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Iron in PDB 3j16: Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners

Other elements in 3j16:

The structure of Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners (pdb code 3j16). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners, PDB code: 3j16:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3j16

Go back to Iron Binding Sites List in 3j16
Iron binding site 1 out of 8 in the Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe703

b:29.9
occ:1.00
 FE1 B:SF4703 0.0 29.9 1.0
SG B:CYS29 1.5 0.0 1.0
S2 B:SF4703 2.3 25.1 1.0
S4 B:SF4703 2.3 27.7 1.0
S3 B:SF4703 2.3 27.7 1.0
FE3 B:SF4703 2.7 29.9 1.0
FE2 B:SF4703 2.7 30.5 1.0
FE4 B:SF4703 2.8 30.0 1.0
CB B:CYS29 3.1 0.0 1.0
SG B:CYS38 3.6 0.0 1.0
CG2 B:VAL31 3.8 0.0 1.0
S1 B:SF4703 3.9 29.6 1.0
CA B:CYS29 4.0 0.0 1.0
CB B:CYS38 4.1 0.0 1.0
SG B:CYS58 4.1 0.0 1.0
CD B:PRO30 4.3 0.0 1.0
CG1 B:VAL31 4.5 0.0 1.0
CG1 B:ILE39 4.5 0.0 1.0
N B:PRO30 4.6 0.0 1.0
CG1 B:ILE56 4.6 0.0 1.0
C B:CYS29 4.6 0.0 1.0
SG B:CYS55 4.6 0.0 1.0
CB B:VAL31 4.8 0.0 1.0
N B:VAL31 4.8 0.0 1.0
CD1 B:ILE56 4.9 0.0 1.0
CG B:PRO30 4.9 0.0 1.0
CD1 B:ILE50 5.0 0.0 1.0
CD1 B:ILE60 5.0 0.0 1.0

Iron binding site 2 out of 8 in 3j16

Go back to Iron Binding Sites List in 3j16
Iron binding site 2 out of 8 in the Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe703

b:30.5
occ:1.00
 FE2 B:SF4703 0.0 30.5 1.0
SG B:CYS55 2.0 0.0 1.0
S4 B:SF4703 2.2 27.7 1.0
S3 B:SF4703 2.2 27.7 1.0
S1 B:SF4703 2.3 29.6 1.0
FE4 B:SF4703 2.7 30.0 1.0
FE1 B:SF4703 2.7 29.9 1.0
FE3 B:SF4703 2.8 29.9 1.0
CB B:CYS55 3.2 0.0 1.0
SG B:CYS38 3.3 0.0 1.0
CA B:CYS55 3.6 0.0 1.0
N B:ILE56 3.6 0.0 1.0
S2 B:SF4703 3.8 25.1 1.0
CD1 B:ILE50 3.8 0.0 1.0
N B:GLY57 4.0 0.0 1.0
C B:CYS55 4.0 0.0 1.0
CG1 B:ILE56 4.1 0.0 1.0
SG B:CYS58 4.1 0.0 1.0
SG B:CYS29 4.2 0.0 1.0
CA B:ILE56 4.6 0.0 1.0
CB B:CYS38 4.6 0.0 1.0
N B:CYS58 4.7 0.0 1.0
C B:ILE56 4.8 0.0 1.0
CG1 B:ILE50 4.8 0.0 1.0
CA B:GLY57 4.8 0.0 1.0
N B:CYS55 4.9 0.0 1.0
SG B:CYS61 4.9 0.0 1.0
CB B:ILE56 4.9 0.0 1.0

Iron binding site 3 out of 8 in 3j16

Go back to Iron Binding Sites List in 3j16
Iron binding site 3 out of 8 in the Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe703

b:29.9
occ:1.00
 FE3 B:SF4703 0.0 29.9 1.0
S4 B:SF4703 2.2 27.7 1.0
S2 B:SF4703 2.2 25.1 1.0
S1 B:SF4703 2.3 29.6 1.0
SG B:CYS61 2.5 0.0 1.0
FE4 B:SF4703 2.7 30.0 1.0
FE1 B:SF4703 2.7 29.9 1.0
FE2 B:SF4703 2.8 30.5 1.0
CB B:CYS61 3.1 0.0 1.0
S3 B:SF4703 3.8 27.7 1.0
SG B:CYS58 3.9 0.0 1.0
N B:CYS61 3.9 0.0 1.0
SG B:CYS29 3.9 0.0 1.0
CD1 B:ILE50 4.1 0.0 1.0
CA B:CYS61 4.1 0.0 1.0
SG B:CYS55 4.5 0.0 1.0
CD1 B:ILE60 4.5 0.0 1.0
CG1 B:ILE60 4.6 0.0 1.0
CB B:CYS29 4.7 0.0 1.0
N B:GLY59 4.8 0.0 1.0
N B:ILE60 4.8 0.0 1.0
SG B:CYS38 4.9 0.0 1.0
CD1 B:ILE39 5.0 0.0 1.0

Iron binding site 4 out of 8 in 3j16

Go back to Iron Binding Sites List in 3j16
Iron binding site 4 out of 8 in the Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe703

b:30.0
occ:1.00
 FE4 B:SF4703 0.0 30.0 1.0
SG B:CYS58 1.5 0.0 1.0
S3 B:SF4703 2.1 27.7 1.0
S1 B:SF4703 2.1 29.6 1.0
S2 B:SF4703 2.2 25.1 1.0
FE3 B:SF4703 2.7 29.9 1.0
FE2 B:SF4703 2.7 30.5 1.0
FE1 B:SF4703 2.8 29.9 1.0
CG1 B:ILE56 3.2 0.0 1.0
CB B:CYS58 3.2 0.0 1.0
CD1 B:ILE56 3.5 0.0 1.0
N B:CYS58 3.6 0.0 1.0
N B:GLY59 3.7 0.0 1.0
S4 B:SF4703 3.8 27.7 1.0
CG1 B:ILE60 3.8 0.0 1.0
CA B:CYS58 3.8 0.0 1.0
SG B:CYS29 3.9 0.0 1.0
C B:CYS58 4.2 0.0 1.0
N B:ILE60 4.2 0.0 1.0
SG B:CYS55 4.4 0.0 1.0
CD B:PRO30 4.4 0.0 1.0
N B:GLY57 4.4 0.0 1.0
CG B:PRO30 4.5 0.0 1.0
CD1 B:ILE60 4.5 0.0 1.0
CB B:ILE56 4.6 0.0 1.0
C B:GLY57 4.7 0.0 1.0
SG B:CYS61 4.7 0.0 1.0
CA B:GLY59 4.7 0.0 1.0
N B:CYS61 4.7 0.0 1.0
N B:ILE56 4.8 0.0 1.0
CB B:ILE60 4.9 0.0 1.0
C B:GLY59 5.0 0.0 1.0

Iron binding site 5 out of 8 in 3j16

Go back to Iron Binding Sites List in 3j16
Iron binding site 5 out of 8 in the Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe704

b:22.7
occ:1.00
 FE1 B:SF4704 0.0 22.7 1.0
S4 B:SF4704 2.3 20.4 1.0
S2 B:SF4704 2.3 20.2 1.0
S3 B:SF4704 2.3 21.1 1.0
FE3 B:SF4704 2.7 23.3 1.0
FE2 B:SF4704 2.7 23.3 1.0
FE4 B:SF4704 2.8 22.6 1.0
SG B:CYS25 3.1 0.0 1.0
SG B:CYS21 3.6 0.0 1.0
S1 B:SF4704 3.9 21.6 1.0
CB B:CYS21 3.9 0.0 1.0
SG B:CYS16 4.2 0.0 1.0
SG B:CYS65 4.4 0.0 1.0
O B:ARG22 4.5 0.0 1.0
N B:CYS25 4.5 0.0 1.0
CB B:CYS25 4.6 0.0 1.0
N B:GLU24 4.9 0.0 1.0

Iron binding site 6 out of 8 in 3j16

Go back to Iron Binding Sites List in 3j16
Iron binding site 6 out of 8 in the Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe704

b:23.3
occ:1.00
 FE2 B:SF4704 0.0 23.3 1.0
SG B:CYS21 1.1 0.0 1.0
CB B:CYS21 1.7 0.0 1.0
S4 B:SF4704 2.2 20.4 1.0
S3 B:SF4704 2.2 21.1 1.0
S1 B:SF4704 2.3 21.6 1.0
FE4 B:SF4704 2.7 22.6 1.0
FE1 B:SF4704 2.7 22.7 1.0
FE3 B:SF4704 2.8 23.3 1.0
CA B:CYS21 3.0 0.0 1.0
O B:LYS17 3.4 0.0 1.0
N B:CYS21 3.4 0.0 1.0
O B:ARG22 3.7 0.0 1.0
S2 B:SF4704 3.8 20.2 1.0
C B:CYS21 4.0 0.0 1.0
CG B:PRO66 4.0 0.0 1.0
CD B:PRO66 4.2 0.0 1.0
N B:ARG22 4.3 0.0 1.0
C B:LYS17 4.3 0.0 1.0
CA B:PRO18 4.3 0.0 1.0
CE1 B:PHE67 4.5 0.0 1.0
O B:PRO18 4.7 0.0 1.0
N B:PRO18 4.7 0.0 1.0
C B:LYS20 4.7 0.0 1.0
C B:PRO18 4.7 0.0 1.0
CD1 B:PHE67 4.9 0.0 1.0
O B:CYS21 4.9 0.0 1.0
C B:ARG22 4.9 0.0 1.0

Iron binding site 7 out of 8 in 3j16

Go back to Iron Binding Sites List in 3j16
Iron binding site 7 out of 8 in the Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe704

b:23.3
occ:1.00
 FE3 B:SF4704 0.0 23.3 1.0
S2 B:SF4704 2.2 20.2 1.0
S4 B:SF4704 2.2 20.4 1.0
S1 B:SF4704 2.3 21.6 1.0
SG B:CYS65 2.6 0.0 1.0
FE4 B:SF4704 2.6 22.6 1.0
FE1 B:SF4704 2.7 22.7 1.0
FE2 B:SF4704 2.8 23.3 1.0
SG B:CYS21 2.8 0.0 1.0
CD1 B:PHE67 3.4 0.0 1.0
CD B:PRO66 3.5 0.0 1.0
S3 B:SF4704 3.8 21.1 1.0
CG B:PRO66 3.8 0.0 1.0
CE1 B:PHE67 3.9 0.0 1.0
CB B:CYS65 3.9 0.0 1.0
N B:PRO66 3.9 0.0 1.0
CA B:CYS65 4.1 0.0 1.0
CB B:CYS21 4.2 0.0 1.0
N B:PHE67 4.3 0.0 1.0
C B:CYS65 4.4 0.0 1.0
CB B:ALA69 4.5 0.0 1.0
CG B:PHE67 4.5 0.0 1.0
SG B:CYS16 4.7 0.0 1.0
CB B:PHE67 4.8 0.0 1.0
CA B:PRO66 4.9 0.0 1.0
O B:LYS17 4.9 0.0 1.0
CB B:PRO66 5.0 0.0 1.0

Iron binding site 8 out of 8 in 3j16

Go back to Iron Binding Sites List in 3j16
Iron binding site 8 out of 8 in the Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Models of Ribosome-Bound DOM34P and RLI1P and Their Ribosomal Binding Partners within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe704

b:22.6
occ:1.00
 FE4 B:SF4704 0.0 22.6 1.0
S3 B:SF4704 2.1 21.1 1.0
S1 B:SF4704 2.1 21.6 1.0
S2 B:SF4704 2.1 20.2 1.0
SG B:CYS16 2.5 0.0 1.0
FE3 B:SF4704 2.6 23.3 1.0
FE2 B:SF4704 2.7 23.3 1.0
FE1 B:SF4704 2.8 22.7 1.0
N B:LYS17 3.1 0.0 1.0
O B:LYS17 3.1 0.0 1.0
SG B:CYS21 3.3 0.0 1.0
C B:LYS17 3.3 0.0 1.0
CB B:CYS16 3.6 0.0 1.0
CA B:CYS16 3.6 0.0 1.0
S4 B:SF4704 3.8 20.4 1.0
C B:CYS16 3.8 0.0 1.0
N B:PRO18 3.8 0.0 1.0
CA B:LYS17 3.9 0.0 1.0
CA B:PRO18 4.1 0.0 1.0
CD B:PRO18 4.2 0.0 1.0
CE1 B:PHE67 4.3 0.0 1.0
CB B:CYS21 4.3 0.0 1.0
CD1 B:PHE67 4.4 0.0 1.0
CG B:PRO18 4.5 0.0 1.0
CB B:PRO18 4.9 0.0 1.0
SG B:CYS65 4.9 0.0 1.0
O B:CYS16 4.9 0.0 1.0
O B:LYS15 4.9 0.0 1.0
N B:CYS16 4.9 0.0 1.0
CB B:LYS17 5.0 0.0 1.0

Reference:

T.Becker, S.Franckenberg, S.Wickles, C.J.Shoemaker, A.M.Anger, J.-P.Armache, H.Sieber, C.Ungewickell, O.Berninghausen, I.Daberkow, A.Karcher, M.Thomm, K.P.Hopfner, R.Green, R.Beckmann. Structural Basis of Highly Conserved Ribosome Recycling in Eukaryotes and Archaea. Nature V. 482 501 2012.
ISSN: ISSN 0028-0836
PubMed: 22358840
DOI: 10.1038/NATURE10829
Page generated: Sun Aug 4 12:40:05 2024

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