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Manganese in PDB 1gg1: Crystal Structure Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate

Enzymatic activity of Crystal Structure Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate

All present enzymatic activity of Crystal Structure Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate:
4.1.2.15;

Protein crystallography data

The structure of Crystal Structure Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate, PDB code: 1gg1 was solved by T.Wagner, 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 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 210.357, 53.188, 149.392, 90.00, 116.09, 90.00
R / Rfree (%) 20.9 / 23.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate (pdb code 1gg1). 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 Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate, PDB code: 1gg1:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1gg1

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Manganese binding site 1 out of 4 in the Crystal Structure Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn371

b:41.0
occ:1.00
 OE1 A:GLU302 2.2 35.1 1.0
OD2 A:ASP326 2.2 38.9 1.0
NE2 A:HIS268 2.4 33.4 1.0
O2 A:PGA372 2.4 38.5 1.0
SG A:CYS61 2.8 36.1 1.0
CD A:GLU302 3.2 34.0 1.0
CD2 A:HIS268 3.2 33.3 1.0
CG A:ASP326 3.3 41.9 1.0
CE1 A:HIS268 3.4 34.2 1.0
C1 A:PGA372 3.4 40.7 1.0
OE2 A:GLU302 3.5 35.9 1.0
NZ A:LYS97 3.6 37.1 1.0
CB A:ASP326 3.7 40.6 1.0
CB A:CYS61 3.8 35.0 1.0
C2 A:PGA372 3.9 42.2 1.0
NH2 A:ARG92 4.2 35.2 1.0
O1 A:PGA372 4.3 37.6 1.0
O A:HOH1435 4.3 36.8 1.0
OD1 A:ASP326 4.4 41.0 1.0
CA A:CYS61 4.4 36.5 1.0
CG A:HIS268 4.4 36.3 1.0
ND1 A:HIS268 4.4 34.4 1.0
CG A:GLU302 4.5 35.0 1.0
O A:HOH1460 4.5 49.2 1.0
O A:CYS61 4.9 36.7 1.0
CE A:LYS97 4.9 39.3 1.0
O1P A:PGA372 5.0 44.4 1.0

Manganese binding site 2 out of 4 in 1gg1

Go back to Manganese Binding Sites List in 1gg1
Manganese binding site 2 out of 4 in the Crystal Structure Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn371

b:17.4
occ:1.00
 OE2 B:GLU302 2.0 16.7 1.0
OD2 B:ASP326 2.1 19.7 1.0
O B:HOH2375 2.3 24.2 1.0
NE2 B:HIS268 2.4 13.9 1.0
O2 B:PGA372 2.5 23.4 1.0
SG B:CYS61 2.7 12.2 1.0
CD B:GLU302 3.0 11.7 1.0
CG B:ASP326 3.1 19.4 1.0
CE1 B:HIS268 3.3 20.6 1.0
C1 B:PGA372 3.3 27.9 1.0
CD2 B:HIS268 3.4 12.8 1.0
OE1 B:GLU302 3.5 13.9 1.0
CB B:ASP326 3.6 16.3 1.0
CB B:CYS61 3.7 15.6 1.0
C2 B:PGA372 3.8 25.3 1.0
NZ B:LYS97 3.9 15.2 1.0
OD1 B:ASP326 4.2 20.2 1.0
NH2 B:ARG92 4.2 11.1 1.0
O B:HOH2448 4.2 23.2 1.0
O1 B:PGA372 4.3 24.9 1.0
CG B:GLU302 4.3 15.8 1.0
CA B:CYS61 4.3 15.1 1.0
ND1 B:HIS268 4.4 12.8 1.0
CG B:HIS268 4.5 18.9 1.0
O B:HOH2384 4.6 18.1 1.0
O B:HOH2571 4.7 25.7 1.0
O B:HOH2553 4.7 25.6 1.0
CE B:LYS97 4.7 18.6 1.0
O B:CYS61 4.8 17.1 1.0
NZ B:LYS273 4.9 35.4 1.0
CA B:ASP326 4.9 13.8 1.0
N B:ASP326 4.9 15.4 1.0
O1P B:PGA372 4.9 26.1 1.0
C B:CYS61 4.9 17.9 1.0
CZ B:ARG92 5.0 16.3 1.0

Manganese binding site 3 out of 4 in 1gg1

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Manganese binding site 3 out of 4 in the Crystal Structure Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn371

b:36.8
occ:1.00
 OD2 C:ASP326 1.9 36.5 1.0
OE2 C:GLU302 2.0 36.1 1.0
O2 C:PGA372 2.3 44.3 1.0
O C:HOH3375 2.5 35.9 1.0
NE2 C:HIS268 2.5 32.9 1.0
SG C:CYS61 2.8 35.1 1.0
CG C:ASP326 3.0 38.9 1.0
CD C:GLU302 3.0 37.5 1.0
OE1 C:GLU302 3.2 37.0 1.0
CD2 C:HIS268 3.2 34.4 1.0
C1 C:PGA372 3.3 44.7 1.0
CB C:ASP326 3.5 40.0 1.0
CE1 C:HIS268 3.6 32.7 1.0
CB C:CYS61 3.7 38.2 1.0
C2 C:PGA372 3.8 44.5 1.0
NZ C:LYS97 3.8 32.1 1.0
OD1 C:ASP326 4.0 37.7 1.0
O1 C:PGA372 4.1 43.6 1.0
O C:HOH3397 4.3 37.2 1.0
CA C:CYS61 4.3 38.2 1.0
CG C:GLU302 4.3 37.6 1.0
NH2 C:ARG92 4.4 30.0 1.0
CG C:HIS268 4.5 35.1 1.0
O C:HOH3376 4.6 38.6 1.0
O C:HOH3442 4.6 40.9 1.0
ND1 C:HIS268 4.6 34.3 1.0
CE C:LYS97 4.7 35.2 1.0
CA C:ASP326 4.8 41.6 1.0
O1P C:PGA372 4.9 46.1 1.0

Manganese binding site 4 out of 4 in 1gg1

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Manganese binding site 4 out of 4 in the Crystal Structure Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure Analysis of Dahp Synthase in Complex with MN2+ and 2-Phosphoglycolate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn371

b:24.7
occ:1.00
 OD2 D:ASP326 2.1 26.2 1.0
OE1 D:GLU302 2.1 24.5 1.0
O D:HOH4375 2.2 28.7 1.0
NE2 D:HIS268 2.3 26.7 1.0
O2 D:PGA372 2.5 33.9 1.0
SG D:CYS61 2.6 24.2 1.0
CD D:GLU302 3.0 22.3 1.0
CG D:ASP326 3.2 25.2 1.0
CD2 D:HIS268 3.2 25.4 1.0
OE2 D:GLU302 3.3 25.5 1.0
CE1 D:HIS268 3.4 26.2 1.0
C1 D:PGA372 3.4 34.8 1.0
CB D:ASP326 3.6 23.7 1.0
CB D:CYS61 3.7 21.1 1.0
NZ D:LYS97 3.9 28.2 1.0
C2 D:PGA372 4.0 34.6 1.0
O D:HOH4430 4.1 32.8 1.0
O1 D:PGA372 4.2 35.3 1.0
OD1 D:ASP326 4.2 25.6 1.0
NH2 D:ARG92 4.3 24.5 1.0
CA D:CYS61 4.3 20.7 1.0
CG D:GLU302 4.4 22.7 1.0
O D:HOH4394 4.4 22.0 1.0
CG D:HIS268 4.4 26.4 1.0
ND1 D:HIS268 4.4 25.7 1.0
O D:HOH4534 4.5 32.0 1.0
O D:HOH4535 4.6 37.1 1.0
CE D:LYS97 4.7 25.7 1.0
O D:CYS61 4.8 22.0 1.0
NZ D:LYS273 4.9 50.0 1.0
CA D:ASP326 4.9 22.2 1.0
C D:CYS61 5.0 22.0 1.0
N D:ASP326 5.0 22.4 1.0

Reference:

T.Wagner, I.A.Shumilin, R.Bauerle, R.H.Kretsinger. Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Escherichia Coli: Comparison of the Mn(2+)*2-Phosphoglycolate and the Pb(2+)*2-Phosphoenolpyruvate Complexes and Implications For Catalysis. J.Mol.Biol. V. 301 389 2000.
ISSN: ISSN 0022-2836
PubMed: 10926516
DOI: 10.1006/JMBI.2000.3957
Page generated: Sat Oct 5 10:32:18 2024

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