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Fluorine in PDB 1shz: Crystal Structure of the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera

Protein crystallography data

The structure of Crystal Structure of the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera, PDB code: 1shz was solved by Z.Chen, W.D.Singer, P.C.Sternweis, S.R.Sprang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.49 / 2.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 199.747, 105.274, 71.748, 90.00, 96.91, 90.00
R / Rfree (%) 22.9 / 29.7

Other elements in 1shz:

The structure of Crystal Structure of the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera (pdb code 1shz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera, PDB code: 1shz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 1shz

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Fluorine binding site 1 out of 8 in the Crystal Structure of the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera


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 the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:26.2
occ:1.00
 F1 A:ALF378 0.0 26.2 1.0
AL A:ALF378 1.8 21.6 1.0
O3B A:GDP475 2.4 45.3 1.0
F4 A:ALF378 2.5 29.9 1.0
F2 A:ALF378 2.5 36.9 1.0
O A:HOH543 2.7 50.9 1.0
N A:GLU58 2.8 37.8 1.0
NE2 A:GLN226 2.9 53.6 1.0
NH2 A:ARG200 3.3 31.5 1.0
CA A:GLY57 3.4 38.3 1.0
F3 A:ALF378 3.5 22.8 1.0
C A:GLY57 3.6 40.8 1.0
NH1 A:ARG200 3.7 33.9 1.0
CD A:GLN226 3.7 41.7 1.0
CA A:GLU58 3.8 34.5 1.0
OE1 A:GLN226 3.8 52.1 1.0
PB A:GDP475 3.8 36.0 1.0
CZ A:ARG200 3.9 30.3 1.0
CG A:GLU58 4.1 49.6 1.0
O1B A:GDP475 4.3 56.0 1.0
CB A:GLU58 4.5 36.6 1.0
O3A A:GDP475 4.6 48.6 1.0
O2B A:GDP475 4.6 35.8 1.0
N A:GLY57 4.7 40.2 1.0
O A:GLY57 4.7 46.6 1.0
N A:GLY225 4.8 23.8 1.0
NZ A:LYS61 5.0 26.2 1.0

Fluorine binding site 2 out of 8 in 1shz

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Fluorine binding site 2 out of 8 in the Crystal Structure of the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera


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 the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:36.9
occ:1.00
 F2 A:ALF378 0.0 36.9 1.0
AL A:ALF378 1.8 21.6 1.0
F3 A:ALF378 2.4 22.8 1.0
O3B A:GDP475 2.4 45.3 1.0
F1 A:ALF378 2.5 26.2 1.0
O A:HOH543 2.6 50.9 1.0
N A:THR203 3.1 37.6 1.0
NH1 A:ARG200 3.2 33.9 1.0
MG A:MG377 3.3 8.2 1.0
NH2 A:ARG200 3.4 31.5 1.0
F4 A:ALF378 3.5 29.9 1.0
O2B A:GDP475 3.6 35.8 1.0
CZ A:ARG200 3.6 30.3 1.0
PB A:GDP475 3.6 36.0 1.0
CA A:PRO202 3.8 28.6 1.0
CB A:THR203 3.8 39.6 1.0
C A:PRO202 3.9 36.3 1.0
CA A:THR203 4.0 37.7 1.0
OG1 A:THR203 4.0 51.4 1.0
O A:ARG201 4.1 42.1 1.0
O A:THR203 4.2 37.5 1.0
O2A A:GDP475 4.2 40.4 1.0
O A:HOH503 4.4 77.4 1.0
O3A A:GDP475 4.6 48.6 1.0
C A:THR203 4.6 38.9 1.0
OE1 A:GLN226 4.6 52.1 1.0
NE2 A:GLN226 4.7 53.6 1.0
O1B A:GDP475 4.8 56.0 1.0
NE A:ARG200 4.8 24.5 1.0
N A:PRO202 4.8 33.6 1.0
CB A:PRO202 4.8 31.3 1.0
C A:ARG201 4.8 32.4 1.0
N A:GLU58 4.9 37.8 1.0
PA A:GDP475 4.9 42.7 1.0

Fluorine binding site 3 out of 8 in 1shz

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Fluorine binding site 3 out of 8 in the Crystal Structure of the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera


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 the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:22.8
occ:1.00
 F3 A:ALF378 0.0 22.8 1.0
AL A:ALF378 1.7 21.6 1.0
F2 A:ALF378 2.4 36.9 1.0
F4 A:ALF378 2.4 29.9 1.0
MG A:MG377 2.5 8.2 1.0
O A:HOH543 2.7 50.9 1.0
O3B A:GDP475 2.8 45.3 1.0
O2B A:GDP475 2.9 35.8 1.0
PB A:GDP475 3.2 36.0 1.0
F1 A:ALF378 3.5 26.2 1.0
O A:VAL223 3.5 34.2 1.0
CB A:THR203 3.5 39.6 1.0
CE A:LYS61 3.8 24.4 1.0
CA A:GLY224 3.8 31.0 1.0
O1B A:GDP475 3.8 56.0 1.0
N A:GLY225 4.0 23.8 1.0
OG1 A:THR203 4.0 51.4 1.0
NZ A:LYS61 4.1 26.2 1.0
O A:THR203 4.2 37.5 1.0
N A:THR203 4.3 37.6 1.0
CA A:THR203 4.4 37.7 1.0
CG2 A:THR203 4.4 40.6 1.0
C A:VAL223 4.4 35.7 1.0
C A:GLY224 4.4 29.0 1.0
N A:GLY224 4.6 32.0 1.0
C A:THR203 4.7 38.9 1.0
O3A A:GDP475 4.7 48.6 1.0
CB A:LYS61 5.0 28.6 1.0

Fluorine binding site 4 out of 8 in 1shz

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Fluorine binding site 4 out of 8 in the Crystal Structure of the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera


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 the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F378

b:29.9
occ:1.00
 F4 A:ALF378 0.0 29.9 1.0
AL A:ALF378 1.7 21.6 1.0
F3 A:ALF378 2.4 22.8 1.0
O A:HOH543 2.5 50.9 1.0
F1 A:ALF378 2.5 26.2 1.0
N A:GLY225 2.7 23.8 1.0
NZ A:LYS61 2.9 26.2 1.0
O3B A:GDP475 2.9 45.3 1.0
CA A:GLY225 3.3 28.4 1.0
CA A:GLY57 3.3 38.3 1.0
CE A:LYS61 3.4 24.4 1.0
F2 A:ALF378 3.5 36.9 1.0
O1B A:GDP475 3.5 56.0 1.0
PB A:GDP475 3.6 36.0 1.0
N A:GLU58 3.7 37.8 1.0
C A:GLY224 3.8 29.0 1.0
O A:ALA56 4.0 39.9 1.0
CA A:GLY224 4.0 31.0 1.0
C A:GLY57 4.1 40.8 1.0
N A:GLY57 4.1 40.2 1.0
OE1 A:GLN226 4.2 52.1 1.0
C A:GLY225 4.2 28.0 1.0
O2B A:GDP475 4.2 35.8 1.0
N A:GLN226 4.3 32.2 1.0
C A:ALA56 4.3 39.9 1.0
NE2 A:GLN226 4.4 53.6 1.0
CD A:GLN226 4.5 41.7 1.0
O A:VAL223 4.5 34.2 1.0
MG A:MG377 4.8 8.2 1.0
CD A:LYS61 4.8 22.7 1.0
O A:GLY224 4.9 27.8 1.0
CA A:GLU58 4.9 34.5 1.0

Fluorine binding site 5 out of 8 in 1shz

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Fluorine binding site 5 out of 8 in the Crystal Structure of the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera


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 the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F378

b:32.3
occ:1.00
 F1 D:ALF378 0.0 32.3 1.0
AL D:ALF378 1.7 20.8 1.0
F4 D:ALF378 2.4 34.5 1.0
F2 D:ALF378 2.5 43.3 1.0
O3B D:GDP476 2.5 33.2 1.0
O D:HOH550 2.7 48.6 1.0
NH2 D:ARG200 2.8 32.3 1.0
NE2 D:GLN226 2.8 47.8 1.0
N D:GLU58 2.9 34.8 1.0
NH1 D:ARG200 3.2 35.5 1.0
CA D:GLY57 3.4 32.7 1.0
CZ D:ARG200 3.4 28.0 1.0
F3 D:ALF378 3.4 41.9 1.0
C D:GLY57 3.7 33.8 1.0
CD D:GLN226 3.8 46.0 1.0
CA D:GLU58 3.9 37.4 1.0
OE1 D:GLN226 4.0 63.3 1.0
PB D:GDP476 4.0 28.0 1.0
O1B D:GDP476 4.6 47.1 1.0
O3A D:GDP476 4.7 44.2 1.0
CB D:GLU58 4.7 51.9 1.0
N D:GLY57 4.7 36.9 1.0
NE D:ARG200 4.7 26.8 1.0
N D:GLY225 4.8 27.9 1.0
O2B D:GDP476 4.8 38.3 1.0
O D:GLY57 4.9 39.5 1.0

Fluorine binding site 6 out of 8 in 1shz

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Fluorine binding site 6 out of 8 in the Crystal Structure of the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera


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 the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F378

b:43.3
occ:1.00
 F2 D:ALF378 0.0 43.3 1.0
AL D:ALF378 1.8 20.8 1.0
F3 D:ALF378 2.3 41.9 1.0
F1 D:ALF378 2.5 32.3 1.0
O3B D:GDP476 2.7 33.2 1.0
O D:HOH550 2.8 48.6 1.0
NH2 D:ARG200 2.9 32.3 1.0
N D:THR203 2.9 39.5 1.0
MG D:MG377 3.2 9.6 1.0
CZ D:ARG200 3.4 28.0 1.0
F4 D:ALF378 3.4 34.5 1.0
NH1 D:ARG200 3.4 35.5 1.0
CA D:PRO202 3.6 37.1 1.0
CB D:THR203 3.7 38.0 1.0
C D:PRO202 3.7 38.1 1.0
CA D:THR203 3.8 40.6 1.0
PB D:GDP476 4.0 28.0 1.0
O2B D:GDP476 4.0 38.3 1.0
O D:ARG201 4.1 52.5 1.0
O D:THR203 4.1 37.2 1.0
OG1 D:THR203 4.2 34.5 1.0
NE D:ARG200 4.4 26.8 1.0
NE2 D:GLN226 4.4 47.8 1.0
C D:THR203 4.5 39.6 1.0
O2A D:GDP476 4.5 39.5 1.0
N D:PRO202 4.5 40.6 1.0
CB D:PRO202 4.6 34.7 1.0
OE1 D:GLN226 4.6 63.3 1.0
C D:ARG201 4.7 45.4 1.0
O D:HOH502 4.7 51.9 1.0
O3A D:GDP476 4.9 44.2 1.0
O D:PRO202 4.9 28.6 1.0
CG2 D:THR203 5.0 30.0 1.0
CD D:GLN226 5.0 46.0 1.0

Fluorine binding site 7 out of 8 in 1shz

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Fluorine binding site 7 out of 8 in the Crystal Structure of the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera


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 the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F378

b:41.9
occ:1.00
 F3 D:ALF378 0.0 41.9 1.0
AL D:ALF378 1.7 20.8 1.0
F2 D:ALF378 2.3 43.3 1.0
F4 D:ALF378 2.4 34.5 1.0
MG D:MG377 2.6 9.6 1.0
O D:HOH550 2.6 48.6 1.0
O3B D:GDP476 2.8 33.2 1.0
O D:HOH502 3.0 51.9 1.0
NZ D:LYS61 3.1 41.1 1.0
O2B D:GDP476 3.2 38.3 1.0
CB D:THR203 3.2 38.0 1.0
PB D:GDP476 3.4 28.0 1.0
F1 D:ALF378 3.4 32.3 1.0
N D:GLY225 3.6 27.9 1.0
CA D:GLY224 3.7 27.1 1.0
O D:VAL223 3.8 30.0 1.0
CG2 D:THR203 3.9 30.0 1.0
O D:THR203 4.0 37.2 1.0
OG1 D:THR203 4.0 34.5 1.0
N D:THR203 4.0 39.5 1.0
CA D:THR203 4.1 40.6 1.0
O1B D:GDP476 4.1 47.1 1.0
C D:GLY224 4.1 28.9 1.0
C D:THR203 4.4 39.6 1.0
CE D:LYS61 4.5 24.8 1.0
C D:VAL223 4.6 32.1 1.0
N D:GLY224 4.6 28.4 1.0
CA D:GLY225 4.6 27.4 1.0
OG D:SER62 4.8 27.9 1.0
OE1 D:GLN226 4.9 63.3 1.0
O3A D:GDP476 4.9 44.2 1.0

Fluorine binding site 8 out of 8 in 1shz

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Fluorine binding site 8 out of 8 in the Crystal Structure of the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera


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 the P115RHOGEF Rgrgs Domain in A Complex with Galpha(13):Galpha(I1) Chimera within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F378

b:34.5
occ:1.00
 F4 D:ALF378 0.0 34.5 1.0
AL D:ALF378 1.6 20.8 1.0
F3 D:ALF378 2.4 41.9 1.0
F1 D:ALF378 2.4 32.3 1.0
O3B D:GDP476 2.5 33.2 1.0
O D:HOH550 2.6 48.6 1.0
NZ D:LYS61 2.9 41.1 1.0
N D:GLY225 3.0 27.9 1.0
CA D:GLY57 3.1 32.7 1.0
CA D:GLY225 3.2 27.4 1.0
O1B D:GDP476 3.3 47.1 1.0
PB D:GDP476 3.3 28.0 1.0
F2 D:ALF378 3.4 43.3 1.0
N D:GLU58 3.6 34.8 1.0
CE D:LYS61 3.7 24.8 1.0
C D:GLY57 3.8 33.8 1.0
O D:ALA56 3.9 41.6 1.0
N D:GLY57 3.9 36.9 1.0
O2B D:GDP476 4.0 38.3 1.0
C D:GLY224 4.1 28.9 1.0
C D:ALA56 4.2 35.5 1.0
NE2 D:GLN226 4.2 47.8 1.0
C D:GLY225 4.2 31.2 1.0
OE1 D:GLN226 4.4 63.3 1.0
N D:GLN226 4.4 23.7 1.0
CA D:GLY224 4.6 27.1 1.0
CD D:GLN226 4.6 46.0 1.0
MG D:MG377 4.6 9.6 1.0
O3A D:GDP476 4.6 44.2 1.0
CA D:GLU58 4.7 37.4 1.0
O D:VAL223 4.8 30.0 1.0
N D:SER59 4.9 27.4 1.0
NH1 D:ARG200 5.0 35.5 1.0
O D:GLY57 5.0 39.5 1.0
O D:GLY55 5.0 42.8 1.0

Reference:

Z.Chen, W.D.Singer, P.C.Sternweis, S.R.Sprang. Structure of the P115RHOGEF Rgrgs Domain-GALPHA13/I1 Chimera Complex Suggests Convergent Evolution of A Gtpase Activator. Nat.Struct.Mol.Biol. V. 12 191 2005.
ISSN: ISSN 1545-9993
PubMed: 15665872
DOI: 10.1038/NSMB888
Page generated: Wed Jul 31 12:50:13 2024

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