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Iodine in PDB 3m6m: Crystal Structure of Rpff Complexed with Rec Domain of Rpfc

Enzymatic activity of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc

All present enzymatic activity of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc:
2.7.13.3;

Protein crystallography data

The structure of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc, PDB code: 3m6m was solved by Z.Cheng, S.C.Lim, R.Qamra, H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 130.913, 130.913, 156.471, 90.00, 90.00, 120.00
R / Rfree (%) 25 / 27.1

Other elements in 3m6m:

The structure of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc (pdb code 3m6m). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 14 binding sites of Iodine where determined in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc, PDB code: 3m6m:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 14 in 3m6m

Go back to Iodine Binding Sites List in 3m6m
Iodine binding site 1 out of 14 in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I1

b:64.4
occ:1.00
 CA A:ALA279 3.8 58.4 1.0
CG D:MET535 3.9 49.7 1.0
CB D:ALA502 3.9 57.1 1.0
CB A:ALA279 4.1 57.4 1.0
CA D:ALA502 4.1 57.3 1.0
N A:ALA279 4.1 57.4 1.0
CE D:MET535 4.2 48.1 1.0
O A:ARG278 4.2 58.3 1.0
C A:ARG278 4.3 57.5 1.0
SD D:MET535 4.4 47.8 1.0
CG A:ARG278 4.5 60.9 1.0
CB D:MET535 4.5 50.1 1.0
CE D:MET530 4.8 42.5 1.0
N D:ALA502 4.9 55.4 1.0
CB A:ARG278 4.9 58.6 1.0

Iodine binding site 2 out of 14 in 3m6m

Go back to Iodine Binding Sites List in 3m6m
Iodine binding site 2 out of 14 in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I2

b:86.2
occ:1.00
 CE E:MET535 3.8 75.9 1.0
CA B:ALA279 3.9 65.0 1.0
CB B:ALA279 4.0 63.6 1.0
CG E:MET535 4.0 77.1 1.0
CB E:ALA502 4.2 0.0 1.0
N B:ALA279 4.2 64.1 1.0
CA E:ALA502 4.4 0.1 1.0
CB E:MET535 4.5 77.3 1.0
C B:ARG278 4.6 64.5 1.0
O B:ARG278 4.6 65.5 1.0
SD E:MET535 4.8 75.0 1.0
CG B:ARG278 4.8 69.1 1.0
CE E:MET530 4.8 69.0 1.0

Iodine binding site 3 out of 14 in 3m6m

Go back to Iodine Binding Sites List in 3m6m
Iodine binding site 3 out of 14 in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I3

b:0.6
occ:1.00
 N E:VAL568 3.2 0.3 1.0
OD1 E:ASN473 3.7 0.1 1.0
CG1 E:VAL568 3.7 0.4 1.0
CB E:VAL568 3.8 0.3 1.0
CA E:PRO567 3.9 0.0 1.0
C E:PRO567 4.0 0.3 1.0
CA E:VAL568 4.1 0.8 1.0
CD2 E:LEU477 4.4 0.2 1.0
CG E:LEU477 4.4 0.2 1.0
CG E:LYS566 4.4 0.5 1.0
CD1 E:LEU477 4.5 0.3 1.0
CB E:PRO567 4.5 0.0 1.0
CE E:LYS566 4.6 0.7 1.0
CG E:ASN473 4.8 0.5 1.0
CD1 E:LEU543 4.8 0.6 1.0
CB E:LYS566 5.0 0.4 1.0

Iodine binding site 4 out of 14 in 3m6m

Go back to Iodine Binding Sites List in 3m6m
Iodine binding site 4 out of 14 in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I4

b:0.6
occ:1.00
 CA C:ALA279 3.8 71.2 1.0
CA F:ALA502 3.8 86.5 1.0
CG F:MET535 3.9 69.4 1.0
CB C:ALA279 3.9 69.7 1.0
O F:ALA502 3.9 91.3 1.0
CE F:MET535 4.2 66.8 1.0
CB F:ALA502 4.2 87.7 1.0
N C:ALA279 4.2 69.8 1.0
C F:ALA502 4.4 89.2 1.0
SD F:MET535 4.4 66.2 1.0
O C:ARG278 4.4 71.9 1.0
CB F:MET535 4.5 70.4 1.0
C C:ARG278 4.5 70.3 1.0
CG C:ARG278 4.7 74.5 1.0
O F:MET501 4.8 83.1 1.0
N F:ALA502 4.9 84.0 1.0

Iodine binding site 5 out of 14 in 3m6m

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Iodine binding site 5 out of 14 in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I6

b:0.3
occ:1.00
 N D:VAL568 3.7 74.8 1.0
CG1 D:VAL568 3.9 75.0 1.0
CG2 D:VAL476 4.0 72.2 1.0
CG D:LYS566 4.1 69.7 1.0
CE D:LYS566 4.1 69.0 1.0
CB D:VAL568 4.2 74.2 1.0
OD1 D:ASN473 4.2 64.9 1.0
CA D:PRO567 4.2 74.9 1.0
CG D:LEU477 4.5 69.6 1.0
C D:PRO567 4.5 75.2 1.0
CA D:VAL568 4.6 75.3 1.0
CD D:LYS566 4.6 68.7 1.0
CD1 D:LEU477 4.7 68.0 1.0
CB D:LYS566 4.7 70.8 1.0
CG D:ASN473 4.8 64.5 1.0
CD2 D:LEU477 4.8 69.7 1.0
O D:ASN473 4.8 65.7 1.0
CD1 D:LEU543 4.9 55.1 1.0
CB D:ASN473 4.9 64.2 1.0
CB D:PRO567 4.9 76.4 1.0

Iodine binding site 6 out of 14 in 3m6m

Go back to Iodine Binding Sites List in 3m6m
Iodine binding site 6 out of 14 in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I7

b:0.4
occ:1.00
 ND2 F:ASN473 3.3 0.5 1.0
N F:VAL568 3.9 95.5 1.0
CG1 F:VAL568 4.0 88.5 1.0
CE F:LYS566 4.0 97.7 1.0
CA F:PRO567 4.2 0.7 1.0
CG F:ASN473 4.4 0.1 1.0
CG F:LYS566 4.5 96.7 1.0
C F:PRO567 4.6 99.3 1.0
CD2 F:LEU477 4.6 0.4 1.0
CB F:PRO567 4.6 1.0 1.0
CG F:LEU477 4.7 0.3 1.0
CD1 F:LEU477 4.7 0.2 1.0
CB F:VAL568 4.8 90.2 1.0
CD F:LYS566 4.8 96.9 1.0
CD1 F:LEU543 4.8 76.5 1.0
CB F:ASN473 4.8 0.4 1.0
CA F:VAL568 4.9 93.5 1.0
CG2 F:VAL476 4.9 0.9 1.0
CB F:LYS566 5.0 0.6 1.0

Iodine binding site 7 out of 14 in 3m6m

Go back to Iodine Binding Sites List in 3m6m
Iodine binding site 7 out of 14 in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I290

b:0.1
occ:1.00
 N C:GLY154 3.5 53.8 1.0
N C:GLU198 3.5 47.8 1.0
CB C:GLU198 3.7 51.6 1.0
N C:ALA197 3.9 46.5 1.0
CB C:SER196 4.0 50.0 1.0
CA C:GLU153 4.1 53.2 1.0
CB C:ALA197 4.1 46.0 1.0
OG C:SER196 4.1 50.2 1.0
CA C:GLU198 4.2 48.8 1.0
C C:GLU153 4.3 54.0 1.0
CA C:ALA197 4.3 45.4 1.0
CA C:GLY154 4.3 54.8 1.0
C C:ALA197 4.4 45.7 1.0
CB C:GLU153 4.4 55.6 1.0
C C:SER196 4.7 46.2 1.0
OE1 C:GLU198 4.7 61.4 1.0
CG C:GLU153 4.7 55.9 1.0
CA C:SER196 4.8 47.8 1.0
CG1 C:VAL209 4.9 48.5 1.0
CG C:GLU198 5.0 54.2 1.0

Iodine binding site 8 out of 14 in 3m6m

Go back to Iodine Binding Sites List in 3m6m
Iodine binding site 8 out of 14 in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I290

b:1.0
occ:1.00
 N B:GLY154 3.4 45.9 1.0
N B:GLU198 3.7 42.4 1.0
CB B:GLU198 3.9 45.8 1.0
CA B:GLU153 3.9 45.5 1.0
N B:ALA197 4.1 40.8 1.0
C B:GLU153 4.1 45.9 1.0
CB B:SER196 4.2 43.4 1.0
CB B:ALA197 4.2 40.4 1.0
CB B:GLU153 4.2 47.6 1.0
CA B:GLY154 4.3 46.5 1.0
OG B:SER196 4.3 43.8 1.0
CA B:GLU198 4.4 43.6 1.0
CA B:ALA197 4.5 40.1 1.0
CG B:GLU153 4.5 48.3 1.0
C B:ALA197 4.6 40.7 1.0
OE1 B:GLU198 4.7 54.5 1.0
C B:SER196 4.9 40.7 1.0
CG1 B:VAL209 4.9 42.9 1.0

Iodine binding site 9 out of 14 in 3m6m

Go back to Iodine Binding Sites List in 3m6m
Iodine binding site 9 out of 14 in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I290

b:0.9
occ:1.00
 N A:GLU198 3.4 38.8 1.0
N A:GLY154 3.4 41.1 1.0
CB A:GLU198 3.7 41.6 1.0
N A:ALA197 3.8 37.4 1.0
CB A:ALA197 3.9 36.9 1.0
CA A:GLU153 4.0 40.7 1.0
CB A:SER196 4.1 39.6 1.0
CA A:GLU198 4.1 39.9 1.0
CA A:ALA197 4.2 36.8 1.0
C A:GLU153 4.2 41.0 1.0
OG A:SER196 4.2 40.1 1.0
C A:ALA197 4.2 37.4 1.0
CB A:GLU153 4.4 42.3 1.0
CA A:GLY154 4.4 41.6 1.0
C A:SER196 4.6 37.4 1.0
CG A:GLU153 4.6 43.0 1.0
CG1 A:VAL209 4.7 38.7 1.0
OE1 A:GLU198 4.8 49.7 1.0
CA A:SER196 4.9 38.3 1.0
CG A:GLU198 5.0 44.1 1.0

Iodine binding site 10 out of 14 in 3m6m

Go back to Iodine Binding Sites List in 3m6m
Iodine binding site 10 out of 14 in the Crystal Structure of Rpff Complexed with Rec Domain of Rpfc


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Rpff Complexed with Rec Domain of Rpfc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I291

b:0.8
occ:1.00
 CG B:MET252 3.8 41.8 1.0
CA B:GLU249 3.9 44.3 1.0
N B:GLU249 4.2 42.5 1.0
CB B:GLU249 4.2 46.1 1.0
CB B:MET252 4.4 42.1 1.0
CD2 B:LEU248 4.4 41.2 1.0
CG B:LEU248 4.4 40.6 1.0
C B:LEU248 4.6 40.8 1.0
CG B:GLU249 4.8 49.7 1.0
O B:LEU248 4.8 40.4 1.0
CB B:LEU248 4.9 40.3 1.0

Reference:

Z.Cheng, Y.W.He, S.C.Lim, R.Qamra, M.A.Walsh, L.H.Zhang, H.Song. Structural Basis of the Sensor-Synthase Interaction in Autoinduction of the Quorum Sensing Signal Dsf Biosynthesis Structure V. 18 1199 2010.
ISSN: ISSN 0969-2126
PubMed: 20826346
DOI: 10.1016/J.STR.2010.06.011
Page generated: Sun Aug 11 15:40:51 2024

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