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Calcium in PDB 5yq0: Crystal Structure of Secreted Protein Cofj From Etec.

Protein crystallography data

The structure of Crystal Structure of Secreted Protein Cofj From Etec., PDB code: 5yq0 was solved by H.Oki, K.Kawahara, T.Maruno, T.Imai, Y.Muroga, S.Fukakusa, T.Iwashita, Y.Kobayashi, S.Matsuda, T.Kodama, T.Iida, T.Yoshida, T.Ohkubo, S.Nakamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.23 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 142.208, 147.540, 149.306, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Secreted Protein Cofj From Etec. (pdb code 5yq0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Secreted Protein Cofj From Etec., PDB code: 5yq0:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5yq0

Go back to Calcium Binding Sites List in 5yq0
Calcium binding site 1 out of 4 in the Crystal Structure of Secreted Protein Cofj From Etec.


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 Secreted Protein Cofj From Etec. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:23.2
occ:0.63
 O C:HOH568 2.3 41.8 1.0
O C:HOH682 2.3 35.6 1.0
OD1 C:ASP138 2.4 22.6 1.0
O D:HOH542 2.4 26.3 1.0
O D:THR79 2.4 16.6 1.0
O D:HOH501 3.0 34.0 1.0
CG C:ASP138 3.1 26.4 1.0
OD2 C:ASP138 3.1 34.5 1.0
C D:THR79 3.6 21.6 1.0
OD1 D:ASN140 4.0 29.6 1.0
O D:HOH537 4.2 28.2 1.0
O D:HOH535 4.3 30.2 1.0
OE1 C:GLU80 4.4 47.0 1.0
CA D:THR79 4.4 17.4 1.0
CB D:THR79 4.4 17.6 1.0
O D:HOH523 4.4 21.1 1.0
CG D:GLU80 4.6 29.6 1.0
N D:GLU80 4.6 15.8 1.0
CB C:ASP138 4.6 18.3 1.0
CA D:GLU80 4.7 16.5 1.0
O D:HOH598 4.8 28.3 1.0
O C:HOH557 4.9 27.6 1.0
OE2 C:GLU80 4.9 44.7 1.0
CD C:GLU80 4.9 51.8 1.0
CG D:ASN140 5.0 24.4 1.0

Calcium binding site 2 out of 4 in 5yq0

Go back to Calcium Binding Sites List in 5yq0
Calcium binding site 2 out of 4 in the Crystal Structure of Secreted Protein Cofj From Etec.


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 Secreted Protein Cofj From Etec. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:28.4
occ:0.55
 O C:HOH802 2.2 35.0 1.0
O D:HOH559 2.2 33.5 1.0
OE2 C:GLU80 2.3 44.7 1.0
O C:HOH508 2.4 25.0 1.0
O C:THR79 2.5 16.4 1.0
OD1 D:ASP138 2.5 28.3 1.0
CD C:GLU80 3.0 51.8 1.0
OE1 C:GLU80 3.4 47.0 1.0
CG D:ASP138 3.5 30.1 1.0
C C:THR79 3.7 20.5 1.0
OD2 D:ASP138 3.7 32.0 1.0
O C:HOH823 3.9 39.3 1.0
O D:HOH753 4.1 41.4 1.0
CG C:GLU80 4.1 30.4 1.0
O D:HOH537 4.2 28.2 1.0
OD1 C:ASN140 4.2 28.8 1.0
CB C:THR79 4.5 20.2 1.0
CA C:THR79 4.6 18.0 1.0
O C:HOH568 4.6 41.8 1.0
O D:HOH404 4.6 44.6 1.0
O C:HOH619 4.6 25.4 1.0
N C:GLU80 4.6 18.0 1.0
CA C:GLU80 4.7 16.3 1.0
O D:HOH587 4.7 29.9 1.0
O C:HOH544 4.8 31.9 1.0
CB D:ASP138 4.8 19.9 1.0
CB C:GLU80 4.9 20.1 1.0

Calcium binding site 3 out of 4 in 5yq0

Go back to Calcium Binding Sites List in 5yq0
Calcium binding site 3 out of 4 in the Crystal Structure of Secreted Protein Cofj From Etec.


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 Secreted Protein Cofj From Etec. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:20.8
occ:0.72
 O F:HOH492 2.2 29.9 1.0
OD2 E:ASP138 2.3 30.4 1.0
OD1 F:ASP138 2.3 27.8 1.0
O F:HOH407 2.4 26.4 1.0
O F:HOH496 2.5 26.9 1.0
O E:HOH791 2.5 30.9 1.0
O E:HOH784 2.5 26.7 1.0
OD1 E:ASP138 2.8 27.4 1.0
CG E:ASP138 2.9 21.2 1.0
CG F:ASP138 3.3 31.1 1.0
CB F:ASP138 3.9 17.0 1.0
OG E:SER137 4.1 25.8 1.0
OE1 F:GLU80 4.1 30.2 1.0
CA F:ASP138 4.2 16.6 1.0
OD2 F:ASP138 4.2 30.2 1.0
OE2 F:GLU80 4.2 35.0 1.0
O E:HOH765 4.2 31.3 1.0
CB E:ASP138 4.4 18.1 1.0
OD1 F:ASN140 4.4 24.6 1.0
ND2 F:ASN140 4.5 27.1 1.0
CD F:GLU80 4.6 36.0 1.0
O F:HOH729 4.6 42.6 1.0
O E:HOH778 4.6 36.9 1.0
O E:HOH813 4.7 45.5 1.0
CB E:SER137 4.9 19.2 1.0
CG F:ASN140 4.9 21.6 1.0
O F:HOH632 4.9 22.9 1.0
O F:HOH500 5.0 33.0 1.0

Calcium binding site 4 out of 4 in 5yq0

Go back to Calcium Binding Sites List in 5yq0
Calcium binding site 4 out of 4 in the Crystal Structure of Secreted Protein Cofj From Etec.


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 Secreted Protein Cofj From Etec. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca401

b:26.0
occ:0.49
 O H:HOH534 2.0 35.6 1.0
O G:HOH418 2.1 39.7 1.0
O H:HOH553 2.2 36.8 1.0
O H:GLU118 2.4 25.0 1.0
O G:HOH511 2.5 42.5 1.0
C H:GLU118 3.4 23.7 1.0
OD1 G:ASP138 3.5 58.5 1.0
O H:HOH808 3.7 40.2 1.0
OE1 G:GLU80 3.8 39.8 1.0
ND2 G:ASN140 3.8 42.5 1.0
CA H:GLU118 3.8 24.9 1.0
CG G:ASP138 3.9 55.7 1.0
OD1 G:ASN140 4.0 45.1 1.0
OE2 G:GLU80 4.1 40.3 1.0
CB G:ASP138 4.1 29.9 1.0
CA G:ASP138 4.2 28.3 1.0
CG H:GLU118 4.3 42.3 1.0
CG G:ASN140 4.3 32.5 1.0
CD G:GLU80 4.4 35.0 1.0
O H:GLY117 4.4 25.7 1.0
O H:HOH805 4.4 33.3 1.0
N H:TYR119 4.5 20.0 1.0
O G:HOH586 4.7 25.4 1.0
CB H:GLU118 4.7 27.3 1.0
OD2 G:ASP138 4.7 53.6 1.0
N H:GLU118 5.0 26.4 1.0
CA H:TYR119 5.0 21.9 1.0

Reference:

H.Oki, K.Kawahara, T.Maruno, T.Imai, Y.Muroga, S.Fukakusa, T.Iwashita, Y.Kobayashi, S.Matsuda, T.Kodama, T.Iida, T.Yoshida, T.Ohkubo, S.Nakamura. Interplay of A Secreted Protein with Type Ivb Pilus For Efficient Enterotoxigenicescherichia Colicolonization Proc. Natl. Acad. Sci. V. 115 7422 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29941571
DOI: 10.1073/PNAS.1805671115
Page generated: Mon Jul 15 15:33:06 2024

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