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Fluorine in PDB 1l5y: Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd

Protein crystallography data

The structure of Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd, PDB code: 1l5y was solved by S.Park, M.Meyer, A.D.Jones, H.P.Yennawar, N.H.Yennawar, B.T.Nixon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.005, 76.837, 77.853, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.9

Other elements in 1l5y:

The structure of Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 33;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd (pdb code 1l5y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 33 binding sites of Fluorine where determined in the Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd, PDB code: 1l5y:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 33 in 1l5y

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Fluorine binding site 1 out of 33 in the Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F660

b:12.7
occ:1.00
 F1 A:BEF660 0.0 12.7 1.0
BE A:BEF660 1.5 13.2 1.0
MG A:MG701 2.1 17.8 1.0
F3 A:BEF660 2.5 12.4 1.0
F2 A:BEF660 2.5 11.3 1.0
OD1 A:ASP55 2.8 7.7 1.0
O A:ARG57 2.9 13.7 1.0
O A:HOH709 3.1 12.9 1.0
OD2 A:ASP55 3.1 10.1 1.0
O A:HOH710 3.2 16.6 1.0
CG A:ASP55 3.3 10.8 1.0
ND1 A:HIS85 3.3 17.8 1.0
CB A:ARG57 3.4 11.8 1.0
N A:ARG57 3.4 12.4 1.0
CE1 A:HIS85 3.6 16.7 1.0
CA A:ARG57 3.7 12.1 1.0
C A:ARG57 3.7 13.8 1.0
O1 A:SO4707 3.8 35.8 1.0
OD1 A:ASP12 4.2 16.6 1.0
NZ A:LYS105 4.3 13.8 1.0
O3 A:SO4707 4.3 35.1 1.0
CG A:ARG57 4.5 20.9 1.0
N A:ILE56 4.5 11.6 1.0
C A:ILE56 4.6 12.9 1.0
CG A:HIS85 4.6 17.4 1.0
S A:SO4707 4.6 34.9 1.0
CB A:ASP55 4.8 12.1 1.0
NE2 A:HIS85 4.8 17.7 1.0
O A:HOH805 4.9 28.0 1.0
OG1 A:THR83 4.9 9.8 1.0
N A:GLY84 5.0 11.2 1.0

Fluorine binding site 2 out of 33 in 1l5y

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Fluorine binding site 2 out of 33 in the Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F660

b:11.3
occ:1.00
 F2 A:BEF660 0.0 11.3 1.0
BE A:BEF660 1.5 13.2 1.0
F1 A:BEF660 2.5 12.7 1.0
F3 A:BEF660 2.5 12.4 1.0
N A:ARG57 2.7 12.4 1.0
OG1 A:THR83 2.7 9.8 1.0
OD1 A:ASP55 2.8 7.7 1.0
N A:ILE56 3.1 11.6 1.0
CB A:ILE56 3.4 9.3 1.0
CA A:ILE56 3.4 11.0 1.0
C A:ILE56 3.5 12.9 1.0
CB A:THR83 3.5 7.8 1.0
CG A:ASP55 3.6 10.8 1.0
CB A:ARG57 3.7 11.8 1.0
CA A:ARG57 3.7 12.1 1.0
ND1 A:HIS85 3.7 17.8 1.0
CA A:THR83 3.8 11.2 1.0
OD2 A:ASP55 4.0 10.1 1.0
N A:GLY84 4.0 11.2 1.0
CG A:ARG57 4.0 20.9 1.0
O A:VAL82 4.1 15.1 1.0
MG A:MG701 4.2 17.8 1.0
C A:ASP55 4.2 11.8 1.0
O A:ARG57 4.3 13.7 1.0
CG2 A:ILE56 4.3 12.6 1.0
N A:HIS85 4.4 11.5 1.0
C A:THR83 4.4 13.2 1.0
C A:ARG57 4.5 13.8 1.0
CG1 A:ILE56 4.5 10.8 1.0
CB A:HIS85 4.5 13.8 1.0
CG A:HIS85 4.6 17.4 1.0
CE1 A:HIS85 4.7 16.7 1.0
CA A:ASP55 4.7 11.6 1.0
O A:ILE56 4.7 10.1 1.0
CB A:ASP55 4.7 12.1 1.0
CG2 A:THR83 4.9 8.8 1.0
N A:THR83 4.9 13.5 1.0
C A:VAL82 5.0 15.2 1.0

Fluorine binding site 3 out of 33 in 1l5y

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Fluorine binding site 3 out of 33 in the Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F660

b:12.4
occ:1.00
 F3 A:BEF660 0.0 12.4 1.0
BE A:BEF660 1.5 13.2 1.0
F1 A:BEF660 2.5 12.7 1.0
OD1 A:ASP55 2.5 7.7 1.0
F2 A:BEF660 2.5 11.3 1.0
N A:GLY84 2.8 11.2 1.0
NZ A:LYS105 3.0 13.8 1.0
CE A:LYS105 3.2 13.4 1.0
CD A:LYS105 3.4 12.5 1.0
CA A:THR83 3.5 11.2 1.0
ND1 A:HIS85 3.5 17.8 1.0
C A:THR83 3.6 13.2 1.0
CG A:ASP55 3.7 10.8 1.0
OG1 A:THR83 3.7 9.8 1.0
O A:HOH709 3.8 12.9 1.0
CA A:GLY84 3.8 13.3 1.0
CE1 A:HIS85 4.0 16.7 1.0
MG A:MG701 4.1 17.8 1.0
CB A:THR83 4.2 7.8 1.0
OD2 A:ASP55 4.2 10.1 1.0
N A:HIS85 4.3 11.5 1.0
O A:VAL82 4.3 15.1 1.0
C A:GLY84 4.4 14.8 1.0
CG A:LYS105 4.4 15.3 1.0
N A:THR83 4.5 13.5 1.0
O A:HOH720 4.5 16.4 1.0
N A:ILE56 4.7 11.6 1.0
CG A:HIS85 4.7 17.4 1.0
O A:THR83 4.8 14.0 1.0
C A:VAL82 4.8 15.2 1.0
CB A:ASP55 4.9 12.1 1.0
O1 A:SO4707 4.9 35.8 1.0
OD2 A:ASP11 4.9 13.9 1.0
O4 A:SO4707 4.9 38.4 1.0
N A:ARG57 4.9 12.4 1.0
O3 A:SO4707 4.9 35.1 1.0

Fluorine binding site 4 out of 33 in 1l5y

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Fluorine binding site 4 out of 33 in the Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F662

b:40.5
occ:1.00
 F1 A:BF2662 0.0 40.5 1.0
BE A:BF2662 1.5 39.4 1.0
F2 A:BF2662 2.4 36.9 1.0
OE2 A:GLU141 3.1 34.1 1.0
OE1 A:GLU141 3.7 35.5 1.0
CD A:GLU141 3.7 35.3 1.0

Fluorine binding site 5 out of 33 in 1l5y

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Fluorine binding site 5 out of 33 in the Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F662

b:36.9
occ:1.00
 F2 A:BF2662 0.0 36.9 1.0
BE A:BF2662 1.5 39.4 1.0
F1 A:BF2662 2.4 40.5 1.0
OE1 A:GLU141 3.2 35.5 1.0
OE2 A:GLU141 3.6 34.1 1.0
CD A:GLU141 3.8 35.3 1.0

Fluorine binding site 6 out of 33 in 1l5y

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Fluorine binding site 6 out of 33 in the Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F663

b:39.8
occ:1.00
 F1 A:BF2663 0.0 39.8 1.0
BE A:BF2663 1.5 38.6 1.0
F2 A:BF2663 2.4 39.1 1.0
NH2 A:ARG124 2.8 34.9 1.0
CZ A:ARG124 3.8 36.7 1.0
NE A:ARG124 4.1 32.2 1.0
CD A:LYS121 4.3 25.6 1.0
CG A:LYS121 4.4 21.4 1.0
CE A:LYS121 4.7 27.2 1.0
CB A:LYS121 4.8 18.0 1.0
NZ A:LYS121 4.8 30.9 1.0
NH1 A:ARG124 4.8 36.9 1.0

Fluorine binding site 7 out of 33 in 1l5y

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Fluorine binding site 7 out of 33 in the Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F663

b:39.1
occ:1.00
 F2 A:BF2663 0.0 39.1 1.0
BE A:BF2663 1.5 38.6 1.0
F1 A:BF2663 2.4 39.8 1.0
NZ A:LYS121 3.3 30.9 1.0
CE A:LYS121 3.9 27.2 1.0
CD A:LYS121 4.2 25.6 1.0
CG A:LYS121 4.9 21.4 1.0

Fluorine binding site 8 out of 33 in 1l5y

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Fluorine binding site 8 out of 33 in the Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F664

b:36.0
occ:1.00
 F1 A:BF2664 0.0 36.0 1.0
BE A:BF2664 1.5 36.5 1.0
F2 A:BF2664 2.5 36.9 1.0
O A:ILE95 3.5 14.8 1.0
O A:GLN96 3.6 19.2 1.0
O A:HOH719 4.0 20.1 1.0
CA A:GLN96 4.1 17.8 1.0
C A:GLN96 4.2 17.7 1.0
C A:ILE95 4.4 16.6 1.0
N A:GLY98 4.7 15.4 1.0
N A:GLN96 4.8 16.1 1.0
CA A:GLY98 4.9 16.5 1.0

Fluorine binding site 9 out of 33 in 1l5y

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Fluorine binding site 9 out of 33 in the Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F664

b:36.9
occ:1.00
 F2 A:BF2664 0.0 36.9 1.0
BE A:BF2664 1.5 36.5 1.0
F1 A:BF2664 2.5 36.0 1.0
O A:HOH737 3.5 26.4 1.0
CA A:GLN96 3.8 17.8 1.0
CG A:GLN96 4.1 15.0 1.0
O B:HOH734 4.1 24.2 1.0
CG2 B:ILE295 4.1 15.1 1.0
O A:ILE95 4.2 14.8 1.0
CB A:GLN96 4.3 16.6 1.0
O A:GLN96 4.4 19.2 1.0
N A:GLN96 4.5 16.1 1.0
C A:GLN96 4.6 17.7 1.0
O B:HOH799 4.6 30.0 1.0
C A:ILE95 4.6 16.6 1.0
O B:ILE295 4.9 9.7 1.0
CG2 A:ILE95 4.9 12.8 1.0

Fluorine binding site 10 out of 33 in 1l5y

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Fluorine binding site 10 out of 33 in the Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of MG2+ / BEF3-Bound Receiver Domain of Sinorhizobium Meliloti Dctd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F665

b:38.4
occ:1.00
 F1 A:BF2665 0.0 38.4 1.0
BE A:BF2665 1.5 33.8 1.0
F2 A:BF2665 2.4 31.9 1.0
NE A:ARG111 2.7 26.0 1.0
O A:HOH784 2.9 29.7 1.0
O A:HOH754 3.5 27.8 1.0
CD A:ARG111 3.5 27.3 1.0
CG2 A:ILE103 3.5 15.2 1.0
CZ A:ARG111 3.6 23.7 1.0
CG A:ARG111 3.7 21.0 1.0
NH2 A:ARG111 3.7 28.1 1.0
O A:HOH748 4.0 27.8 1.0
CA A:ILE103 4.1 14.8 1.0
N A:ALA104 4.1 14.7 1.0
CB A:ILE103 4.2 14.0 1.0
CG1 A:ILE103 4.4 13.7 1.0
C A:ILE103 4.6 15.5 1.0
O A:ALA104 4.7 16.9 1.0
CG B:PRO289 4.7 20.8 1.0
NH1 A:ARG111 4.8 24.7 1.0
O A:PHE102 4.8 13.8 1.0
CB B:PRO289 4.9 19.0 1.0
CB A:ARG111 4.9 20.8 1.0

Reference:

S.Park, M.Meyer, A.D.Jones, H.P.Yennawar, N.H.Yennawar, B.T.Nixon. Two-Component Signaling in the Aaa + Atpase Dctd: Binding MG2+ and BEF3- Selects Between Alternate Dimeric States of the Receiver Domain Faseb J. V. 16 1964 2002.
ISSN: ISSN 0892-6638
PubMed: 12368235
Page generated: Wed Jul 31 11:46:39 2024

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