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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

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