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Fluorine in PDB 3ab3: Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13

Protein crystallography data

The structure of Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13, PDB code: 3ab3 was solved by M.Kukimoto-Niino, C.Mishima, M.Shirouzu, T.Kozasa, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.88 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.481, 70.640, 88.078, 77.77, 84.45, 80.11
R / Rfree (%) 20.5 / 28

Other elements in 3ab3:

The structure of Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13 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 P115RHOGEF Rgs Domain in Complex with G Alpha 13 (pdb code 3ab3). 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 P115RHOGEF Rgs Domain in Complex with G Alpha 13, PDB code: 3ab3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3ab3

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Fluorine binding site 1 out of 8 in the Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13


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 P115RHOGEF Rgs Domain in Complex with G Alpha 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:45.5
occ:1.00
 F1 A:ALF601 0.0 45.5 1.0
AL A:ALF601 1.8 42.7 1.0
F3 A:ALF601 2.4 41.6 1.0
O1B A:GDP401 2.7 40.3 1.0
F4 A:ALF601 2.7 33.3 1.0
NH2 A:ARG200 2.9 30.5 1.0
N A:GLU58 3.0 25.7 1.0
NE2 A:GLN226 3.0 28.9 1.0
CA A:GLY57 3.5 27.4 1.0
F2 A:ALF601 3.5 51.8 1.0
NH1 A:ARG200 3.5 32.9 1.0
OE1 A:GLN226 3.6 36.9 1.0
CZ A:ARG200 3.6 30.2 1.0
C A:GLY57 3.7 25.8 1.0
CD A:GLN226 3.7 29.8 1.0
CA A:GLU58 3.9 29.4 1.0
PB A:GDP401 4.1 25.1 1.0
CG A:GLU58 4.2 43.3 1.0
CB A:GLU58 4.6 30.1 1.0
N A:GLY225 4.7 21.8 1.0
NZ A:LYS61 4.8 37.5 1.0
CA A:PRO202 4.8 34.4 1.0
N A:THR203 4.8 32.4 1.0
N A:GLY57 4.8 30.2 1.0
O2B A:GDP401 4.8 31.8 1.0
O3A A:GDP401 4.9 24.2 1.0
O A:GLY57 4.9 30.6 1.0
NE A:ARG200 4.9 32.9 1.0
O A:HOH408 4.9 19.6 1.0
O3B A:GDP401 4.9 35.2 1.0

Fluorine binding site 2 out of 8 in 3ab3

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Fluorine binding site 2 out of 8 in the Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13


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 P115RHOGEF Rgs Domain in Complex with G Alpha 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:51.8
occ:1.00
 F2 A:ALF601 0.0 51.8 1.0
AL A:ALF601 1.7 42.7 1.0
F3 A:ALF601 2.5 41.6 1.0
F4 A:ALF601 2.5 33.3 1.0
MG A:MG501 2.6 30.3 1.0
CB A:THR203 3.0 25.8 1.0
O A:HOH409 3.1 48.8 1.0
CA A:GLY224 3.3 27.1 1.0
O A:VAL223 3.3 32.5 1.0
O1B A:GDP401 3.5 40.3 1.0
F1 A:ALF601 3.5 45.5 1.0
N A:THR203 3.6 32.4 1.0
N A:GLY225 3.6 21.8 1.0
OG1 A:THR203 3.6 35.7 1.0
O A:THR203 3.7 31.4 1.0
CA A:THR203 3.8 29.9 1.0
CE A:LYS61 3.9 30.5 1.0
O3B A:GDP401 3.9 35.2 1.0
C A:GLY224 3.9 25.9 1.0
NZ A:LYS61 4.0 37.5 1.0
CG2 A:THR203 4.0 27.8 1.0
PB A:GDP401 4.0 25.1 1.0
C A:VAL223 4.0 36.2 1.0
O A:HOH408 4.1 19.6 1.0
N A:GLY224 4.1 32.9 1.0
C A:THR203 4.1 31.2 1.0
OE1 A:GLN226 4.6 36.9 1.0
O2B A:GDP401 4.7 31.8 1.0
CA A:GLY225 4.8 22.3 1.0
C A:PRO202 4.8 33.0 1.0
OG A:SER62 4.9 4.1 0.5

Fluorine binding site 3 out of 8 in 3ab3

Go back to Fluorine Binding Sites List in 3ab3
Fluorine binding site 3 out of 8 in the Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13


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 P115RHOGEF Rgs Domain in Complex with G Alpha 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:41.6
occ:1.00
 F3 A:ALF601 0.0 41.6 1.0
AL A:ALF601 1.8 42.7 1.0
F1 A:ALF601 2.4 45.5 1.0
F2 A:ALF601 2.5 51.8 1.0
N A:THR203 2.7 32.4 1.0
O1B A:GDP401 2.9 40.3 1.0
O A:HOH408 2.9 19.6 1.0
NH1 A:ARG200 3.1 32.9 1.0
MG A:MG501 3.2 30.3 1.0
CA A:PRO202 3.2 34.4 1.0
NH2 A:ARG200 3.3 30.5 1.0
C A:PRO202 3.4 33.0 1.0
F4 A:ALF601 3.6 33.3 1.0
CZ A:ARG200 3.6 30.2 1.0
CA A:THR203 3.7 29.9 1.0
CB A:THR203 3.8 25.8 1.0
PB A:GDP401 3.9 25.1 1.0
OG1 A:THR203 3.9 35.7 1.0
O3B A:GDP401 4.0 35.2 1.0
O A:ARG201 4.0 35.5 1.0
O A:THR203 4.1 31.4 1.0
CB A:PRO202 4.2 35.4 1.0
N A:PRO202 4.3 33.4 1.0
C A:THR203 4.4 31.2 1.0
O2A A:GDP401 4.5 24.1 1.0
OE1 A:GLN226 4.5 36.9 1.0
C A:ARG201 4.6 32.5 1.0
O A:PRO202 4.6 37.2 1.0
NE2 A:GLN226 4.8 28.9 1.0
O3A A:GDP401 4.8 24.2 1.0
NE A:ARG200 4.9 32.9 1.0
N A:GLU58 4.9 25.7 1.0
O A:HOH409 5.0 48.8 1.0

Fluorine binding site 4 out of 8 in 3ab3

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Fluorine binding site 4 out of 8 in the Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13


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 P115RHOGEF Rgs Domain in Complex with G Alpha 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:33.3
occ:1.00
 F4 A:ALF601 0.0 33.3 1.0
AL A:ALF601 1.8 42.7 1.0
N A:GLY225 2.5 21.8 1.0
F2 A:ALF601 2.5 51.8 1.0
F1 A:ALF601 2.7 45.5 1.0
NZ A:LYS61 2.7 37.5 1.0
CA A:GLY225 3.0 22.3 1.0
O1B A:GDP401 3.2 40.3 1.0
CA A:GLY57 3.3 27.4 1.0
CE A:LYS61 3.4 30.5 1.0
C A:GLY224 3.5 25.9 1.0
F3 A:ALF601 3.6 41.6 1.0
OE1 A:GLN226 3.8 36.9 1.0
N A:GLU58 3.8 25.7 1.0
O A:ALA56 3.8 30.8 1.0
CA A:GLY224 3.9 27.1 1.0
C A:GLY225 3.9 26.7 1.0
N A:GLY57 4.0 30.2 1.0
PB A:GDP401 4.0 25.1 1.0
C A:GLY57 4.1 25.8 1.0
O2B A:GDP401 4.1 31.8 1.0
N A:GLN226 4.1 30.3 1.0
C A:ALA56 4.2 26.8 1.0
NE2 A:GLN226 4.3 28.9 1.0
O A:VAL223 4.4 32.5 1.0
CD A:GLN226 4.4 29.8 1.0
O A:HOH409 4.6 48.8 1.0
O A:GLY224 4.6 22.8 1.0
MG A:MG501 4.6 30.3 1.0
O A:GLY55 4.7 30.3 1.0
O3B A:GDP401 4.8 35.2 1.0
CD A:LYS61 4.9 29.5 1.0
O A:GLY225 4.9 28.3 1.0
N A:GLY224 5.0 32.9 1.0

Fluorine binding site 5 out of 8 in 3ab3

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Fluorine binding site 5 out of 8 in the Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13


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 P115RHOGEF Rgs Domain in Complex with G Alpha 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F602

b:48.6
occ:1.00
 F1 C:ALF602 0.0 48.6 1.0
AL C:ALF602 1.8 47.4 1.0
F3 C:ALF602 2.4 47.7 1.0
F4 C:ALF602 2.6 49.5 1.0
NH2 C:ARG200 2.7 27.5 1.0
O1B C:GDP402 2.7 38.2 1.0
NE2 C:GLN226 2.8 30.6 1.0
N C:GLU58 3.0 32.6 1.0
NH1 C:ARG200 3.2 25.9 1.0
CZ C:ARG200 3.4 34.4 1.0
CA C:GLY57 3.4 29.1 1.0
F2 C:ALF602 3.5 61.2 1.0
OE1 C:GLN226 3.5 37.2 1.0
CD C:GLN226 3.6 36.9 1.0
C C:GLY57 3.7 34.4 1.0
CA C:GLU58 4.0 37.6 1.0
PB C:GDP402 4.1 28.9 1.0
CG C:GLU58 4.2 40.3 1.0
CA C:PRO202 4.6 37.0 1.0
CB C:GLU58 4.6 32.5 1.0
NE C:ARG200 4.7 30.8 1.0
N C:THR203 4.7 37.8 1.0
N C:GLY225 4.8 25.0 1.0
O3B C:GDP402 4.8 37.6 1.0
N C:GLY57 4.8 33.4 1.0
O C:GLY57 4.9 30.4 1.0
CB C:PRO202 4.9 37.4 1.0
O2B C:GDP402 4.9 31.3 1.0
O3A C:GDP402 4.9 35.2 1.0
O C:HOH1 5.0 27.9 1.0

Fluorine binding site 6 out of 8 in 3ab3

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Fluorine binding site 6 out of 8 in the Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13


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 P115RHOGEF Rgs Domain in Complex with G Alpha 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F602

b:61.2
occ:1.00
 F2 C:ALF602 0.0 61.2 1.0
AL C:ALF602 1.7 47.4 1.0
F3 C:ALF602 2.4 47.7 1.0
F4 C:ALF602 2.5 49.5 1.0
MG C:MG502 2.6 34.9 1.0
O C:HOH388 2.9 30.0 1.0
CB C:THR203 3.0 31.4 1.0
CA C:GLY224 3.3 35.7 1.0
O C:VAL223 3.4 41.3 1.0
F1 C:ALF602 3.5 48.6 1.0
N C:THR203 3.5 37.8 1.0
O C:THR203 3.6 44.7 1.0
O1B C:GDP402 3.6 38.2 1.0
CA C:THR203 3.7 40.4 1.0
CG2 C:THR203 3.7 40.6 1.0
O3B C:GDP402 3.7 37.6 1.0
N C:GLY225 3.8 25.0 1.0
OG1 C:THR203 3.9 45.5 1.0
O C:HOH1 3.9 27.9 1.0
C C:THR203 4.0 42.0 1.0
PB C:GDP402 4.0 28.9 1.0
CE C:LYS61 4.0 22.4 1.0
C C:GLY224 4.0 28.4 1.0
C C:VAL223 4.0 39.5 1.0
N C:GLY224 4.0 40.5 1.0
NZ C:LYS61 4.1 28.3 1.0
OE1 C:GLN226 4.6 37.2 1.0
O2B C:GDP402 4.7 31.3 1.0
C C:PRO202 4.7 39.1 1.0
OG C:SER62 4.8 15.6 0.5
NH1 C:ARG200 5.0 25.9 1.0

Fluorine binding site 7 out of 8 in 3ab3

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Fluorine binding site 7 out of 8 in the Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13


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 P115RHOGEF Rgs Domain in Complex with G Alpha 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F602

b:47.7
occ:1.00
 F3 C:ALF602 0.0 47.7 1.0
AL C:ALF602 1.8 47.4 1.0
F1 C:ALF602 2.4 48.6 1.0
F2 C:ALF602 2.4 61.2 1.0
N C:THR203 2.7 37.8 1.0
NH1 C:ARG200 2.9 25.9 1.0
O C:HOH1 3.0 27.9 1.0
CA C:PRO202 3.1 37.0 1.0
O1B C:GDP402 3.1 38.2 1.0
C C:PRO202 3.3 39.1 1.0
MG C:MG502 3.3 34.9 1.0
NH2 C:ARG200 3.4 27.5 1.0
CZ C:ARG200 3.5 34.4 1.0
F4 C:ALF602 3.6 49.5 1.0
CA C:THR203 3.7 40.4 1.0
CB C:THR203 3.7 31.4 1.0
O C:ARG201 3.9 35.4 1.0
O3B C:GDP402 3.9 37.6 1.0
CB C:PRO202 4.0 37.4 1.0
PB C:GDP402 4.0 28.9 1.0
O C:THR203 4.1 44.7 1.0
OG1 C:THR203 4.2 45.5 1.0
N C:PRO202 4.2 34.3 1.0
O2A C:GDP402 4.4 36.6 1.0
C C:THR203 4.4 42.0 1.0
C C:ARG201 4.4 35.8 1.0
O C:PRO202 4.5 33.5 1.0
OE1 C:GLN226 4.6 37.2 1.0
NE C:ARG200 4.7 30.8 1.0
NE2 C:GLN226 4.7 30.6 1.0
O C:HOH388 4.8 30.0 1.0
CG C:PRO202 4.9 35.1 1.0
O3A C:GDP402 4.9 35.2 1.0
N C:GLU58 5.0 32.6 1.0

Fluorine binding site 8 out of 8 in 3ab3

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Fluorine binding site 8 out of 8 in the Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13


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 P115RHOGEF Rgs Domain in Complex with G Alpha 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F602

b:49.5
occ:1.00
 F4 C:ALF602 0.0 49.5 1.0
AL C:ALF602 1.8 47.4 1.0
N C:GLY225 2.5 25.0 1.0
F2 C:ALF602 2.5 61.2 1.0
F1 C:ALF602 2.6 48.6 1.0
NZ C:LYS61 2.9 28.3 1.0
CA C:GLY57 3.0 29.1 1.0
CA C:GLY225 3.1 24.2 1.0
O1B C:GDP402 3.2 38.2 1.0
C C:GLY224 3.5 28.4 1.0
OE1 C:GLN226 3.6 37.2 1.0
F3 C:ALF602 3.6 47.7 1.0
CE C:LYS61 3.6 22.4 1.0
N C:GLU58 3.8 32.6 1.0
CA C:GLY224 3.8 35.7 1.0
N C:GLY57 3.9 33.4 1.0
C C:GLY57 3.9 34.4 1.0
C C:GLY225 3.9 23.2 1.0
O C:ALA56 4.0 35.3 1.0
PB C:GDP402 4.0 28.9 1.0
N C:GLN226 4.0 25.8 1.0
NE2 C:GLN226 4.0 30.6 1.0
O2B C:GDP402 4.0 31.3 1.0
CD C:GLN226 4.1 36.9 1.0
C C:ALA56 4.2 33.9 1.0
O C:VAL223 4.3 41.3 1.0
O C:HOH388 4.4 30.0 1.0
O C:GLY224 4.6 32.6 1.0
O3B C:GDP402 4.6 37.6 1.0
MG C:MG502 4.7 34.9 1.0
O C:GLY55 4.8 37.3 1.0
N C:GLY224 4.9 40.5 1.0
O C:GLY225 5.0 21.1 1.0
O C:THR203 5.0 44.7 1.0

Reference:

N.Hajicek, M.Kukimoto-Niino, C.Mishima-Tsumagari, C.R.Chow, M.Shirouzu, T.Terada, M.Patel, S.Yokoyama, T.Kozasa. Identification of Critical Residues in G(Alpha)13 For Stimulation of P115RHOGEF Activity and the Structure of the G(Alpha)13-P115RHOGEF Regulator of G Protein Signaling Homology (Rh) Domain Complex. J.Biol.Chem. V. 286 20625 2011.
ISSN: ISSN 0021-9258
PubMed: 21507947
DOI: 10.1074/JBC.M110.201392
Page generated: Mon Jul 14 15:10:29 2025

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