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Cadmium in PDB 1mms: Crystal Structure of the Ribosomal Protein L11-Rna Complex

Protein crystallography data

The structure of Crystal Structure of the Ribosomal Protein L11-Rna Complex, PDB code: 1mms was solved by B.T.Wimberly, R.Guymon, J.P.Mccutcheon, S.W.White, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.890, 84.260, 155.510, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 25.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Ribosomal Protein L11-Rna Complex (pdb code 1mms). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Crystal Structure of the Ribosomal Protein L11-Rna Complex, PDB code: 1mms:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 1mms

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Cadmium binding site 1 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd201

b:77.5
occ:0.91
O C:HOH262 2.3 39.1 1.0
O C:HOH264 2.4 49.4 1.0
N7 C:G1071 2.6 31.3 1.0
O C:HOH263 3.3 31.5 1.0
O C:HOH266 3.5 54.5 1.0
O6 C:G1071 3.5 31.9 1.0
C5 C:G1071 3.6 14.6 1.0
C8 C:G1071 3.6 20.4 1.0
C6 C:G1071 3.9 28.2 1.0
N1 C:G1089 4.3 10.6 1.0
OP1 C:G1071 4.3 39.0 1.0
O C:HOH218 4.3 23.4 1.0
O6 C:G1089 4.5 38.0 1.0
O C:HOH267 4.6 21.2 1.0
N4 C:C1072 4.6 23.9 1.0
C6 C:G1089 4.8 23.5 1.0
C4 C:G1071 4.8 11.2 1.0
N9 C:G1071 4.8 22.6 1.0
OP1 C:A1098 4.8 56.4 1.0
OP2 C:A1098 4.9 22.0 1.0

Cadmium binding site 2 out of 8 in 1mms

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Cadmium binding site 2 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd202

b:32.4
occ:0.91
O C:HOH445 1.9 3.6 1.0
O C:HOH446 2.0 19.5 1.0
O C:HOH447 2.0 12.2 1.0
N7 C:G1087 2.1 9.4 1.0
O2' C:A1086 2.5 37.4 1.0
C8 C:G1087 3.1 23.9 1.0
C5 C:G1087 3.2 16.6 1.0
C2' C:A1086 3.5 40.9 1.0
O6 C:G1087 3.6 25.8 1.0
C6 C:G1087 3.8 25.6 1.0
O3' C:A1086 3.9 30.6 1.0
N1 C:A1103 4.0 23.8 1.0
OP2 C:A1057 4.0 50.5 1.0
OP2 C:G1087 4.1 19.3 1.0
O2' C:G1056 4.2 36.3 1.0
N9 C:G1087 4.3 19.6 1.0
C3' C:A1086 4.3 38.3 1.0
C6 C:G1089 4.3 23.5 1.0
C4 C:G1087 4.4 16.3 1.0
C5 C:G1089 4.4 14.4 1.0
O6 C:G1089 4.4 38.0 1.0
N7 C:G1089 4.6 20.2 1.0
N7 C:A1057 4.6 16.5 1.0
P C:G1087 4.6 31.0 1.0
C2 C:A1103 4.6 20.5 1.0
C1' C:A1086 4.7 29.9 1.0
N1 C:G1089 4.8 10.6 1.0
C6 C:A1103 4.8 17.5 1.0
N6 C:A1103 4.8 18.4 1.0
O5' C:G1087 4.9 29.6 1.0
C4 C:G1089 4.9 10.9 1.0

Cadmium binding site 3 out of 8 in 1mms

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Cadmium binding site 3 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd211

b:48.0
occ:0.91
O C:HOH254 2.2 20.4 1.0
O D:HOH256 2.2 15.3 1.0
OP1 D:A1095 2.3 64.6 1.0
O D:HOH255 2.3 15.6 1.0
N7 C:A1067 2.4 21.4 1.0
C8 C:A1067 3.3 13.3 1.0
C5 C:A1067 3.5 7.0 1.0
P D:A1095 3.7 43.6 1.0
N6 C:A1067 3.7 26.0 1.0
O3' D:U1094 4.0 48.0 1.0
C6 C:A1067 4.0 18.5 1.0
O6 C:G1068 4.0 26.9 1.0
O D:HOH427 4.3 17.3 1.0
O2' C:U1066 4.4 33.4 1.0
O5' D:A1095 4.4 28.9 1.0
N9 C:A1067 4.5 16.6 1.0
OP1 C:A1067 4.6 52.4 1.0
C4 C:A1067 4.6 16.3 1.0
O3' C:U1066 4.6 45.3 1.0
C6 C:G1068 4.8 23.5 1.0
OP2 D:A1095 4.8 36.6 1.0
C8 D:A1095 4.9 20.4 1.0

Cadmium binding site 4 out of 8 in 1mms

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Cadmium binding site 4 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd302

b:31.5
occ:0.91
O D:HOH461 2.0 2.0 1.0
O D:HOH462 2.0 22.2 1.0
N7 D:G1087 2.1 6.6 1.0
O D:HOH463 2.2 27.4 1.0
O2' D:A1086 2.4 53.2 1.0
O D:HOH460 2.4 28.4 1.0
C8 D:G1087 3.0 13.2 1.0
C5 D:G1087 3.2 11.8 1.0
C2' D:A1086 3.4 42.6 1.0
O6 D:G1087 3.7 28.3 1.0
C6 D:G1087 3.8 26.4 1.0
O3' D:A1086 3.8 33.2 1.0
N1 D:A1103 4.0 26.2 1.0
OP2 D:G1087 4.0 28.8 1.0
OP2 D:A1057 4.1 40.3 1.0
O2' D:G1056 4.1 28.7 1.0
C3' D:A1086 4.2 36.9 1.0
N9 D:G1087 4.2 24.4 1.0
C4 D:G1087 4.3 16.4 1.0
C6 D:G1089 4.4 26.6 1.0
C5 D:G1089 4.5 20.6 1.0
P D:G1087 4.5 31.8 1.0
O6 D:G1089 4.5 34.4 1.0
C2 D:A1103 4.6 23.0 1.0
O D:HOH372 4.7 29.1 1.0
N7 D:A1057 4.7 23.7 1.0
C1' D:A1086 4.7 38.4 1.0
N7 D:G1089 4.8 20.2 1.0
O5' D:G1087 4.8 32.9 1.0
C6 D:A1103 4.8 19.9 1.0
N1 D:G1089 4.8 18.2 1.0
N6 D:A1103 4.8 16.8 1.0
C4 D:G1089 5.0 15.8 1.0

Cadmium binding site 5 out of 8 in 1mms

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Cadmium binding site 5 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd311

b:76.3
occ:0.91
N7 D:A1067 2.5 23.2 1.0
OP1 C:A1095 3.1 62.5 1.0
C8 D:A1067 3.4 19.0 1.0
C5 D:A1067 3.6 12.6 1.0
N6 D:A1067 3.8 21.1 1.0
C6 D:A1067 4.2 16.3 1.0
O6 D:G1068 4.2 32.9 1.0
P C:A1095 4.3 56.2 1.0
O2' D:U1066 4.3 47.2 1.0
O3' C:U1094 4.5 56.8 1.0
N9 D:A1067 4.7 18.5 1.0
O3' D:U1066 4.7 47.2 1.0
C8 C:A1095 4.7 21.4 1.0
OP1 D:A1067 4.8 61.4 1.0
C4 D:A1067 4.8 22.3 1.0
O5' C:A1095 4.8 37.3 1.0
N7 C:A1095 4.8 21.3 1.0
C6 D:G1068 5.0 18.6 1.0

Cadmium binding site 6 out of 8 in 1mms

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Cadmium binding site 6 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd390

b:66.3
occ:1.00
O D:HOH392 2.4 74.8 1.0
N7 D:G1071 2.5 24.2 1.0
O D:HOH394 2.6 55.7 1.0
O D:HOH396 2.7 38.7 1.0
O D:HOH391 3.1 26.1 1.0
O6 D:G1071 3.4 34.1 1.0
C5 D:G1071 3.4 13.4 1.0
C8 D:G1071 3.5 17.7 1.0
C6 D:G1071 3.7 24.4 1.0
N1 D:G1089 4.1 18.2 1.0
OP1 D:G1071 4.4 43.0 1.0
O6 D:G1089 4.4 34.4 1.0
O D:HOH395 4.6 23.2 1.0
N4 D:C1072 4.6 21.6 1.0
C6 D:G1089 4.6 26.6 1.0
C4 D:G1071 4.6 12.7 1.0
MG D:MG318 4.6 17.5 1.0
N9 D:G1071 4.7 20.7 1.0
O D:HOH452 4.8 47.9 1.0
OP1 D:A1098 4.9 56.5 1.0
N2 D:G1089 4.9 24.0 1.0
C2 D:G1089 4.9 22.5 1.0

Cadmium binding site 7 out of 8 in 1mms

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Cadmium binding site 7 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd413

b:33.4
occ:0.10
O A:ALA118 2.9 45.8 1.0
SD A:MET113 3.0 47.3 1.0
CE A:MET113 3.5 49.6 1.0
N A:SER120 3.8 48.4 1.0
CG A:MET113 3.8 45.8 1.0
C A:ALA118 3.9 43.8 1.0
C A:ASN119 3.9 48.1 1.0
C A:SER120 4.0 45.9 1.0
CA A:SER120 4.2 43.9 1.0
O A:SER120 4.2 53.7 1.0
O A:ASN119 4.3 53.1 1.0
N A:LEU121 4.4 47.0 1.0
CA A:ASN119 4.4 42.4 1.0
N A:ASN119 4.5 42.1 1.0
CB A:ALA118 4.8 41.3 1.0
CA A:ALA118 4.9 41.2 1.0
CA A:LEU121 5.0 44.8 1.0

Cadmium binding site 8 out of 8 in 1mms

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Cadmium binding site 8 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd414

b:14.1
occ:0.10
NZ A:LYS112 2.2 28.6 1.0
OP2 C:U1060 2.8 31.4 1.0
O A:THR72 3.1 51.4 1.0
OD2 A:ASP115 3.2 58.2 1.0
OG1 A:THR72 3.3 56.8 1.0
CE A:LYS112 3.3 31.0 1.0
CB A:ASP115 3.5 48.7 1.0
CG A:ASP115 3.5 57.4 1.0
O3' C:G1059 3.6 34.1 1.0
P C:U1060 3.8 31.4 1.0
C A:THR72 4.1 47.2 1.0
CB A:LYS71 4.1 41.2 1.0
N A:THR72 4.2 51.6 1.0
CG A:PRO55 4.5 66.7 1.0
OD1 A:ASP115 4.5 51.5 1.0
CB A:THR72 4.5 49.4 1.0
CA A:THR72 4.5 48.5 1.0
CD A:LYS71 4.5 47.8 1.0
O A:PRO73 4.6 41.4 1.0
C5' C:G1059 4.6 22.7 1.0
CD A:LYS112 4.6 35.7 1.0
C3' C:G1059 4.7 26.7 1.0
O5' C:U1060 4.8 22.6 1.0
C4' C:G1059 4.8 24.8 1.0
C A:PRO73 4.9 38.4 1.0

Reference:

B.T.Wimberly, R.Guymon, J.P.Mccutcheon, S.W.White, V.Ramakrishnan. A Detailed View of A Ribosomal Active Site: the Structure of the L11-Rna Complex. Cell(Cambridge,Mass.) V. 97 491 1999.
ISSN: ISSN 0092-8674
PubMed: 10338213
DOI: 10.1016/S0092-8674(00)80759-X
Page generated: Fri Aug 28 12:11:54 2020
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