD2 C:ASP155 2.4 66.9 1.0
OD1 C:ASP157 2.6 64.5 1.0
O C:ASN159 2.6 80.9 1.0
OE2 C:GLU167 2.8 69.8 1.0
OD1 C:ASP155 3.0 75.9 1.0
CG C:ASP155 3.0 70.3 1.0
CG C:ASP157 3.5 69.5 1.0
CG C:ASP152 3.6 75.8 1.0
OD2 C:ASP157 3.6 72.0 1.0
C C:ASN159 3.6 76.0 1.0
N C:GLN161 3.9 80.3 1.0
CA C:ASP152 4.0 68.4 1.0
CD C:GLU167 4.0 73.2 1.0
CB C:GLN161 4.1 78.7 1.0
N C:ASN159 4.3 70.6 1.0
CA C:CA403 4.3 68.7 1.0
C C:PRO160 4.3 80.5 1.0
CB C:ASP152 4.4 72.0 1.0
CA C:PRO160 4.4 78.8 1.0
N C:PRO160 4.4 74.1 1.0
OD2 C:ASP152 4.5 78.0 1.0
CB C:ASP155 4.5 67.5 1.0
CA C:ASN159 4.5 72.4 1.0
CG C:GLU167 4.6 75.6 1.0
CA C:GLN161 4.6 77.8 1.0
O C:ASP152 4.6 69.9 1.0
N C:ASP152 4.8 68.0 1.0
C C:ASP152 4.8 69.3 1.0
C C:GLN158 4.8 77.0 1.0
O C:ASP157 4.9 72.3 1.0
CB C:ASP157 4.9 69.4 1.0
C C:ASP157 4.9 75.1 1.0
O C:ALA151 4.9 66.6 1.0
CB C:ASN159 5.0 68.4 1.0
OE1 C:GLU167 5.0 76.8 1.0

Calcium binding site 3 out of 9 in 6utu

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Calcium binding site 3 out of 9 in the Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:68.7
occ:1.00
 O C:ASP157 2.4 72.3 1.0
OD1 C:ASP155 2.4 75.9 1.0
O C:ASP152 2.5 69.9 1.0
OD1 C:ASN182 2.5 79.3 1.0
OE2 C:GLU167 2.6 69.8 1.0
O C:ASP155 2.7 63.7 1.0
OE1 C:GLU167 2.7 76.8 1.0
CD C:GLU167 3.0 73.2 1.0
CG C:ASN182 3.4 82.5 1.0
C C:ASP157 3.5 75.1 1.0
C C:ASP152 3.6 69.3 1.0
C C:ASP155 3.6 70.7 1.0
CG C:ASP155 3.7 70.3 1.0
CB C:ASN182 4.1 76.0 1.0
N C:ASP157 4.2 65.5 1.0
OD1 C:ASP157 4.2 64.5 1.0
N C:ASP155 4.3 72.8 1.0
CA C:ASN182 4.3 70.8 1.0
CA C:CA402 4.3 73.4 1.0
CA C:GLN158 4.3 77.1 1.0
CA C:ASP152 4.3 68.4 1.0
N C:GLN158 4.3 81.1 1.0
ND2 C:ASN182 4.3 79.4 1.0
CA C:ASP155 4.3 71.0 1.0
C C:ALA156 4.4 70.0 1.0
CA C:ASP157 4.4 71.6 1.0
OD2 C:ASP155 4.5 66.9 1.0
CG C:GLU167 4.5 75.6 1.0
N C:TRP153 4.6 70.7 1.0
CB C:ASP155 4.6 67.5 1.0
O C:ALA156 4.6 70.1 1.0
N C:ALA156 4.6 78.3 1.0
CA C:TRP153 4.8 67.2 1.0
C C:TRP153 4.8 66.5 1.0
CG C:ASP157 4.8 69.5 1.0
CA C:ALA156 4.9 72.8 1.0
N C:ASN182 4.9 69.5 1.0
OD1 C:ASP152 4.9 74.2 1.0
O C:ALA151 4.9 66.6 1.0
C C:LEU154 5.0 74.8 1.0
O C:TRP153 5.0 66.6 1.0

Calcium binding site 4 out of 9 in 6utu

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Calcium binding site 4 out of 9 in the Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca401

b:95.0
occ:1.00
 OD1 F:ASP65 2.0 85.5 1.0
O F:VAL77 2.3 91.6 1.0
OD2 F:ASP78 2.6 87.2 1.0
CG F:ASP78 2.9 88.0 1.0
OE2 F:GLU82 3.0 93.6 1.0
CG F:ASP65 3.1 85.1 1.0
OE1 F:GLU82 3.2 81.3 1.0
C F:VAL77 3.2 93.8 1.0
CA F:ASP78 3.3 87.1 1.0
CD F:GLU82 3.5 83.6 1.0
CB F:ASP78 3.5 95.2 1.0
OD1 F:ASP78 3.5 82.7 1.0
OD2 F:ASP65 3.6 84.9 1.0
N F:ASP78 3.6 87.8 1.0
O F:ASP65 4.2 89.9 1.0
CB F:ASP65 4.3 90.7 1.0
CA F:VAL77 4.5 92.5 1.0
CD2 F:LEU66 4.6 85.7 1.0
C F:ASP78 4.6 77.9 1.0
N F:VAL77 4.6 94.8 1.0
C F:ASP65 4.8 90.6 1.0
NE1 F:TRP84 4.8 85.4 1.0
CA F:ASP65 4.9 90.2 1.0
N F:HIS79 4.9 81.0 1.0
CG F:GLU82 5.0 81.7 1.0

Calcium binding site 5 out of 9 in 6utu

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Calcium binding site 5 out of 9 in the Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca402

b:78.0
occ:1.00
 OD1 F:ASP152 2.3 79.7 1.0
OD2 F:ASP157 2.4 85.5 1.0
OE2 F:GLU167 2.4 88.3 1.0
O F:ASN159 2.5 84.7 1.0
OD2 F:ASP155 2.7 78.3 1.0
CG F:ASP152 3.4 83.4 1.0
CG F:ASP157 3.4 81.6 1.0
CG F:ASP155 3.4 80.7 1.0
OD1 F:ASP155 3.5 76.6 1.0
C F:ASN159 3.6 88.5 1.0
CD F:GLU167 3.6 83.4 1.0
CA F:ASP152 3.9 75.7 1.0
OD1 F:ASP157 3.9 73.9 1.0
N F:ASN159 4.1 88.5 1.0
CB F:ASP152 4.2 75.6 1.0
O F:ASP152 4.3 78.4 1.0
OD2 F:ASP152 4.3 85.7 1.0
CA F:ASN159 4.4 89.0 1.0
CA F:CA403 4.4 83.3 1.0
N F:PRO160 4.4 89.8 1.0
CG F:GLU167 4.5 78.0 1.0
OE1 F:GLU167 4.5 80.1 1.0
O F:ASP157 4.5 87.4 1.0
CA F:PRO160 4.5 91.6 1.0
O F:PRO160 4.6 81.0 1.0
CB F:ASP157 4.6 83.9 1.0
C F:ASP152 4.6 78.0 1.0
C F:ASP157 4.7 83.5 1.0
C F:PRO160 4.8 92.6 1.0
N F:ASP152 4.9 76.8 1.0
CB F:ASP155 4.9 78.7 1.0
CB F:ASN159 4.9 92.6 1.0
C F:GLN158 4.9 88.6 1.0

Calcium binding site 6 out of 9 in 6utu

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Calcium binding site 6 out of 9 in the Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca403

b:83.3
occ:1.00
 O F:ASP152 2.4 78.4 1.0
OE1 F:GLU167 2.4 80.1 1.0
O F:ASP157 2.5 87.4 1.0
OD1 F:ASP155 2.5 76.6 1.0
ND2 F:ASN182 2.6 84.8 1.0
OE2 F:GLU167 3.1 88.3 1.0
CD F:GLU167 3.1 83.4 1.0
O F:ASP155 3.3 76.9 1.0
CG F:ASN182 3.4 86.0 1.0
C F:ASP152 3.6 78.0 1.0
C F:ASP157 3.7 83.5 1.0
CG F:ASP155 3.8 80.7 1.0
C F:ASP155 4.0 83.0 1.0
CA F:ASN182 4.0 76.4 1.0
CB F:ASN182 4.1 77.1 1.0
OD1 F:ASN182 4.1 88.8 1.0
N F:ASP157 4.2 85.1 1.0
CA F:CA402 4.4 78.0 1.0
C F:ALA156 4.4 85.8 1.0
N F:TRP153 4.4 79.7 1.0
CA F:ASP152 4.5 75.7 1.0
OD2 F:ASP155 4.5 78.3 1.0
CA F:TRP153 4.5 75.0 1.0
N F:ASP155 4.5 82.7 1.0
CA F:ASP157 4.5 82.6 1.0
C F:TRP153 4.6 71.5 1.0
CG F:GLU167 4.6 78.0 1.0
N F:GLN158 4.6 83.0 1.0
CA F:GLN158 4.6 86.3 1.0
CA F:ASP155 4.7 81.4 1.0
N F:ASN182 4.7 73.9 1.0
O F:ALA156 4.7 92.5 1.0
N F:ALA156 4.8 83.0 1.0
O F:TRP153 4.8 71.7 1.0
CB F:ASP155 4.8 78.7 1.0
N F:LEU154 4.9 70.9 1.0
OD2 F:ASP157 5.0 85.5 1.0

Calcium binding site 7 out of 9 in 6utu

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Calcium binding site 7 out of 9 in the Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca401

b:88.9
occ:1.00
 OE2 I:GLU82 2.2 78.2 1.0
OD2 I:ASP65 2.2 82.0 1.0
OD1 I:ASP78 2.3 82.2 1.0
O I:VAL77 2.3 80.4 1.0
OE1 I:GLU82 2.7 85.5 1.0
CD I:GLU82 2.8 81.2 1.0
CG I:ASP65 2.9 79.3 1.0
OD1 I:ASP65 2.9 80.5 1.0
CG I:ASP78 3.3 82.2 1.0
C I:VAL77 3.4 80.5 1.0
CA I:ASP78 3.4 81.4 1.0
CB I:ASP78 3.7 79.5 1.0
N I:ASP78 3.8 84.5 1.0
CG I:GLU82 4.2 74.5 1.0
CB I:ASP65 4.3 84.1 1.0
OD2 I:ASP78 4.4 84.0 1.0
NE1 I:TRP84 4.5 79.9 1.0
CA I:VAL77 4.7 79.4 1.0
C I:ASP78 4.7 77.7 1.0
N I:VAL77 4.8 77.5 1.0
CG2 I:VAL77 4.9 69.1 1.0
N I:HIS79 4.9 74.2 1.0
CD1 I:TRP84 5.0 82.1 1.0

Calcium binding site 8 out of 9 in 6utu

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Calcium binding site 8 out of 9 in the Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca402

b:79.6
occ:1.00
 OD1 I:ASP152 2.2 71.6 1.0
OD2 I:ASP155 2.5 70.9 1.0
OD1 I:ASP155 2.6 74.6 1.0
OE2 I:GLU167 2.7 78.5 1.0
OD1 I:ASP157 2.7 75.3 1.0
CG I:ASP155 2.9 75.0 1.0
O I:ASN159 2.9 79.8 1.0
OD2 I:ASP157 3.2 78.6 1.0
CG I:ASP157 3.3 76.3 1.0
CG I:ASP152 3.4 79.2 1.0
CD I:GLU167 3.8 73.1 1.0
C I:ASN159 3.9 81.5 1.0
OD2 I:ASP152 4.1 86.3 1.0
N I:ASN159 4.3 80.0 1.0
CA I:CA403 4.3 75.4 1.0
CA I:ASP152 4.4 70.3 1.0
CB I:ASP155 4.4 74.4 1.0
CG I:GLU167 4.4 71.5 1.0
CB I:ASP152 4.5 75.3 1.0
O I:ASP152 4.6 75.9 1.0
CA I:ASN159 4.7 81.0 1.0
N I:GLN161 4.7 85.2 1.0
CB I:ASP157 4.7 80.0 1.0
CB I:GLN161 4.7 94.0 1.0
O I:ASP157 4.7 84.0 1.0
OE1 I:GLU167 4.8 76.7 1.0
N I:PRO160 4.8 81.8 1.0
C I:ASP157 4.8 78.8 1.0
CA I:PRO160 4.8 81.5 1.0
C I:PRO160 5.0 85.3 1.0
C I:ASP152 5.0 75.2 1.0

Calcium binding site 9 out of 9 in 6utu

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Calcium binding site 9 out of 9 in the Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Minor Pseudopilin Ternary Complex of Xcpvwx From the Type 2 Secretion System of Pseudomonas Aeruginosa in the P3 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca403

b:75.4
occ:1.00
 OD1 I:ASN182 2.3 71.1 1.0
OE1 I:GLU167 2.4 76.7 1.0
O I:ASP152 2.4 75.9 1.0
O I:ASP157 2.5 84.0 1.0
O I:ASP155 2.6 72.4 1.0
OE2 I:GLU167 2.7 78.5 1.0
OD1 I:ASP155 2.8 74.6 1.0
CD I:GLU167 2.8 73.1 1.0
CG I:ASN182 3.4 73.8 1.0
C I:ASP157 3.7 78.8 1.0
C I:ASP152 3.7 75.2 1.0
C I:ASP155 3.8 75.8 1.0
CG I:ASP155 3.9 75.0 1.0
N I:ASP157 4.2 86.0 1.0
N I:ASP155 4.2 71.8 1.0
ND2 I:ASN182 4.2 75.0 1.0
OD1 I:ASP152 4.2 71.6 1.0
CG I:GLU167 4.3 71.5 1.0
CB I:ASN182 4.3 69.2 1.0
CA I:CA402 4.3 79.6 1.0
CA I:ASP155 4.4 75.9 1.0
CA I:ASN182 4.5 62.9 1.0
CA I:ASP152 4.5 70.3 1.0
CA I:ASP157 4.5 81.6 1.0
N I:GLN158 4.6 75.0 1.0
C I:TRP153 4.6 68.1 1.0
N I:TRP153 4.6 75.7 1.0
CA I:TRP153 4.6 69.4 1.0
OD2 I:ASP155 4.6 70.9 1.0
OD1 I:ASP157 4.6 75.3 1.0
CA I:GLN158 4.6 74.4 1.0
CB I:ALA180 4.7 66.9 1.0
CB I:ASP155 4.7 74.4 1.0
O I:TRP153 4.8 69.4 1.0
N I:LEU154 4.8 67.8 1.0
C I:ALA156 4.8 80.6 1.0
N I:ALA156 4.8 79.9 1.0
CG I:ASP157 4.9 76.3 1.0
C I:LEU154 5.0 77.5 1.0
CG I:ASP152 5.0 79.2 1.0

Reference:

Y.Zhang, S.Wang, Z.Jia. In Situ Proteolysis Condition-Induced Crystallization of the Xcpvwx Complex in Different Lattices. Int J Mol Sci V. 21 2020.
ISSN: ESSN 1422-0067
PubMed: 31906428
DOI: 10.3390/IJMS21010308
Page generated: Tue Jul 16 16:01:29 2024

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