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Cadmium in PDB 8r4p: Structure of Baba From Helicobacter Pylori Strain 17875

Protein crystallography data

The structure of Structure of Baba From Helicobacter Pylori Strain 17875, PDB code: 8r4p was solved by K.Persson, T.Boren, J.Bugaytsova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.64 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.613, 96.953, 97.408, 90, 90, 90
R / Rfree (%) 21.1 / 24.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Baba From Helicobacter Pylori Strain 17875 (pdb code 8r4p). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the Structure of Baba From Helicobacter Pylori Strain 17875, PDB code: 8r4p:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 8r4p

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Cadmium binding site 1 out of 10 in the Structure of Baba From Helicobacter Pylori Strain 17875


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Baba From Helicobacter Pylori Strain 17875 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd601

b:70.5
occ:0.77
 OE1 A:GLU34 2.4 78.2 1.0
OD1 A:ASP31 2.4 69.6 1.0
OE2 A:GLU34 2.5 68.5 1.0
CD A:GLU34 2.8 70.9 1.0
O A:HOH870 3.0 58.9 1.0
CG A:ASP31 3.3 70.1 1.0
OD2 A:ASP31 3.7 69.7 1.0
CG A:GLU34 4.3 54.5 1.0
CB A:ASP31 4.6 54.3 1.0
CB A:GLU34 4.9 45.5 1.0

Cadmium binding site 2 out of 10 in 8r4p

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Cadmium binding site 2 out of 10 in the Structure of Baba From Helicobacter Pylori Strain 17875


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Baba From Helicobacter Pylori Strain 17875 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd602

b:35.4
occ:1.00
 OD2 A:ASP76 2.5 27.2 1.0
OD1 A:ASN72 2.7 28.6 1.0
O A:HOH853 2.7 25.1 1.0
OD1 A:ASP76 2.8 29.9 1.0
CG A:ASP76 3.0 27.9 1.0
CG A:ASN72 3.4 34.7 1.0
ND2 A:ASN72 4.0 29.3 1.0
O A:HOH818 4.2 37.2 1.0
O A:HOH832 4.2 47.6 1.0
CB A:ASN72 4.3 29.2 1.0
O A:HOH833 4.4 42.4 1.0
CB A:ASP76 4.4 27.5 1.0
ND2 A:ASN79 4.6 34.5 1.0
CA A:ASN72 4.7 27.2 1.0
CB A:ASN79 4.7 28.3 1.0

Cadmium binding site 3 out of 10 in 8r4p

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Cadmium binding site 3 out of 10 in the Structure of Baba From Helicobacter Pylori Strain 17875


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Baba From Helicobacter Pylori Strain 17875 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd603

b:35.6
occ:1.00
 OE1 A:GLU176 2.6 37.5 1.0
O A:HOH789 2.7 18.2 1.0
OE2 A:GLU176 2.8 31.2 1.0
CD A:GLU176 3.1 39.6 1.0
ND2 A:ASN178 4.2 41.4 1.0
O A:HOH809 4.3 44.0 1.0
CG A:GLU176 4.6 32.0 1.0
CB A:ASN178 4.7 29.8 1.0
CG A:ASN178 5.0 38.4 1.0

Cadmium binding site 4 out of 10 in 8r4p

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Cadmium binding site 4 out of 10 in the Structure of Baba From Helicobacter Pylori Strain 17875


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Baba From Helicobacter Pylori Strain 17875 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd604

b:50.1
occ:0.43
 O A:HOH729 2.8 25.0 1.0
OD2 A:ASP253 2.8 44.4 0.3
OD1 A:ASP253 2.9 37.1 0.3
CG A:ASP253 3.1 37.8 0.3
O A:HOH723 3.7 34.7 1.0
N A:GLY254 3.9 31.1 1.0
CB A:ASP253 4.4 38.1 0.7
CA A:GLY254 4.4 30.0 1.0
CB A:ASP253 4.5 38.4 0.3
C A:ASP253 4.6 35.8 0.7
C A:ASP253 4.7 35.8 0.3
OG A:SER182 4.7 37.6 1.0
OD1 A:ASP253 4.8 35.8 0.7
CA A:ASP253 4.8 35.7 0.7
CA A:ASP253 4.8 35.8 0.3
CG A:ASP253 4.9 40.2 0.7

Cadmium binding site 5 out of 10 in 8r4p

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Cadmium binding site 5 out of 10 in the Structure of Baba From Helicobacter Pylori Strain 17875


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Baba From Helicobacter Pylori Strain 17875 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd605

b:62.2
occ:0.57
 OE2 A:GLU303 2.7 59.0 1.0
OE1 A:GLU303 2.8 49.0 1.0
O A:HOH854 2.8 35.5 1.0
O A:HOH726 2.8 49.9 1.0
CD A:GLU303 3.1 50.0 1.0
O A:THR381 3.7 48.3 1.0
CB A:PHE384 4.3 36.2 1.0
CG2 A:THR381 4.4 48.6 1.0
C A:THR381 4.6 52.2 1.0
CG A:GLU303 4.6 44.4 1.0
O A:HOH893 4.9 46.6 1.0
CD2 A:PHE384 5.0 32.4 1.0

Cadmium binding site 6 out of 10 in 8r4p

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Cadmium binding site 6 out of 10 in the Structure of Baba From Helicobacter Pylori Strain 17875


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Baba From Helicobacter Pylori Strain 17875 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd606

b:77.5
occ:0.79
 OE2 A:GLU317 2.7 53.3 1.0
OE1 A:GLU317 2.8 43.6 1.0
CD A:GLU317 3.1 45.3 1.0
OE1 A:GLN321 4.5 36.8 1.0
ND2 A:ASN320 4.6 42.1 1.0
CG A:GLU317 4.7 34.4 1.0
O A:HOH788 4.9 54.9 1.0
CB A:ASN320 4.9 30.9 1.0
NZ A:LYS363 5.0 51.9 1.0

Cadmium binding site 7 out of 10 in 8r4p

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Cadmium binding site 7 out of 10 in the Structure of Baba From Helicobacter Pylori Strain 17875


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Baba From Helicobacter Pylori Strain 17875 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd607

b:103.0
occ:1.00
 NE2 A:HIS328 2.8 38.8 1.0
O A:HOH871 3.1 61.8 1.0
CE1 A:HIS328 3.1 34.9 1.0
CD2 A:HIS328 4.1 30.3 1.0
ND1 A:HIS328 4.4 37.1 1.0
O A:HOH899 4.5 50.6 1.0
CB A:ALA356 4.9 33.4 1.0
CG A:HIS328 4.9 39.7 1.0

Cadmium binding site 8 out of 10 in 8r4p

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Cadmium binding site 8 out of 10 in the Structure of Baba From Helicobacter Pylori Strain 17875


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Baba From Helicobacter Pylori Strain 17875 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd608

b:42.6
occ:0.72
 O A:HOH850 2.7 21.6 1.0
O A:HOH851 2.7 28.7 1.0
O A:HOH827 2.8 34.5 1.0
O A:HOH891 2.8 44.7 1.0
CA A:TYR425 4.0 33.1 1.0
CB A:CYS395 4.2 39.5 1.0
N A:TYR425 4.3 29.2 1.0
C A:THR394 4.5 41.3 1.0
O A:THR394 4.5 38.5 1.0
O A:HOH756 4.6 30.8 1.0
CD1 A:TYR425 4.6 38.4 1.0
C A:TYR425 4.8 28.9 1.0
N A:CYS395 4.8 34.6 1.0
CA A:THR394 4.8 37.3 1.0
CB A:GLU427 4.9 27.9 1.0
CG A:TYR425 4.9 40.1 1.0
N A:VAL426 4.9 26.5 1.0
O A:ALA393 5.0 39.2 1.0

Cadmium binding site 9 out of 10 in 8r4p

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Cadmium binding site 9 out of 10 in the Structure of Baba From Helicobacter Pylori Strain 17875


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Baba From Helicobacter Pylori Strain 17875 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd609

b:48.0
occ:0.42
 OD1 A:ASN434 2.8 36.6 1.0
O A:HOH828 2.8 37.6 1.0
O A:HOH834 2.8 40.9 0.5
O A:HOH861 2.9 55.2 1.0
O A:HOH834 3.0 36.2 0.5
NE2 A:HIS369 3.0 55.6 1.0
O A:HOH776 3.2 41.2 1.0
CG A:ASN434 3.4 28.6 1.0
ND2 A:ASN434 3.5 38.5 1.0
CD2 A:HIS369 3.6 48.0 1.0
CE1 A:HIS369 4.1 57.2 1.0
ND2 A:ASN376 4.4 41.4 1.0
CB A:ASN434 4.6 28.5 1.0
O A:HOH874 4.7 58.6 1.0
CG A:HIS369 4.8 53.3 1.0
CG A:GLN373 4.8 39.4 1.0
ND1 A:HIS369 5.0 51.4 1.0

Cadmium binding site 10 out of 10 in 8r4p

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Cadmium binding site 10 out of 10 in the Structure of Baba From Helicobacter Pylori Strain 17875


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of Baba From Helicobacter Pylori Strain 17875 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd610

b:71.2
occ:0.48
 OG1 A:THR431 3.3 23.6 1.0
OE2 A:GLU427 3.4 42.6 1.0
O A:HOH863 3.5 58.9 1.0
O A:HOH706 3.9 35.9 1.0
CG2 A:ILE430 4.4 28.2 1.0
CB A:THR431 4.5 28.9 1.0
CD A:GLU427 4.5 38.7 1.0
O A:HOH799 4.5 58.7 1.0
CA A:THR431 4.7 32.4 1.0
N A:THR431 4.8 27.5 1.0
O A:GLU427 4.8 26.1 1.0

Reference:

K.Persson, T.Boren, J.Bugaytsova. Structure of Baba From Helicobacter Pylori Strain 17875 To Be Published.
Page generated: Wed Nov 27 16:42:13 2024

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