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Manganese in PDB 1kfl: Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe

Enzymatic activity of Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe

All present enzymatic activity of Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe:
4.1.2.15;

Protein crystallography data

The structure of Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe, PDB code: 1kfl was solved by I.A.Shumilin, C.Zhao, R.Bauerle, R.H.Kretsinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 290.097, 90.097, 155.798, 90.00, 120.77, 90.00
R / Rfree (%) 21.8 / 24.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe (pdb code 1kfl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe, PDB code: 1kfl:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1kfl

Go back to Manganese Binding Sites List in 1kfl
Manganese binding site 1 out of 8 in the Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1351

b:33.3
occ:1.00
 OD2 A:ASP326 2.1 57.5 1.0
OE2 A:GLU302 2.1 17.7 1.0
NE2 A:HIS268 2.4 19.1 1.0
SG A:CYS61 2.7 34.4 1.0
CD A:GLU302 2.9 29.4 1.0
CG A:ASP326 3.0 50.7 1.0
OE1 A:GLU302 3.2 31.0 1.0
CD2 A:HIS268 3.3 24.3 1.0
CE1 A:HIS268 3.4 30.6 1.0
CB A:ASP326 3.5 45.5 1.0
NH2 A:ARG92 3.7 18.0 1.0
CB A:CYS61 3.8 34.1 1.0
NZ A:LYS97 3.9 48.7 1.0
CD A:LYS97 4.1 43.3 1.0
OD1 A:ASP326 4.1 53.6 1.0
O2P A:PEP1352 4.2 46.4 1.0
CA A:CYS61 4.3 37.6 1.0
CG A:GLU302 4.3 14.4 1.0
ND1 A:HIS268 4.4 40.3 1.0
CG A:HIS268 4.4 34.4 1.0
CE A:LYS97 4.5 35.6 1.0
O A:CYS61 4.6 40.3 1.0
CZ A:ARG92 4.6 17.9 1.0
O2 A:PEP1352 4.7 49.1 1.0
CA A:ASP326 4.8 37.5 1.0
C A:CYS61 4.8 43.2 1.0
P A:PEP1352 4.9 47.1 1.0
N A:ASP326 4.9 37.8 1.0
O1P A:PEP1352 4.9 29.7 1.0

Manganese binding site 2 out of 8 in 1kfl

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Manganese binding site 2 out of 8 in the Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2351

b:57.6
occ:1.00
 OE2 B:GLU302 2.1 45.3 1.0
OD2 B:ASP326 2.3 63.9 1.0
NE2 B:HIS268 2.5 63.9 1.0
SG B:CYS61 2.8 52.0 1.0
CD B:GLU302 3.0 43.5 1.0
OE1 B:GLU302 3.2 45.4 1.0
CG B:ASP326 3.3 63.0 1.0
CE1 B:HIS268 3.3 61.8 1.0
NH2 B:ARG92 3.4 49.0 1.0
CD2 B:HIS268 3.5 63.9 1.0
CB B:ASP326 3.7 58.7 1.0
CB B:CYS61 3.8 57.0 1.0
O2P B:PEP2352 4.0 81.0 1.0
NZ B:LYS97 4.1 72.0 1.0
CD B:LYS97 4.2 71.8 1.0
CA B:CYS61 4.2 58.9 1.0
CZ B:ARG92 4.3 51.5 1.0
CG B:GLU302 4.4 28.1 1.0
OD1 B:ASP326 4.4 58.3 1.0
O B:CYS61 4.4 58.3 1.0
ND1 B:HIS268 4.5 69.2 1.0
O2 B:PEP2352 4.5 77.6 1.0
CG B:HIS268 4.6 66.2 1.0
CE B:LYS97 4.6 65.6 1.0
C B:CYS61 4.7 62.1 1.0
P B:PEP2352 4.8 79.0 1.0
O1P B:PEP2352 5.0 67.1 1.0
NE B:ARG92 5.0 50.8 1.0

Manganese binding site 3 out of 8 in 1kfl

Go back to Manganese Binding Sites List in 1kfl
Manganese binding site 3 out of 8 in the Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn3351

b:72.0
occ:1.00
 OD2 C:ASP326 2.1 78.4 1.0
OE2 C:GLU302 2.3 72.3 1.0
NE2 C:HIS268 2.5 71.4 1.0
SG C:CYS61 2.8 71.4 1.0
CG C:ASP326 3.1 69.8 1.0
CD C:GLU302 3.1 68.0 1.0
OE1 C:GLU302 3.2 73.6 1.0
CD2 C:HIS268 3.3 68.1 1.0
CE1 C:HIS268 3.4 65.4 1.0
CB C:ASP326 3.5 72.6 1.0
NH2 C:ARG92 3.8 55.9 1.0
NZ C:LYS97 3.9 0.0 0.0
CB C:CYS61 3.9 65.3 1.0
OD1 C:ASP326 4.1 62.0 1.0
CD C:LYS97 4.1 0.0 0.0
O2P C:PEP3352 4.2 0.1 1.0
ND1 C:HIS268 4.4 71.6 1.0
CE C:LYS97 4.4 0.0 0.0
CG C:HIS268 4.4 68.3 1.0
CA C:CYS61 4.5 63.6 1.0
CG C:GLU302 4.5 60.2 1.0
O2 C:PEP3352 4.6 99.1 1.0
CZ C:ARG92 4.7 63.8 1.0
O C:CYS61 4.8 60.9 1.0
CA C:ASP326 4.8 78.8 1.0
P C:PEP3352 4.9 0.1 1.0
C C:CYS61 4.9 64.3 1.0
N C:ASP326 4.9 82.3 1.0

Manganese binding site 4 out of 8 in 1kfl

Go back to Manganese Binding Sites List in 1kfl
Manganese binding site 4 out of 8 in the Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn4351

b:47.1
occ:1.00
 OD2 D:ASP326 2.1 68.2 1.0
OE2 D:GLU302 2.2 33.1 1.0
NE2 D:HIS268 2.3 58.6 1.0
SG D:CYS61 2.6 48.1 1.0
CD D:GLU302 3.0 44.0 1.0
CG D:ASP326 3.0 63.6 1.0
OE1 D:GLU302 3.1 62.5 1.0
CD2 D:HIS268 3.2 60.4 1.0
CE1 D:HIS268 3.3 50.4 1.0
CB D:ASP326 3.5 62.1 1.0
NH2 D:ARG92 3.7 30.5 1.0
CB D:CYS61 3.8 48.0 1.0
NZ D:LYS97 4.0 72.8 1.0
OD1 D:ASP326 4.1 56.1 1.0
O2P D:PEP4352 4.1 74.3 1.0
CD D:LYS97 4.2 72.0 1.0
CG D:HIS268 4.3 62.9 1.0
ND1 D:HIS268 4.3 57.3 1.0
CG D:GLU302 4.4 37.7 1.0
CA D:CYS61 4.4 51.3 1.0
O2 D:PEP4352 4.5 70.6 1.0
CE D:LYS97 4.5 70.5 1.0
CZ D:ARG92 4.7 43.7 1.0
O D:CYS61 4.7 49.6 1.0
P D:PEP4352 4.8 67.1 1.0
CA D:ASP326 4.8 62.1 1.0
C D:CYS61 4.9 53.7 1.0
O1P D:PEP4352 5.0 56.0 1.0
N D:ASP326 5.0 65.2 1.0

Manganese binding site 5 out of 8 in 1kfl

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Manganese binding site 5 out of 8 in the Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn5351

b:64.6
occ:1.00
 OD2 E:ASP326 2.1 59.4 1.0
OE2 E:GLU302 2.2 58.6 1.0
NE2 E:HIS268 2.4 58.5 1.0
SG E:CYS61 2.8 64.7 1.0
CD E:GLU302 3.0 58.1 1.0
CG E:ASP326 3.1 57.2 1.0
OE1 E:GLU302 3.2 62.4 1.0
CD2 E:HIS268 3.2 64.0 1.0
CE1 E:HIS268 3.3 51.5 1.0
CB E:ASP326 3.5 64.1 1.0
NH2 E:ARG92 3.8 38.6 1.0
CB E:CYS61 3.8 60.8 1.0
NZ E:LYS97 4.0 70.2 1.0
OD1 E:ASP326 4.2 57.9 1.0
O2P E:PEP5352 4.2 75.2 1.0
CD E:LYS97 4.3 60.5 1.0
CA E:CYS61 4.4 61.9 1.0
CG E:HIS268 4.4 61.7 1.0
ND1 E:HIS268 4.4 54.7 1.0
CG E:GLU302 4.4 55.8 1.0
O2 E:PEP5352 4.6 76.5 1.0
CE E:LYS97 4.6 61.3 1.0
CZ E:ARG92 4.7 40.7 1.0
O E:CYS61 4.7 62.3 1.0
CA E:ASP326 4.8 69.3 1.0
C E:CYS61 4.9 65.8 1.0
P E:PEP5352 4.9 76.4 1.0

Manganese binding site 6 out of 8 in 1kfl

Go back to Manganese Binding Sites List in 1kfl
Manganese binding site 6 out of 8 in the Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn6351

b:61.7
occ:1.00
 OD2 F:ASP326 2.0 76.0 1.0
OE2 F:GLU302 2.2 54.3 1.0
NE2 F:HIS268 2.6 54.0 1.0
SG F:CYS61 2.7 49.5 1.0
CG F:ASP326 3.0 71.4 1.0
CD F:GLU302 3.1 54.6 1.0
OE1 F:GLU302 3.2 71.5 1.0
CD2 F:HIS268 3.4 59.4 1.0
CE1 F:HIS268 3.5 60.6 1.0
CB F:ASP326 3.5 66.1 1.0
NH2 F:ARG92 3.6 65.8 1.0
CB F:CYS61 3.8 60.6 1.0
NZ F:LYS97 3.9 58.7 1.0
OD1 F:ASP326 4.0 77.5 1.0
CD F:LYS97 4.1 63.0 1.0
O2P F:PEP6352 4.1 70.6 1.0
CA F:CYS61 4.3 56.2 1.0
CE F:LYS97 4.4 53.7 1.0
CG F:GLU302 4.5 55.1 1.0
ND1 F:HIS268 4.5 60.8 1.0
O F:CYS61 4.5 45.1 1.0
CG F:HIS268 4.5 66.8 1.0
O2 F:PEP6352 4.6 90.3 1.0
CZ F:ARG92 4.6 65.8 1.0
C F:CYS61 4.8 55.1 1.0
CA F:ASP326 4.8 64.2 1.0
P F:PEP6352 4.9 82.0 1.0
N F:ASP326 4.9 64.4 1.0

Manganese binding site 7 out of 8 in 1kfl

Go back to Manganese Binding Sites List in 1kfl
Manganese binding site 7 out of 8 in the Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn7351

b:77.1
occ:1.00
 OD2 G:ASP326 2.1 86.0 1.0
OE2 G:GLU302 2.1 60.8 1.0
NE2 G:HIS268 2.4 86.3 1.0
SG G:CYS61 2.9 66.2 1.0
CD G:GLU302 3.0 59.1 1.0
CG G:ASP326 3.1 78.3 1.0
OE1 G:GLU302 3.2 66.2 1.0
CE1 G:HIS268 3.2 84.8 1.0
CD2 G:HIS268 3.3 79.2 1.0
CB G:ASP326 3.5 76.4 1.0
NH2 G:ARG92 3.8 53.0 1.0
CB G:CYS61 3.8 54.4 1.0
NZ G:LYS97 3.9 83.6 1.0
OD1 G:ASP326 4.1 80.5 1.0
CD G:LYS97 4.2 85.8 1.0
O2P G:PEP7352 4.3 0.1 1.0
ND1 G:HIS268 4.3 78.7 1.0
CG G:HIS268 4.4 75.9 1.0
CG G:GLU302 4.4 54.1 1.0
CA G:CYS61 4.4 55.9 1.0
CE G:LYS97 4.5 89.0 1.0
O2 G:PEP7352 4.5 94.4 1.0
CZ G:ARG92 4.7 57.5 1.0
O G:CYS61 4.8 53.2 1.0
CA G:ASP326 4.9 74.3 1.0
P G:PEP7352 4.9 99.1 1.0
C G:CYS61 4.9 59.3 1.0

Manganese binding site 8 out of 8 in 1kfl

Go back to Manganese Binding Sites List in 1kfl
Manganese binding site 8 out of 8 in the Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Phenylalanine-Regulated 3-Deoxy-D- Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From E.Coli Complexed with MN2+, Pep, and Phe within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn8351

b:69.0
occ:1.00
 OE2 H:GLU302 2.1 68.4 1.0
OD2 H:ASP326 2.2 75.1 1.0
NE2 H:HIS268 2.4 72.2 1.0
SG H:CYS61 2.7 63.6 1.0
CD H:GLU302 3.0 72.3 1.0
CG H:ASP326 3.2 70.0 1.0
OE1 H:GLU302 3.2 75.9 1.0
CE1 H:HIS268 3.3 74.9 1.0
CD2 H:HIS268 3.3 68.3 1.0
CB H:ASP326 3.5 65.9 1.0
NH2 H:ARG92 3.6 62.1 1.0
CB H:CYS61 3.8 52.7 1.0
NZ H:LYS97 4.1 65.2 1.0
CD H:LYS97 4.2 66.9 1.0
O2P H:PEP8352 4.2 92.4 1.0
OD1 H:ASP326 4.3 59.0 1.0
CA H:CYS61 4.3 59.3 1.0
CG H:GLU302 4.4 63.7 1.0
ND1 H:HIS268 4.4 77.7 1.0
CG H:HIS268 4.4 75.8 1.0
CE H:LYS97 4.5 69.2 1.0
CZ H:ARG92 4.6 56.9 1.0
O H:CYS61 4.6 59.3 1.0
O2 H:PEP8352 4.6 96.3 1.0
C H:CYS61 4.8 62.4 1.0
CA H:ASP326 4.8 67.2 1.0
P H:PEP8352 4.9 91.1 1.0
N H:ASP326 5.0 65.2 1.0
O1P H:PEP8352 5.0 84.4 1.0

Reference:

I.A.Shumilin, C.Zhao, R.Bauerle, R.H.Kretsinger. Allosteric Inhibition of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase Alters the Coordination of Both Substrates. J.Mol.Biol. V. 320 1147 2002.
ISSN: ISSN 0022-2836
PubMed: 12126632
DOI: 10.1016/S0022-2836(02)00545-4
Page generated: Sat Oct 5 11:20:16 2024

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