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Manganese in PDB 5hud: Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog

Enzymatic activity of Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog

All present enzymatic activity of Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog:
5.4.99.5;

Protein crystallography data

The structure of Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog, PDB code: 5hud was solved by D.Burschowsky, J.B.Heim, H.V.Thorbjoernsrud, U.Krengel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 117.622, 110.481, 134.652, 90.00, 101.41, 90.00
R / Rfree (%) 25 / 29.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog (pdb code 5hud). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog, PDB code: 5hud:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5hud

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Manganese binding site 1 out of 4 in the Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:40.1
occ:1.00
 OD2 A:ASP451 2.2 40.3 1.0
OE1 A:GLU421 2.3 36.0 1.0
NE2 A:HIS379 2.4 36.5 1.0
SG A:CYS97 2.5 31.5 1.0
O A:HOH704 2.6 33.8 1.0
OE2 A:GLU421 2.7 39.0 1.0
CD A:GLU421 2.8 36.0 1.0
CG A:ASP451 3.2 36.8 1.0
CE1 A:HIS379 3.3 35.9 1.0
CD2 A:HIS379 3.3 35.3 1.0
CB A:ASP451 3.5 35.2 1.0
CB A:CYS97 3.5 29.4 1.0
CA A:CYS97 4.2 27.6 1.0
NH2 A:ARG392 4.3 34.1 1.0
OD1 A:ASP451 4.3 38.6 1.0
CG A:GLU421 4.3 34.7 1.0
O A:HOH671 4.3 27.9 1.0
NH2 A:ARG136 4.4 31.7 1.0
ND1 A:HIS379 4.4 35.1 1.0
CG A:HIS379 4.5 34.3 1.0
O A:HOH716 4.7 36.3 1.0
CA A:ASP451 4.7 35.0 1.0
N A:ASP451 4.7 35.1 1.0
O A:CYS97 4.8 25.5 1.0
C A:CYS97 4.8 25.9 1.0
CZ A:ARG136 4.9 30.0 1.0
NH1 A:ARG136 5.0 29.7 1.0
SG A:CYS450 5.0 30.3 0.7
NH1 A:ARG392 5.0 33.6 1.0

Manganese binding site 2 out of 4 in 5hud

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Manganese binding site 2 out of 4 in the Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn513

b:40.0
occ:1.00
 OE1 B:GLU421 2.2 39.4 1.0
NE2 B:HIS379 2.3 32.0 1.0
OD2 B:ASP451 2.4 37.8 1.0
SG B:CYS97 2.5 33.0 1.0
OE2 B:GLU421 2.8 39.3 1.0
CD B:GLU421 2.8 36.4 1.0
CD2 B:HIS379 3.2 33.1 1.0
CG B:ASP451 3.3 41.9 1.0
CE1 B:HIS379 3.3 32.3 1.0
CB B:CYS97 3.4 32.9 1.0
CB B:ASP451 3.5 40.5 1.0
CA B:CYS97 4.1 31.7 1.0
NH2 B:ARG392 4.2 46.0 1.0
O B:HOH710 4.3 39.7 1.0
CG B:GLU421 4.3 34.4 1.0
O B:HOH696 4.3 47.6 1.0
NH2 B:ARG136 4.4 33.5 1.0
CG B:HIS379 4.4 33.6 1.0
ND1 B:HIS379 4.4 32.5 1.0
OD1 B:ASP451 4.4 46.8 1.0
O B:HOH686 4.5 26.8 1.0
O B:CYS97 4.7 28.8 1.0
N B:ASP451 4.7 40.0 1.0
C B:CYS97 4.7 29.4 1.0
CA B:ASP451 4.8 39.6 1.0
CZ B:ARG136 4.9 31.7 1.0
NH1 B:ARG136 4.9 32.0 1.0
NH1 B:ARG392 4.9 43.4 1.0

Manganese binding site 3 out of 4 in 5hud

Go back to Manganese Binding Sites List in 5hud
Manganese binding site 3 out of 4 in the Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn530

b:29.0
occ:1.00
 OE1 C:GLU421 2.1 25.3 1.0
NE2 C:HIS379 2.4 29.6 1.0
SG C:CYS97 2.4 26.8 1.0
OD2 C:ASP451 2.5 40.6 1.0
OE2 C:GLU421 2.6 25.0 1.0
CD C:GLU421 2.7 25.8 1.0
O C:HOH758 2.8 24.2 1.0
CG C:ASP451 3.2 38.5 1.0
CD2 C:HIS379 3.3 30.6 1.0
CB C:CYS97 3.4 24.9 1.0
CE1 C:HIS379 3.4 30.5 1.0
CB C:ASP451 3.5 37.7 1.0
CA C:CYS97 4.1 23.3 1.0
O C:HOH716 4.1 37.3 1.0
NH2 C:ARG392 4.1 33.3 1.0
CG C:GLU421 4.2 25.5 1.0
OD1 C:ASP451 4.3 37.3 1.0
NH2 C:ARG136 4.3 27.9 1.0
O C:HOH764 4.5 34.0 1.0
O C:HOH704 4.5 24.0 1.0
ND1 C:HIS379 4.5 30.2 1.0
CG C:HIS379 4.5 29.7 1.0
C C:CYS97 4.7 22.1 1.0
N C:ASP451 4.7 35.4 1.0
CA C:ASP451 4.8 36.6 1.0
O C:CYS97 4.8 21.1 1.0
CZ C:ARG136 4.8 26.8 1.0
NH1 C:ARG136 4.9 28.3 1.0

Manganese binding site 4 out of 4 in 5hud

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Manganese binding site 4 out of 4 in the Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Non-Covalent Complex of and Dahp Synthase and Chorismate Mutase From Corynebacterium Glutamicum with Bound Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn525

b:27.5
occ:1.00
 OE1 D:GLU421 2.1 24.2 1.0
O D:HOH746 2.3 20.8 1.0
SG D:CYS97 2.4 25.0 1.0
NE2 D:HIS379 2.4 31.4 1.0
OD2 D:ASP451 2.5 36.5 1.0
OE2 D:GLU421 2.6 22.5 1.0
CD D:GLU421 2.7 22.7 1.0
CG D:ASP451 3.2 32.8 1.0
CD2 D:HIS379 3.3 32.2 1.0
CB D:CYS97 3.4 22.4 1.0
CE1 D:HIS379 3.4 31.0 1.0
CB D:ASP451 3.5 31.4 1.0
CA D:CYS97 4.0 21.9 1.0
NH2 D:ARG392 4.1 28.1 1.0
O D:HOH764 4.2 32.2 1.0
NH2 D:ARG136 4.2 25.5 1.0
CG D:GLU421 4.2 22.8 1.0
OD1 D:ASP451 4.3 33.0 1.0
O D:HOH715 4.4 34.9 1.0
CG D:HIS379 4.5 30.2 1.0
ND1 D:HIS379 4.5 30.9 1.0
O D:CYS97 4.6 21.3 1.0
C D:CYS97 4.7 21.5 1.0
CA D:ASP451 4.7 30.5 1.0
N D:ASP451 4.7 28.3 1.0
CZ D:ARG136 4.7 24.1 1.0
O D:HOH685 4.7 31.8 1.0
NH1 D:ARG136 4.8 24.0 1.0
NH1 D:ARG392 4.8 27.7 1.0
CZ D:ARG392 5.0 28.6 1.0

Reference:

D.Burschowsky, H.V.Thorbjornsrud, J.B.Heim, J.R.Fahrig-Kamarauskaite, K.Wurth-Roderer, P.Kast, U.Krengel. Inter-Enzyme Allosteric Regulation of Chorismate Mutase in Corynebacterium Glutamicum: Structural Basis of Feedback Activation By Trp. Biochemistry V. 57 557 2018.
ISSN: ISSN 1520-4995
PubMed: 29178787
DOI: 10.1021/ACS.BIOCHEM.7B01018
Page generated: Sun Oct 6 00:34:31 2024

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