Atomistry » Fluorine » PDB 2z78-3az8 » 3ab3
Atomistry »
  Fluorine »
    PDB 2z78-3az8 »
      3ab3 »

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

Go back to Fluorine Binding Sites List in 3ab3
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

Go back to Fluorine Binding Sites List in 3ab3
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

Go back to Fluorine Binding Sites List in 3ab3
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

Go back to Fluorine Binding Sites List in 3ab3
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

Go back to Fluorine Binding Sites List in 3ab3
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

Go back to Fluorine Binding Sites List in 3ab3
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

Go back to Fluorine Binding Sites List in 3ab3
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: Wed Jul 31 17:04:51 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy