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

Go back to Calcium Binding Sites List in 6utu
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

Go back to Calcium Binding Sites List in 6utu
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

Go back to Calcium Binding Sites List in 6utu
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

Go back to Calcium Binding Sites List in 6utu
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

Go back to Calcium Binding Sites List in 6utu
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

Go back to Calcium Binding Sites List in 6utu
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

Go back to Calcium Binding Sites List in 6utu
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

Go back to Calcium Binding Sites List in 6utu
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

Go back to Calcium Binding Sites List in 6utu
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: Sat Dec 12 07:47:41 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy