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Magnesium in PDB 4xgx: Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited

Enzymatic activity of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited

All present enzymatic activity of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited:
2.7.1.180;

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited, PDB code: 4xgx was solved by D.R.Tomchick, C.A.Brautigam, R.K.Deka, M.V.Norgard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.26 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.583, 56.981, 224.766, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited (pdb code 4xgx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited, PDB code: 4xgx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4xgx

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Magnesium binding site 1 out of 4 in the Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:21.1
occ:1.00
 HG1 A:THR284 1.9 30.6 1.0
O A:HOH617 2.3 38.3 1.0
O A:HOH589 2.4 44.0 1.0
OD1 A:ASP280 2.4 25.1 1.0
OG1 A:THR284 2.5 25.5 1.0
O A:ASP280 2.5 16.8 1.0
O A:THR166 2.5 18.2 1.0
HB A:THR166 3.1 27.8 1.0
CG A:ASP280 3.2 19.9 1.0
HA A:ASP280 3.3 15.3 1.0
C A:ASP280 3.3 14.2 1.0
C A:THR166 3.6 16.3 1.0
H A:THR284 3.6 18.5 1.0
HB3 A:ASP283 3.6 24.1 1.0
CA A:ASP280 3.7 12.8 1.0
HA A:THR166 3.7 19.4 1.0
CB A:THR284 3.7 19.0 1.0
HB A:THR284 3.8 22.8 1.0
CB A:ASP280 3.9 15.8 1.0
CB A:THR166 3.9 23.2 1.0
CA A:THR166 4.0 16.1 1.0
HB3 A:ASP280 4.0 18.9 1.0
N A:THR284 4.1 15.4 1.0
OD2 A:ASP280 4.1 18.3 1.0
O A:HOH625 4.4 41.1 1.0
CA A:THR284 4.4 16.2 1.0
O A:HOH614 4.4 37.3 1.0
HA A:ALA281 4.4 12.0 1.0
N A:ALA281 4.4 15.7 1.0
HA A:THR284 4.5 19.5 1.0
HG22 A:THR166 4.5 30.2 1.0
OG A:SER234 4.5 21.8 1.0
O A:HOH574 4.5 15.8 1.0
HA A:VAL167 4.5 11.8 1.0
CB A:ASP283 4.6 20.1 1.0
O A:HOH579 4.6 37.8 1.0
HG A:SER234 4.6 26.1 1.0
CG2 A:THR166 4.7 25.2 1.0
N A:VAL167 4.8 12.7 1.0
HB2 A:ASP280 4.8 18.9 1.0
O2A A:ADP403 4.8 46.7 1.0
HG21 A:THR284 4.8 23.2 1.0
CG2 A:THR284 4.8 19.4 1.0
OG1 A:THR166 4.8 23.4 1.0
CA A:ALA281 4.9 10.0 1.0
OD2 A:ASP283 4.9 30.8 1.0
C A:ASP283 5.0 19.8 1.0
O1A A:ADP403 5.0 64.8 1.0

Magnesium binding site 2 out of 4 in 4xgx

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Magnesium binding site 2 out of 4 in the Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:40.9
occ:1.00
 O3B A:ADP403 2.2 44.5 1.0
O1A A:ADP403 2.5 64.8 1.0
OE2 A:GLU169 2.6 28.3 1.0
HB2 A:TYR239 2.7 32.7 1.0
H A:TYR239 2.8 27.0 1.0
HD2 A:TYR239 3.0 29.1 1.0
HG3 A:ARG240 3.2 36.5 1.0
PB A:ADP403 3.2 48.9 1.0
O3A A:ADP403 3.2 70.5 1.0
PA A:ADP403 3.4 64.3 1.0
CD A:GLU169 3.4 24.4 1.0
HH11 A:ARG240 3.4 40.4 1.0
N A:TYR239 3.5 22.5 1.0
OE1 A:GLU169 3.6 21.7 1.0
HH12 A:ARG240 3.6 40.4 1.0
NH1 A:ARG240 3.6 33.6 1.0
CB A:TYR239 3.6 27.2 1.0
O1B A:ADP403 3.7 49.7 1.0
H A:ARG240 3.7 30.3 1.0
CD2 A:TYR239 3.8 24.3 1.0
HA A:SER238 3.9 33.9 1.0
O A:HOH625 4.0 41.1 1.0
CA A:TYR239 4.0 27.0 1.0
O A:GLY237 4.1 23.1 1.0
CG A:ARG240 4.1 30.4 1.0
N A:ARG240 4.2 25.2 1.0
CG A:TYR239 4.2 24.9 1.0
O A:HOH589 4.2 44.0 1.0
HB3 A:TYR239 4.3 32.7 1.0
CZ A:ARG240 4.4 32.4 1.0
O2A A:ADP403 4.4 46.7 1.0
C A:TYR239 4.5 31.6 1.0
C A:SER238 4.5 27.5 1.0
HG2 A:ARG240 4.5 36.5 1.0
O2B A:ADP403 4.6 50.7 1.0
O A:HOH512 4.6 50.0 1.0
O5' A:ADP403 4.6 43.4 1.0
CA A:SER238 4.7 28.2 1.0
HB2 A:ARG240 4.7 40.4 1.0
H A:GLY194 4.8 17.2 1.0
CG A:GLU169 4.8 17.7 1.0
HD2 A:ARG240 4.8 36.6 1.0
O A:HOH574 4.8 15.8 1.0
HG3 A:GLU169 4.8 21.2 1.0
CD A:ARG240 4.9 30.5 1.0
CB A:ARG240 4.9 33.7 1.0
NE A:ARG240 4.9 35.3 1.0
HA A:TYR239 4.9 32.4 1.0
CE2 A:TYR239 5.0 25.5 1.0

Magnesium binding site 3 out of 4 in 4xgx

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Magnesium binding site 3 out of 4 in the Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:22.5
occ:1.00
 HG1 B:THR166 2.4 35.8 1.0
O B:HOH647 2.4 33.1 1.0
OG1 B:THR284 2.5 19.1 1.0
O B:THR166 2.5 13.2 1.0
O B:ASP280 2.6 10.7 1.0
HG1 B:THR284 2.8 22.9 1.0
OG1 B:THR166 3.2 29.8 1.0
HA B:ASP280 3.2 10.2 1.0
C B:ASP280 3.3 11.5 1.0
OD1 B:ASP280 3.4 37.1 1.0
HB3 B:ASP283 3.5 18.7 1.0
CG B:ASP280 3.5 21.2 1.0
H B:THR284 3.5 16.5 1.0
HB3 B:ASP280 3.5 13.1 1.0
CA B:ASP280 3.6 8.5 1.0
C B:THR166 3.6 10.8 1.0
CB B:ASP280 3.7 10.9 1.0
CB B:THR284 3.8 17.3 1.0
HG23 B:THR166 3.8 14.1 1.0
HB B:THR284 3.9 20.8 1.0
HA B:THR166 3.9 12.3 1.0
N B:THR284 4.0 13.8 1.0
CB B:THR166 4.1 16.5 1.0
OD2 B:ASP280 4.1 17.3 1.0
CA B:THR166 4.1 10.2 1.0
O2 B:NO3405 4.1 41.5 1.0
CA B:THR284 4.4 14.1 1.0
O B:HOH547 4.4 39.9 1.0
CG2 B:THR166 4.4 11.7 1.0
CB B:ASP283 4.5 15.6 1.0
N B:ALA281 4.5 13.8 1.0
HA B:VAL167 4.5 9.2 1.0
HA B:THR284 4.5 16.9 1.0
OG B:SER234 4.5 21.9 1.0
O3 B:NO3405 4.5 39.9 1.0
HA B:ALA281 4.6 14.7 1.0
N B:NO3405 4.6 48.4 1.0
HG B:SER234 4.6 26.3 1.0
HB2 B:ASP280 4.7 13.1 1.0
OD2 B:ASP283 4.7 24.4 1.0
O B:HOH586 4.7 13.2 1.0
HG21 B:THR166 4.8 14.1 1.0
N B:VAL167 4.8 9.8 1.0
O B:HOH518 4.8 23.2 1.0
O1A B:ADP403 4.8 56.9 1.0
HB2 B:ASP283 4.9 18.7 1.0
CG2 B:THR284 4.9 17.8 1.0
HG21 B:THR284 4.9 21.4 1.0
HB B:THR166 4.9 19.8 1.0
C B:ASP283 4.9 18.5 1.0
HG12 B:VAL167 5.0 14.0 1.0

Magnesium binding site 4 out of 4 in 4xgx

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Magnesium binding site 4 out of 4 in the Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, Y60N Mutant, Adp-Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:40.0
occ:1.00
 O2A B:ADP403 2.2 74.9 1.0
HB2 B:TYR239 2.5 27.6 1.0
O3B B:ADP403 2.5 57.0 1.0
OE2 B:GLU169 2.6 21.5 1.0
HD2 B:TYR239 2.7 26.6 1.0
H B:TYR239 2.8 20.1 1.0
O3A B:ADP403 3.1 0.9 1.0
PA B:ADP403 3.1 77.3 1.0
HG3 B:ARG240 3.1 37.5 1.0
PB B:ADP403 3.3 59.6 1.0
CD B:GLU169 3.3 18.2 1.0
HE B:ARG240 3.4 43.7 1.0
OE1 B:GLU169 3.4 13.0 1.0
CB B:TYR239 3.4 23.0 1.0
N B:TYR239 3.5 16.7 1.0
CD2 B:TYR239 3.6 22.1 1.0
O2B B:ADP403 3.7 58.5 1.0
H B:ARG240 3.8 26.8 1.0
HA B:SER238 3.9 18.6 1.0
CG B:TYR239 4.0 18.3 1.0
CA B:TYR239 4.0 23.4 1.0
O1A B:ADP403 4.0 56.9 1.0
O B:GLY237 4.0 16.3 1.0
CG B:ARG240 4.1 31.2 1.0
HB3 B:TYR239 4.1 27.6 1.0
O B:HOH547 4.2 39.9 1.0
NE B:ARG240 4.2 36.4 1.0
N B:ARG240 4.2 22.3 1.0
O5' B:ADP403 4.4 58.9 1.0
C B:SER238 4.5 19.8 1.0
HG2 B:ARG240 4.5 37.5 1.0
C B:TYR239 4.5 23.8 1.0
CA B:SER238 4.6 15.5 1.0
CD B:ARG240 4.6 34.1 1.0
HH21 B:ARG240 4.7 22.5 1.0
H B:GLY194 4.7 14.2 1.0
CG B:GLU169 4.7 12.9 1.0
O1B B:ADP403 4.7 50.0 1.0
CE2 B:TYR239 4.7 13.5 1.0
HD2 B:ARG240 4.7 40.9 1.0
HG3 B:GLU169 4.8 15.5 1.0
HA B:TYR239 4.8 28.1 1.0
O B:HOH586 4.8 13.2 1.0
HE2 B:TYR239 4.9 16.2 1.0
HB2 B:ARG240 4.9 36.1 1.0

Reference:

R.K.Deka, C.A.Brautigam, W.Z.Liu, D.R.Tomchick, M.V.Norgard. Molecular Insights Into the Enzymatic Diversity of Flavin-Trafficking Protein (Ftp; Formerly Apbe) in Flavoprotein Biogenesis in the Bacterial Periplasm. Microbiologyopen V. 5 21 2016.
ISSN: ESSN 2045-8827
PubMed: 26626129
DOI: 10.1002/MBO3.306
Page generated: Mon Dec 14 19:46:39 2020

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