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Cadmium in PDB 3txa: Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae

Protein crystallography data

The structure of Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae, PDB code: 3txa was solved by V.Krishnan, S.V.L.Narayana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.79 / 2.62
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.585, 124.585, 117.839, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 25.6

Other elements in 3txa:

The structure of Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae (pdb code 3txa). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae, PDB code: 3txa:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 3txa

Go back to Cadmium Binding Sites List in 3txa
Cadmium binding site 1 out of 7 in the Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd802

b:96.1
occ:1.00
O A:HOH902 2.2 62.9 1.0
NE2 A:HIS588 2.3 73.4 1.0
O A:HOH901 2.5 55.9 1.0
CE1 A:HIS588 3.0 73.0 1.0
CD2 A:HIS588 3.5 71.1 1.0
ND1 A:HIS588 4.2 71.8 1.0
CG A:HIS588 4.5 68.0 1.0
OE1 A:GLU586 4.8 76.1 1.0
OG1 A:THR211 5.0 61.3 1.0

Cadmium binding site 2 out of 7 in 3txa

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Cadmium binding site 2 out of 7 in the Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd803

b:0.9
occ:1.00
NH1 A:ARG346 3.2 65.4 1.0
NE1 A:TRP302 3.5 38.4 1.0
OE1 A:GLN350 3.8 46.0 1.0
CD1 A:TRP302 3.9 37.2 1.0
OG A:SER299 4.0 56.4 1.0
CZ A:ARG346 4.2 65.3 1.0
NE2 A:GLN350 4.4 41.0 1.0
CB A:SER299 4.5 55.6 1.0
CD A:GLN350 4.5 42.3 1.0
CE2 A:TRP302 4.7 33.4 1.0
NH2 A:ARG346 4.8 65.5 1.0

Cadmium binding site 3 out of 7 in 3txa

Go back to Cadmium Binding Sites List in 3txa
Cadmium binding site 3 out of 7 in the Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd804

b:85.7
occ:1.00
ND1 A:HIS305 2.4 60.9 1.0
OD1 A:ASP303 2.4 57.8 1.0
O A:HOH905 2.4 53.7 1.0
O A:HOH906 2.5 54.9 1.0
OD2 A:ASP303 2.6 52.2 1.0
CG A:ASP303 2.8 51.6 1.0
CE1 A:HIS305 3.3 60.3 1.0
CG A:HIS305 3.4 55.0 1.0
CB A:HIS305 3.7 48.8 1.0
CB A:ASP303 4.2 47.9 1.0
NE2 A:HIS305 4.4 60.3 1.0
CD2 A:HIS305 4.5 59.4 1.0
N A:HIS305 4.6 46.9 1.0
CE2 A:TYR304 4.8 49.9 1.0
CA A:HIS305 4.8 48.0 1.0

Cadmium binding site 4 out of 7 in 3txa

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Cadmium binding site 4 out of 7 in the Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd805

b:43.0
occ:1.00
OE2 A:GLU340 2.0 48.7 1.0
O A:HOH907 2.0 29.8 1.0
O A:HOH908 2.2 25.9 1.0
NE2 A:HIS314 2.2 37.1 1.0
OE1 A:GLU340 2.2 46.2 1.0
CD A:GLU340 2.5 46.0 1.0
CE1 A:HIS314 3.2 38.7 1.0
CD2 A:HIS314 3.2 38.5 1.0
CG A:GLU340 4.0 46.9 1.0
CD1 A:LEU348 4.2 28.4 1.0
CB A:ASP345 4.3 53.1 1.0
ND1 A:HIS314 4.3 37.7 1.0
O A:HOH959 4.4 42.4 1.0
CG A:HIS314 4.4 38.4 1.0
OD2 A:ASP345 4.4 52.9 1.0
O A:HOH917 4.6 43.2 1.0
CG A:ASP345 4.9 53.9 1.0

Cadmium binding site 5 out of 7 in 3txa

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Cadmium binding site 5 out of 7 in the Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd806

b:0.4
occ:1.00
NE2 A:HIS662 2.7 56.1 1.0
O A:HOH964 3.1 51.3 1.0
CE1 A:HIS662 3.4 59.0 1.0
CD2 A:HIS662 3.8 55.2 1.0
ND1 A:HIS662 4.7 59.2 1.0
OG1 A:THR648 4.9 47.0 1.0
CG A:HIS662 4.9 53.3 1.0

Cadmium binding site 6 out of 7 in 3txa

Go back to Cadmium Binding Sites List in 3txa
Cadmium binding site 6 out of 7 in the Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd807

b:90.0
occ:1.00
OE1 A:GLU237 2.6 63.1 1.0
O A:HOH963 2.6 48.8 1.0
ND1 A:HIS341 2.8 72.3 1.0
OD1 A:ASN343 3.2 70.5 1.0
CB A:HIS341 3.4 59.0 1.0
CD A:GLU237 3.4 64.7 1.0
CG A:HIS341 3.5 65.6 1.0
OE2 A:GLU237 3.6 67.2 1.0
CE1 A:HIS341 3.9 74.8 1.0
CG A:ASN343 4.1 66.7 1.0
CA A:HIS341 4.2 57.4 1.0
ND2 A:ASN343 4.3 66.5 1.0
N A:ILE342 4.5 58.0 1.0
C A:HIS341 4.7 57.0 1.0
CD2 A:HIS341 4.7 71.2 1.0
CG2 A:ILE342 4.9 59.7 1.0
N A:ASN343 4.9 60.4 1.0
CG A:GLU237 4.9 56.6 1.0
NE2 A:HIS341 4.9 74.8 1.0

Cadmium binding site 7 out of 7 in 3txa

Go back to Cadmium Binding Sites List in 3txa
Cadmium binding site 7 out of 7 in the Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structural Analysis of Adhesive Tip Pilin, GBS104 From Group B Streptococcus Agalactiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd808

b:82.6
occ:1.00
O A:HOH909 2.1 44.0 1.0
ND1 A:HIS662 2.3 59.2 1.0
OD1 A:ASP592 2.3 64.5 1.0
O A:HOH910 2.4 48.4 1.0
OD2 A:ASP592 2.6 64.9 1.0
CE1 A:HIS662 2.6 59.0 1.0
CG A:ASP592 2.8 60.7 1.0
CG A:HIS662 3.6 53.3 1.0
NE2 A:HIS662 3.8 56.1 1.0
CB A:ASP592 4.2 57.0 1.0
CD2 A:HIS662 4.3 55.2 1.0
CB A:HIS662 4.4 49.8 1.0
CA A:HIS662 4.4 49.0 1.0
OE1 A:GLU702 4.5 83.5 1.0
N A:HIS662 4.6 48.4 1.0
OG A:SER701 4.8 72.5 1.0
OD1 A:ASN594 4.8 69.7 1.0
O A:ASP592 4.8 55.5 1.0
CA A:ASP592 5.0 56.4 1.0

Reference:

V.Krishnan, P.Dwivedi, B.J.Kim, A.Samal, K.Macon, X.Ma, A.Mishra, K.S.Doran, H.Ton-That, S.V.Narayana. Structure of Streptococcus Agalactiae Tip Pilin GBS104: A Model For Gbs Pili Assembly and Host Interactions. Acta Crystallogr.,Sect.D V. 69 1073 2013.
ISSN: ISSN 0907-4449
PubMed: 23695252
DOI: 10.1107/S0907444913004642
Page generated: Sat Dec 12 08:23:17 2020

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