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Manganese in PDB 1n8f: Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep

Enzymatic activity of Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep

All present enzymatic activity of Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep:
4.1.2.15;

Protein crystallography data

The structure of Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep, PDB code: 1n8f was solved by I.A.Shumilin, 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 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 213.224, 53.277, 150.245, 90.00, 116.90, 90.00
R / Rfree (%) 20.9 / 23.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep (pdb code 1n8f). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep, PDB code: 1n8f:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1n8f

Go back to Manganese Binding Sites List in 1n8f
Manganese binding site 1 out of 4 in the Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep


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 E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn351

b:28.9
occ:1.00
 OE2 A:GLU302 2.1 29.5 1.0
OD2 A:ASP326 2.1 28.5 1.0
O A:HOH5416 2.4 35.6 1.0
NE2 A:HIS268 2.4 23.4 1.0
SG A:CYS61 2.6 27.3 1.0
CD A:GLU302 3.0 26.3 1.0
CG A:ASP326 3.1 29.6 1.0
O1 A:PEP1396 3.1 32.7 1.0
OE1 A:GLU302 3.2 27.9 1.0
CD2 A:HIS268 3.3 25.5 1.0
CE1 A:HIS268 3.4 23.6 1.0
CB A:ASP326 3.5 29.0 1.0
CB A:CYS61 3.6 27.3 1.0
C1 A:PEP1396 3.9 28.8 1.0
NZ A:LYS97 4.0 24.5 1.0
OD1 A:ASP326 4.2 28.8 1.0
NH2 A:ARG92 4.2 26.1 1.0
CA A:CYS61 4.3 26.4 1.0
O A:HOH5427 4.3 27.2 1.0
O A:HOH5552 4.3 43.3 1.0
CG A:GLU302 4.4 27.1 1.0
CG A:HIS268 4.4 26.0 1.0
ND1 A:HIS268 4.4 25.4 1.0
C2 A:PEP1396 4.4 27.9 1.0
O A:HOH5566 4.5 43.7 1.0
O A:HOH5525 4.5 46.1 1.0
O2' A:PEP1396 4.6 26.8 1.0
O A:CYS61 4.8 25.2 1.0
CA A:ASP326 4.8 30.3 1.0
CE A:LYS97 4.8 25.3 1.0
N A:ASP326 4.9 30.5 1.0
C A:CYS61 4.9 27.3 1.0
C3 A:PEP1396 4.9 29.8 1.0

Manganese binding site 2 out of 4 in 1n8f

Go back to Manganese Binding Sites List in 1n8f
Manganese binding site 2 out of 4 in the Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep


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 E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn351

b:19.5
occ:1.00
 OE2 B:GLU302 2.1 17.8 1.0
O B:HOH2376 2.1 20.5 1.0
OD2 B:ASP326 2.1 16.9 1.0
NE2 B:HIS268 2.3 12.9 1.0
SG B:CYS61 2.6 15.7 1.0
CD B:GLU302 2.9 11.7 1.0
OE1 B:GLU302 3.1 15.1 1.0
CG B:ASP326 3.1 21.6 1.0
CD2 B:HIS268 3.2 16.9 1.0
O1 B:PEP1397 3.2 21.1 1.0
CE1 B:HIS268 3.2 19.2 1.0
CB B:ASP326 3.5 17.0 1.0
CB B:CYS61 3.6 16.8 1.0
C1 B:PEP1397 3.9 23.3 1.0
NZ B:LYS97 4.0 19.8 1.0
O B:HOH2548 4.1 31.5 1.0
OD1 B:ASP326 4.2 19.3 1.0
CA B:CYS61 4.2 15.3 1.0
O B:HOH2505 4.3 31.6 1.0
O B:HOH2386 4.3 18.7 1.0
ND1 B:HIS268 4.3 15.5 1.0
CG B:GLU302 4.3 15.7 1.0
CG B:HIS268 4.4 17.0 1.0
NH2 B:ARG92 4.4 15.0 1.0
C2 B:PEP1397 4.4 21.2 1.0
O B:HOH2561 4.5 39.2 1.0
O2' B:PEP1397 4.6 18.9 1.0
CE B:LYS97 4.8 18.4 1.0
CA B:ASP326 4.8 16.8 1.0
C3 B:PEP1397 4.8 19.1 1.0
O B:CYS61 4.8 14.2 1.0
N B:ASP326 4.9 17.4 1.0
C B:CYS61 4.9 17.3 1.0

Manganese binding site 3 out of 4 in 1n8f

Go back to Manganese Binding Sites List in 1n8f
Manganese binding site 3 out of 4 in the Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep


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 E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn351

b:31.5
occ:1.00
 OD2 C:ASP326 2.0 25.7 1.0
OE2 C:GLU302 2.1 31.0 1.0
O C:HOH3451 2.4 39.1 1.0
NE2 C:HIS268 2.4 31.0 1.0
SG C:CYS61 2.6 31.3 1.0
O1 C:PEP1398 2.9 37.2 1.0
CD C:GLU302 2.9 30.4 1.0
CG C:ASP326 3.1 31.3 1.0
OE1 C:GLU302 3.1 30.3 1.0
CE1 C:HIS268 3.3 30.7 1.0
CD2 C:HIS268 3.3 30.6 1.0
CB C:ASP326 3.4 31.3 1.0
CB C:CYS61 3.7 32.0 1.0
C1 C:PEP1398 3.7 36.8 1.0
NZ C:LYS97 4.0 29.1 1.0
OD1 C:ASP326 4.2 27.9 1.0
C2 C:PEP1398 4.2 36.2 1.0
NH2 C:ARG92 4.2 31.7 1.0
CA C:CYS61 4.3 31.2 1.0
CG C:GLU302 4.3 31.6 1.0
O C:HOH3462 4.4 32.7 1.0
ND1 C:HIS268 4.4 29.6 1.0
CG C:HIS268 4.4 30.8 1.0
O2' C:PEP1398 4.4 36.5 1.0
C3 C:PEP1398 4.7 35.0 1.0
CE C:LYS97 4.7 27.8 1.0
O2 C:PEP1398 4.7 36.0 1.0
O C:CYS61 4.7 30.3 1.0
CA C:ASP326 4.8 33.0 1.0
N C:ASP326 4.9 32.4 1.0
C C:CYS61 4.9 32.1 1.0

Manganese binding site 4 out of 4 in 1n8f

Go back to Manganese Binding Sites List in 1n8f
Manganese binding site 4 out of 4 in the Crystal Structure of E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep


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 E24Q Mutant of Phenylalanine-Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Escherichia Coli in Complex with MN2+ and Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn351

b:23.5
occ:1.00
 OE2 D:GLU302 2.1 23.2 1.0
OD2 D:ASP326 2.1 25.4 1.0
O D:HOH4414 2.2 29.4 1.0
NE2 D:HIS268 2.3 19.7 1.0
SG D:CYS61 2.6 20.2 1.0
CD D:GLU302 3.0 20.2 1.0
CG D:ASP326 3.1 21.6 1.0
OE1 D:GLU302 3.1 23.7 1.0
CE1 D:HIS268 3.2 24.3 1.0
O1 D:PEP1399 3.2 29.3 1.0
CD2 D:HIS268 3.3 23.3 1.0
CB D:ASP326 3.5 21.7 1.0
CB D:CYS61 3.6 20.9 1.0
C1 D:PEP1399 3.9 30.3 1.0
NZ D:LYS97 4.0 20.2 1.0
O D:HOH4542 4.1 47.3 1.0
O D:HOH4368 4.2 32.1 1.0
OD1 D:ASP326 4.2 25.2 1.0
CA D:CYS61 4.2 20.7 1.0
NH2 D:ARG92 4.3 20.7 1.0
O D:HOH4426 4.3 28.2 1.0
ND1 D:HIS268 4.3 22.2 1.0
CG D:GLU302 4.4 23.8 1.0
C2 D:PEP1399 4.4 30.6 1.0
CG D:HIS268 4.4 23.1 1.0
O D:HOH4550 4.5 44.9 1.0
O2' D:PEP1399 4.7 30.5 1.0
CA D:ASP326 4.8 21.2 1.0
C3 D:PEP1399 4.8 27.1 1.0
N D:ASP326 4.8 20.3 1.0
CE D:LYS97 4.8 21.0 1.0
O D:CYS61 4.9 18.5 1.0
C D:CYS61 4.9 21.6 1.0
O D:HOH4451 5.0 38.0 1.0
O2 D:PEP1399 5.0 28.4 1.0

Reference:

I.A.Shumilin, R.Bauerle, R.H.Kretsinger. The High-Resolution Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase Reveals A Twist in the Plane of Bound Phosphoenolpyruvate Biochemistry V. 42 3766 2003.
ISSN: ISSN 0006-2960
PubMed: 12667068
DOI: 10.1021/BI027257P
Page generated: Tue Dec 15 03:53:13 2020

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