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Cadmium in PDB 3inz: H57T Hfq From Pseudomonas Aeruginosa

Protein crystallography data

The structure of H57T Hfq From Pseudomonas Aeruginosa, PDB code: 3inz was solved by O.Moskaleva, B.Melnik, A.Gabdulkhakov, M.Garber, S.Nikonov, E.Stolboushkina, A.Nikulin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.290, 71.160, 104.410, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 21.8

Other elements in 3inz:

The structure of H57T Hfq From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the H57T Hfq From Pseudomonas Aeruginosa (pdb code 3inz). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the H57T Hfq From Pseudomonas Aeruginosa, PDB code: 3inz:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 3inz

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Cadmium binding site 1 out of 9 in the H57T Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of H57T Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd83

b:56.6
occ:0.65
 OD2 A:ASP9 2.5 47.8 1.0
OD1 A:ASP9 2.5 44.4 1.0
O A:HOH286 2.6 35.4 1.0
O A:HOH287 2.7 42.8 1.0
CG A:ASP9 2.8 44.0 1.0
O A:HOH288 3.1 74.4 1.0
O A:HOH350 3.2 52.6 1.0
CB A:ASP9 4.3 38.1 1.0
CA A:GLN41 4.7 29.7 1.0
OG A:SER6 4.7 60.2 1.0
CB A:GLN41 4.9 34.5 1.0

Cadmium binding site 2 out of 9 in 3inz

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Cadmium binding site 2 out of 9 in the H57T Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of H57T Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd83

b:62.3
occ:0.75
 OD2 B:ASP9 2.4 43.3 1.0
O B:HOH305 2.5 47.1 1.0
O B:HOH365 2.6 76.2 1.0
O B:HOH304 2.7 57.1 1.0
OD1 B:ASP9 2.8 40.3 1.0
CG B:ASP9 3.0 40.7 1.0
N B:HIS5 3.6 55.4 1.0
O B:HOH372 3.7 57.6 1.0
CB B:ASP9 4.4 35.9 1.0
CA B:HIS5 4.9 56.4 1.0
CA B:GLN41 4.9 31.7 1.0

Cadmium binding site 3 out of 9 in 3inz

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Cadmium binding site 3 out of 9 in the H57T Hfq From Pseudomonas Aeruginosa


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of H57T Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd84

b:51.8
occ:0.33
 O B:HOH238 2.4 51.6 1.0
OE2 B:GLU18 2.5 37.2 1.0
O B:HOH236 2.5 32.9 1.0
O B:HOH237 2.6 58.2 1.0
OE1 B:GLU18 2.8 36.6 1.0
CD B:GLU18 2.9 34.8 1.0
NH2 B:ARG69 3.1 65.7 1.0
CZ B:ARG69 3.8 66.4 1.0
NE B:ARG69 4.0 63.6 1.0
CB B:ARG69 4.4 50.1 1.0
CG B:GLU18 4.4 32.1 1.0
O B:ARG69 4.4 47.8 1.0
N B:ARG69 4.8 43.3 1.0
NH1 B:ARG69 4.8 67.8 1.0
NH2 B:ARG66 4.8 37.2 1.0
NH1 B:ARG66 4.9 39.6 1.0
CG2 B:THR14 4.9 31.1 1.0

Cadmium binding site 4 out of 9 in 3inz

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Cadmium binding site 4 out of 9 in the H57T Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of H57T Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd83

b:47.8
occ:0.76
 O C:HOH85 2.3 53.3 1.0
OD1 C:ASP9 2.4 39.0 1.0
OD2 C:ASP9 2.5 40.0 1.0
O C:HOH86 2.5 31.6 1.0
O C:HOH84 2.7 49.2 1.0
CG C:ASP9 2.8 38.6 1.0
CB C:ASP9 4.3 35.1 1.0
N C:HIS5 4.4 63.3 1.0
CA C:HIS5 4.5 61.9 1.0
NZ C:LYS56 4.8 28.0 1.0
CA C:GLN41 4.9 27.6 1.0

Cadmium binding site 5 out of 9 in 3inz

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Cadmium binding site 5 out of 9 in the H57T Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of H57T Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd83

b:63.2
occ:0.59
 OD2 D:ASP9 2.4 37.4 1.0
O D:HOH368 2.6 55.1 1.0
OD1 D:ASP9 2.6 40.2 1.0
O E:HOH87 2.7 61.5 1.0
O D:HOH120 2.8 42.2 1.0
CG D:ASP9 2.8 37.3 1.0
O D:HOH121 3.2 54.7 1.0
N D:HIS5 3.5 82.0 1.0
CB D:HIS5 3.7 83.0 1.0
CA D:HIS5 4.2 80.1 1.0
CB D:ASP9 4.3 31.6 1.0
N E:LYS3 4.6 77.5 1.0
CA D:GLN41 4.7 30.6 1.0
O D:HOH119 4.8 69.2 1.0
O D:HIS5 4.9 71.3 1.0

Cadmium binding site 6 out of 9 in 3inz

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Cadmium binding site 6 out of 9 in the H57T Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of H57T Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd83

b:60.2
occ:0.78
 OD2 E:ASP9 2.3 40.8 1.0
ND1 E:HIS5 2.6 68.8 1.0
O E:HOH156 2.7 33.5 1.0
OD1 E:ASP9 3.0 36.5 1.0
CG E:ASP9 3.0 37.9 1.0
O E:HOH157 3.2 66.7 1.0
CE1 E:HIS5 3.4 69.1 1.0
O E:HOH155 3.5 42.2 1.0
CG E:HIS5 3.6 67.8 1.0
CB E:HIS5 3.9 65.1 1.0
CB E:ASP9 4.5 36.7 1.0
NE2 E:HIS5 4.5 68.7 1.0
CD2 E:HIS5 4.6 68.4 1.0

Cadmium binding site 7 out of 9 in 3inz

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Cadmium binding site 7 out of 9 in the H57T Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of H57T Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cd83

b:56.2
occ:0.70
 OD2 F:ASP9 2.2 38.3 1.0
ND1 F:HIS5 2.5 56.7 1.0
O F:HOH306 2.7 43.5 1.0
O F:HOH373 2.7 72.3 1.0
CG F:ASP9 2.9 36.4 1.0
OD1 F:ASP9 2.9 39.1 1.0
O F:HOH307 3.3 39.8 1.0
O F:HOH374 3.4 62.2 1.0
CE1 F:HIS5 3.4 57.0 1.0
CG F:HIS5 3.4 57.1 1.0
CB F:HIS5 3.7 54.5 1.0
CD A:LYS3 4.0 80.0 1.0
CE A:LYS3 4.3 78.2 1.0
CB F:ASP9 4.4 28.3 1.0
NE2 F:HIS5 4.4 59.2 1.0
CD2 F:HIS5 4.5 58.0 1.0
CA F:HIS5 4.9 53.5 1.0
CG A:LYS3 4.9 80.6 1.0
N F:HIS5 4.9 59.6 1.0

Cadmium binding site 8 out of 9 in 3inz

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Cadmium binding site 8 out of 9 in the H57T Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of H57T Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cd84

b:67.0
occ:0.44
 OE2 F:GLU18 2.4 44.2 1.0
O F:HOH183 2.4 79.4 1.0
O F:HOH182 2.5 71.6 1.0
OE1 F:GLU18 2.6 42.2 1.0
O F:HOH308 2.6 0.1 1.0
CD F:GLU18 2.8 40.6 1.0
O F:HOH181 2.9 52.7 1.0
N F:ARG69 4.3 56.2 1.0
CB F:ARG69 4.3 63.6 1.0
CG F:GLU18 4.3 32.6 1.0
CG1 F:VAL68 4.6 47.4 1.0
O F:ARG69 4.7 68.2 1.0
NH1 F:ARG66 4.8 43.1 1.0
CA F:ARG69 4.8 62.1 1.0
NH2 F:ARG66 4.8 38.1 1.0

Cadmium binding site 9 out of 9 in 3inz

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Cadmium binding site 9 out of 9 in the H57T Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of H57T Hfq From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cd85

b:29.0
occ:0.47
 OD1 F:ASN48 2.5 58.0 1.0
O F:HOH125 2.7 56.5 1.0
O F:HOH126 2.7 63.2 1.0
O F:HOH127 2.8 70.5 1.0
CG F:ASN48 2.9 59.2 1.0
ND2 F:ASN48 3.0 63.0 1.0
CB F:ASN48 4.0 56.0 1.0
CA F:ASN48 4.2 49.9 1.0
C F:ASN48 4.4 50.6 1.0
NZ F:LYS47 4.5 33.5 1.0
O F:ASN48 4.6 53.5 1.0
N F:THR49 5.0 48.5 1.0

Reference:

O.Moskaleva, B.Melnik, A.Gabdulkhakov, M.Garber, S.Nikonov, E.Stolboushkina, A.Nikulin. The Structures of Mutant Forms of Hfq From Pseudomonas Aeruginosa Reveal the Importance of the Conserved HIS57 For the Protein Hexamer Organization. Acta Crystallogr.,Sect.F V. 66 760 2010.
ISSN: ESSN 1744-3091
PubMed: 20606268
DOI: 10.1107/S1744309110017331
Page generated: Sat Dec 12 08:22:06 2020

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