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Cadmium in PDB 1feu: Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.

Protein crystallography data

The structure of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna., PDB code: 1feu was solved by R.V.Fedorov, V.A.Meshcheryakov, G.M.Gongadze, N.P.Fomenkova, N.A.Nevskaya, M.Selmer, M.Laurberg, O.Kristensen, S.Al-Karadaghi, A.Liljas, M.B.Garber, S.V.Nikonov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.30
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 109.904, 109.904, 137.511, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 24.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. (pdb code 1feu). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna., PDB code: 1feu:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13;

Cadmium binding site 1 out of 13 in 1feu

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Cadmium binding site 1 out of 13 in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd296

b:47.0
occ:1.00
NE2 A:HIS54 2.3 35.0 1.0
O A:HOH305 2.4 36.2 1.0
OD2 A:ASP123 2.5 42.7 1.0
O A:HOH307 2.6 33.0 1.0
O A:HOH306 2.8 38.5 1.0
CE1 A:HIS54 3.2 34.6 1.0
CG A:ASP123 3.3 40.6 1.0
CD2 A:HIS54 3.4 34.0 1.0
OD1 A:ASP123 3.4 42.1 1.0
ND1 A:HIS54 4.3 32.9 1.0
CG A:HIS54 4.5 33.0 1.0
CB A:ASP123 4.7 39.1 1.0
OG A:SER52 4.7 29.4 1.0
CD A:ARG122 4.8 58.3 1.0
O A:HOH303 4.9 40.1 1.0
CG A:PRO101 4.9 26.8 1.0
CG A:ARG122 4.9 53.3 1.0

Cadmium binding site 2 out of 13 in 1feu

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Cadmium binding site 2 out of 13 in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd297

b:40.7
occ:1.00
ND1 A:HIS55 2.2 37.5 1.0
O A:MET1 2.3 48.5 1.0
O A:HOH342 2.5 37.4 1.0
OE1 A:GLU135 2.7 43.1 1.0
N A:MET1 2.7 48.4 1.0
OE2 A:GLU135 2.7 42.8 1.0
CD A:GLU135 3.0 42.0 1.0
C A:MET1 3.1 48.0 1.0
CE1 A:HIS55 3.1 38.0 1.0
CA A:MET1 3.2 48.2 1.0
CG A:HIS55 3.2 37.5 1.0
CB A:MET1 3.5 50.3 1.0
CB A:HIS55 3.6 37.5 1.0
CA A:HIS55 4.0 37.2 1.0
NE2 A:HIS55 4.3 38.4 1.0
CD2 A:HIS55 4.3 37.9 1.0
N A:GLU2 4.4 46.9 1.0
CG A:GLU135 4.5 40.8 1.0
O A:HIS54 4.6 36.8 1.0
N A:VAL56 4.8 38.2 1.0
CG A:MET1 4.8 52.8 1.0
C A:HIS55 4.9 38.0 1.0
N A:HIS55 5.0 37.0 1.0

Cadmium binding site 3 out of 13 in 1feu

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Cadmium binding site 3 out of 13 in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd298

b:53.5
occ:1.00
NE2 A:HIS32 2.3 36.0 1.0
OD1 A:ASP93 2.5 50.2 1.0
O A:HOH304 2.6 24.3 1.0
O A:HOH308 2.7 34.2 1.0
CD2 A:HIS32 2.9 33.4 1.0
OG A:SER92 3.0 44.8 1.0
OE2 A:GLU94 3.2 61.3 1.0
CG A:ASP93 3.2 50.5 1.0
OD2 A:ASP93 3.3 51.6 1.0
CE1 A:HIS32 3.5 35.5 1.0
CD A:GLU94 3.9 58.6 1.0
CG A:GLU94 4.0 55.8 1.0
CD A:ARG31 4.2 45.1 1.0
CB A:SER92 4.2 41.3 1.0
CG A:HIS32 4.2 34.2 1.0
CG A:ARG31 4.5 43.7 1.0
ND1 A:HIS32 4.5 34.4 1.0
N A:ASP93 4.6 44.6 1.0
CB A:ASP93 4.7 48.5 1.0
OE1 A:GLU94 4.9 59.0 1.0

Cadmium binding site 4 out of 13 in 1feu

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Cadmium binding site 4 out of 13 in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd299

b:47.6
occ:0.50
OD1 A:ASP154 2.6 37.5 1.0
ND1 A:HIS151 2.9 43.3 1.0
O A:HOH320 3.1 37.2 1.0
CG A:ASP154 3.3 35.1 1.0
OD2 A:ASP154 3.4 36.6 1.0
O A:SER149 3.5 40.8 1.0
CE1 A:HIS151 3.8 43.4 1.0
CG A:HIS151 3.8 42.6 1.0
CB A:HIS151 4.0 39.6 1.0
N A:HIS151 4.1 37.2 1.0
C A:SER149 4.7 40.7 1.0
CA A:HIS151 4.7 37.3 1.0
CB A:ASP154 4.8 33.8 1.0
CA A:LEU150 4.9 37.8 1.0
C A:LEU150 4.9 37.1 1.0
NE2 A:HIS151 4.9 42.4 1.0
O A:HOH310 4.9 32.7 1.0
CD2 A:HIS151 4.9 42.6 1.0
OG A:SER153 5.0 37.6 1.0

Cadmium binding site 5 out of 13 in 1feu

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Cadmium binding site 5 out of 13 in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:43.1
occ:0.50
NE2 A:HIS121 2.5 43.5 1.0
O A:HOH309 2.7 23.2 1.0
OE2 A:GLU169 2.8 58.5 1.0
O A:HOH313 2.9 43.8 1.0
CE1 A:HIS121 3.5 43.4 1.0
CD2 A:HIS121 3.5 42.6 1.0
CD A:GLU169 3.8 55.5 1.0
CG1 A:VAL165 4.1 31.8 1.0
CD A:CD302 4.2 41.7 0.5
CG A:GLU169 4.3 51.0 1.0
ND1 A:HIS121 4.6 42.2 1.0
CB A:VAL165 4.6 32.1 1.0
CG A:HIS121 4.6 41.5 1.0
OE1 A:GLU169 4.8 57.6 1.0

Cadmium binding site 6 out of 13 in 1feu

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Cadmium binding site 6 out of 13 in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:41.7
occ:0.50
O A:ASP123 2.4 35.6 1.0
CD2 A:HIS121 2.7 42.6 1.0
O A:HOH309 2.9 23.2 1.0
O A:HOH311 2.9 28.8 1.0
C A:ASP123 3.4 34.5 1.0
NE2 A:HIS121 3.4 43.5 1.0
CG A:HIS121 3.7 41.5 1.0
CD A:CD301 4.2 43.1 0.5
N A:ASP123 4.2 37.9 1.0
N A:ILE124 4.3 31.1 1.0
CA A:ASP123 4.3 36.6 1.0
CB A:HIS121 4.3 41.0 1.0
CA A:ILE124 4.3 28.8 1.0
O A:HOH312 4.5 38.7 1.0
CB A:ASP123 4.5 39.1 1.0
CE1 A:HIS121 4.6 43.4 1.0
CD2 A:TYR99 4.7 39.1 1.0
CE2 A:TYR99 4.7 39.9 1.0
ND1 A:HIS121 4.7 42.2 1.0
N A:ARG122 4.8 40.4 1.0
CA A:HIS121 4.9 40.1 1.0

Cadmium binding site 7 out of 13 in 1feu

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Cadmium binding site 7 out of 13 in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd300

b:42.5
occ:0.50
OD1 D:ASP93 2.5 45.5 1.0
O D:HOH435 2.6 27.5 1.0
O D:HOH434 2.6 32.0 1.0
OD2 D:ASP93 2.9 45.7 1.0
CG D:ASP93 3.1 44.6 1.0
CB D:ASP93 4.6 40.2 1.0

Cadmium binding site 8 out of 13 in 1feu

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Cadmium binding site 8 out of 13 in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd303

b:33.9
occ:1.00
O D:HOH325 2.2 31.6 1.0
OD1 D:ASP123 2.3 34.6 1.0
O D:HOH323 2.3 28.0 1.0
NE2 D:HIS54 2.4 23.6 1.0
O D:HOH343 2.5 19.0 1.0
O D:HOH324 2.6 30.4 1.0
CG D:ASP123 3.1 34.2 1.0
OD2 D:ASP123 3.2 34.6 1.0
CE1 D:HIS54 3.2 22.8 1.0
CD2 D:HIS54 3.5 22.8 1.0
OG D:SER52 4.4 17.6 1.0
NE D:ARG122 4.4 58.7 1.0
ND1 D:HIS54 4.4 22.1 1.0
CB D:ASP123 4.5 33.0 1.0
CG D:HIS54 4.6 22.8 1.0
CZ D:ARG122 4.7 61.8 1.0
NH2 D:ARG122 4.7 62.8 1.0
CD D:ARG122 4.9 53.0 1.0

Cadmium binding site 9 out of 13 in 1feu

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Cadmium binding site 9 out of 13 in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd304

b:28.6
occ:1.00
OE1 D:GLU135 2.2 31.5 1.0
ND1 D:HIS55 2.5 25.3 1.0
N D:MET1 2.6 34.0 1.0
O D:HOH443 2.6 34.3 1.0
O D:MET1 2.7 32.7 1.0
OE2 D:GLU135 2.8 34.2 1.0
CD D:GLU135 2.8 31.8 1.0
CB D:MET1 3.0 36.8 1.0
CA D:MET1 3.0 34.0 1.0
C D:MET1 3.2 33.1 1.0
CE1 D:HIS55 3.4 25.8 1.0
CG D:HIS55 3.5 25.5 1.0
CB D:HIS55 3.7 22.8 1.0
CA D:HIS55 4.1 20.8 1.0
CG D:GLU135 4.3 28.9 1.0
CG D:MET1 4.3 37.9 1.0
N D:GLU2 4.5 32.9 1.0
NE2 D:HIS55 4.5 25.9 1.0
O D:HOH440 4.5 26.9 1.0
CD2 D:HIS55 4.6 25.9 1.0
N D:VAL56 4.8 21.4 1.0
O D:HOH395 4.9 33.3 1.0
O D:HIS54 4.9 22.0 1.0

Cadmium binding site 10 out of 13 in 1feu

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Cadmium binding site 10 out of 13 in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd305

b:40.1
occ:1.00
OE2 D:GLU94 2.2 46.7 1.0
NE2 D:HIS32 2.3 29.6 1.0
O D:HOH425 2.4 19.2 1.0
OG D:SER92 2.6 32.6 1.0
OE1 D:GLU94 2.8 47.1 1.0
CD D:GLU94 2.8 44.8 1.0
CD2 D:HIS32 3.1 27.3 1.0
O D:HOH353 3.3 36.3 1.0
CE1 D:HIS32 3.4 28.2 1.0
CB D:SER92 3.7 31.3 1.0
CG D:HIS32 4.3 26.5 1.0
CG D:GLU94 4.3 41.6 1.0
N D:ASP93 4.4 35.0 1.0
ND1 D:HIS32 4.4 28.4 1.0
CD D:ARG31 4.5 35.5 1.0
N D:GLU94 4.8 35.1 1.0
CG D:ARG31 4.9 32.9 1.0
CA D:SER92 5.0 31.1 1.0
CB D:ASP93 5.0 40.2 1.0

Cadmium binding site 11 out of 13 in 1feu

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Cadmium binding site 11 out of 13 in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd306

b:30.5
occ:0.50
OD1 D:ASP154 2.5 30.9 1.0
ND1 D:HIS151 2.6 29.6 1.0
CG D:ASP154 3.2 30.9 1.0
OD2 D:ASP154 3.4 31.3 1.0
CE1 D:HIS151 3.5 29.2 1.0
CG D:HIS151 3.6 30.2 1.0
CB D:HIS151 3.9 29.7 1.0
N D:HIS151 4.0 28.2 1.0
O D:SER149 4.2 31.9 1.0
OG D:SER153 4.6 31.5 1.0
CA D:HIS151 4.6 29.8 1.0
NE2 D:HIS151 4.6 28.4 1.0
CB D:ASP154 4.7 30.0 1.0
CD2 D:HIS151 4.7 27.4 1.0
C D:LEU150 4.9 26.7 1.0
CA D:LEU150 5.0 26.8 1.0

Cadmium binding site 12 out of 13 in 1feu

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Cadmium binding site 12 out of 13 in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd307

b:46.1
occ:0.50
NE2 D:HIS121 2.5 34.4 1.0
O D:HOH355 2.6 37.2 1.0
O D:HOH336 2.8 15.3 1.0
OE2 D:GLU169 2.9 46.5 1.0
CD2 D:HIS121 3.2 33.0 1.0
O D:HOH363 3.5 47.4 1.0
CE1 D:HIS121 3.6 32.9 1.0
CD D:GLU169 3.9 45.0 1.0
CG1 D:VAL165 3.9 32.9 1.0
CD D:CD308 4.0 35.6 0.5
CG D:GLU169 4.1 42.8 1.0
CG D:HIS121 4.5 33.8 1.0
CG2 D:VAL165 4.5 31.4 1.0
ND1 D:HIS121 4.6 34.0 1.0
CB D:VAL165 4.9 32.6 1.0

Cadmium binding site 13 out of 13 in 1feu

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Cadmium binding site 13 out of 13 in the Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Crystal Structure of Ribosomal Protein TL5, One of the Ctc Family Proteins, Complexed with A Fragment of 5S Rrna. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd308

b:35.6
occ:0.50
O D:HOH328 2.6 18.0 1.0
CD2 D:HIS121 2.7 33.0 1.0
O D:ASP123 2.9 35.2 1.0
O D:HOH336 3.0 15.3 1.0
CG D:HIS121 3.6 33.8 1.0
NE2 D:HIS121 3.6 34.4 1.0
C D:ASP123 3.7 33.6 1.0
CD D:CD307 4.0 46.1 0.5
CB D:HIS121 4.0 32.8 1.0
N D:ASP123 4.3 33.1 1.0
CA D:ASP123 4.4 33.8 1.0
O D:HOH355 4.5 37.2 1.0
N D:ILE124 4.5 33.0 1.0
CE2 D:TYR99 4.5 24.9 1.0
CB D:ASP123 4.5 33.0 1.0
CA D:ILE124 4.6 31.3 1.0
CA D:HIS121 4.6 33.2 1.0
CD2 D:TYR99 4.6 26.0 1.0
ND1 D:HIS121 4.7 34.0 1.0
CE1 D:HIS121 4.7 32.9 1.0
N D:ARG122 4.8 34.8 1.0

Reference:

R.Fedorov, V.Meshcheryakov, G.Gongadze, N.Fomenkova, N.Nevskaya, M.Selmer, M.Laurberg, O.Kristensen, S.Al-Karadaghi, A.Liljas, M.Garber, S.Nikonov. Structure of Ribosomal Protein TL5 Complexed with Rna Provides New Insights Into the Ctc Family of Stress Proteins. Acta Crystallogr.,Sect.D V. 57 968 2001.
ISSN: ISSN 0907-4449
PubMed: 11418764
DOI: 10.1107/S0907444901006291
Page generated: Fri Aug 28 11:47:14 2020
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