Atomistry » Fluorine » PDB 2q9p-2rbe » 2r25
Atomistry »
  Fluorine »
    PDB 2q9p-2rbe »
      2r25 »

Fluorine in PDB 2r25: Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-

Enzymatic activity of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-

All present enzymatic activity of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-:
2.7.13.3;

Protein crystallography data

The structure of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-, PDB code: 2r25 was solved by D.M.Copeland, X.Zhao, A.S.Soares, A.H.West, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.75 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.013, 75.544, 98.392, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24

Other elements in 2r25:

The structure of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3- also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3- (pdb code 2r25). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-, PDB code: 2r25:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 2r25

Go back to Fluorine Binding Sites List in 2r25
Fluorine binding site 1 out of 3 in the Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:26.6
occ:1.00
F1 B:BEF2 0.0 26.6 1.0
BE B:BEF2 1.5 28.5 1.0
MG B:MG1 2.0 25.9 1.0
F3 B:BEF2 2.4 26.0 1.0
F2 B:BEF2 2.5 25.3 1.0
OD1 B:ASP1144 2.6 33.6 1.0
OD2 B:ASP1144 2.9 28.9 1.0
O B:HOH160 2.9 27.9 1.0
O B:GLN1146 3.0 25.0 1.0
O B:HOH159 3.1 26.8 1.0
CG B:ASP1144 3.1 33.2 1.0
CD2 A:HIS64 3.1 23.0 1.0
NE2 A:HIS64 3.2 27.5 1.0
O A:HOH184 3.4 29.0 1.0
N B:GLN1146 3.5 26.9 1.0
CB B:GLN1146 3.7 29.0 1.0
C B:GLN1146 3.8 26.9 1.0
CA B:GLN1146 3.8 26.5 1.0
OD2 B:ASP1095 4.1 28.0 1.0
CG B:GLN1146 4.4 33.7 1.0
NZ B:LYS1195 4.4 23.7 1.0
CG A:HIS64 4.4 27.2 1.0
O B:HOH164 4.6 27.5 1.0
CE1 A:HIS64 4.6 28.3 1.0
C B:VAL1145 4.6 29.6 1.0
N B:VAL1145 4.6 26.0 1.0
CB B:ASP1144 4.6 30.8 1.0
O B:HOH189 4.9 48.9 1.0
OG1 B:THR1173 4.9 33.0 1.0
N B:ALA1174 4.9 27.4 1.0
OE1 B:GLU1094 5.0 26.7 1.0

Fluorine binding site 2 out of 3 in 2r25

Go back to Fluorine Binding Sites List in 2r25
Fluorine binding site 2 out of 3 in the Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:25.3
occ:1.00
F2 B:BEF2 0.0 25.3 1.0
BE B:BEF2 1.5 28.5 1.0
F1 B:BEF2 2.5 26.6 1.0
F3 B:BEF2 2.5 26.0 1.0
OD1 B:ASP1144 2.5 33.6 1.0
OG1 B:THR1173 2.6 33.0 1.0
NE2 A:HIS64 2.7 27.5 1.0
N B:GLN1146 3.1 26.9 1.0
N B:VAL1145 3.2 26.0 1.0
CB B:THR1173 3.5 27.8 1.0
CB B:VAL1145 3.5 30.5 1.0
CD2 A:HIS64 3.6 23.0 1.0
CG B:ASP1144 3.6 33.2 1.0
CA B:VAL1145 3.6 29.3 1.0
CE1 A:HIS64 3.8 28.3 1.0
N B:ALA1174 3.8 27.4 1.0
C B:VAL1145 3.8 29.6 1.0
CA B:THR1173 3.9 30.2 1.0
CD2 B:PHE1175 4.1 28.5 1.0
OD2 B:ASP1144 4.2 28.9 1.0
CA B:GLN1146 4.2 26.5 1.0
CG2 B:VAL1145 4.3 26.0 1.0
MG B:MG1 4.3 25.9 1.0
CB B:GLN1146 4.3 29.0 1.0
CG B:GLN1146 4.3 33.7 1.0
CE2 B:PHE1175 4.3 32.2 1.0
C B:THR1173 4.3 31.1 1.0
C B:ASP1144 4.3 28.7 1.0
O B:GLN1146 4.5 25.0 1.0
CA B:ASP1144 4.7 30.6 1.0
CG1 B:VAL1145 4.7 30.1 1.0
CB B:ASP1144 4.7 30.8 1.0
CG A:HIS64 4.8 27.2 1.0
N B:PHE1175 4.8 30.1 1.0
C B:GLN1146 4.8 26.9 1.0
CG2 B:THR1173 4.9 32.0 1.0
ND1 A:HIS64 4.9 30.6 1.0
O A:HOH184 4.9 29.0 1.0
CA B:ALA1174 4.9 29.5 1.0
CG B:PHE1175 5.0 29.7 1.0

Fluorine binding site 3 out of 3 in 2r25

Go back to Fluorine Binding Sites List in 2r25
Fluorine binding site 3 out of 3 in the Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex of YPD1 and SLN1-R1 with Bound MG2+ and BEF3- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:26.0
occ:1.00
F3 B:BEF2 0.0 26.0 1.0
BE B:BEF2 1.5 28.5 1.0
F1 B:BEF2 2.4 26.6 1.0
F2 B:BEF2 2.5 25.3 1.0
OD1 B:ASP1144 2.6 33.6 1.0
N B:ALA1174 2.7 27.4 1.0
NZ B:LYS1195 2.9 23.7 1.0
O A:HOH184 2.9 29.0 1.0
NE2 A:HIS64 3.3 27.5 1.0
CA B:THR1173 3.5 30.2 1.0
C B:THR1173 3.5 31.1 1.0
OG1 B:THR1173 3.6 33.0 1.0
CG B:ASP1144 3.6 33.2 1.0
CB B:ALA1174 3.6 30.3 1.0
CE B:LYS1195 3.7 28.5 1.0
O B:HOH160 3.7 27.9 1.0
CA B:ALA1174 3.7 29.5 1.0
CD2 A:HIS64 3.8 23.0 1.0
MG B:MG1 4.0 25.9 1.0
CD B:LYS1195 4.0 26.4 1.0
CB B:THR1173 4.1 27.8 1.0
OD2 B:ASP1144 4.1 28.9 1.0
O B:HOH189 4.2 48.9 1.0
CE1 A:HIS64 4.3 28.3 1.0
O B:LEU1172 4.6 31.4 1.0
O B:THR1173 4.7 30.0 1.0
N B:THR1173 4.7 30.1 1.0
OE2 B:GLU1094 4.7 26.9 1.0
C B:ALA1174 4.8 33.1 1.0
CB B:ASP1144 4.8 30.8 1.0
N B:PHE1175 4.9 30.1 1.0
N B:VAL1145 4.9 26.0 1.0
CG A:HIS64 5.0 27.2 1.0

Reference:

X.Zhao, D.M.Copeland, A.S.Soares, A.H.West. Crystal Structure of A Complex Between the Phosphorelay Protein YPD1 and the Response Regulator Domain of SLN1 Bound to A Phosphoryl Analog J.Mol.Biol. V. 375 1141 2008.
ISSN: ISSN 0022-2836
PubMed: 18076904
DOI: 10.1016/J.JMB.2007.11.045
Page generated: Sun Dec 13 11:39:45 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy