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Manganese in PDB 3nvt: 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E

Enzymatic activity of 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E

All present enzymatic activity of 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E:
2.5.1.54; 5.4.99.5;

Protein crystallography data

The structure of 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E, PDB code: 3nvt was solved by A.S.Halavaty, S.H.Light, G.Minasov, L.Shuvalova, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.04 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.570, 111.787, 81.049, 90.00, 127.63, 90.00
R / Rfree (%) 15.4 / 19.8

Manganese Binding Sites:

The binding sites of Manganese atom in the 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E (pdb code 3nvt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E, PDB code: 3nvt:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3nvt

Go back to Manganese Binding Sites List in 3nvt
Manganese binding site 1 out of 4 in the 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn362

b:18.7
occ:0.60
 MN A:MN362 0.0 18.7 0.6
MN A:MN362 1.4 29.1 0.4
OD2 A:ASP333 2.0 44.4 1.0
OE1 A:GLU322 2.1 33.7 1.0
NE2 A:HIS296 2.1 29.3 1.0
SG A:CYS126 2.5 30.8 1.0
OE2 A:GLU322 2.5 38.4 1.0
CD A:GLU322 2.6 33.0 1.0
CE1 A:HIS296 2.9 32.1 1.0
CG A:ASP333 3.0 44.6 1.0
CD2 A:HIS296 3.1 28.4 1.0
CB A:CYS126 3.1 27.8 1.0
O A:HOH695 3.3 67.4 1.0
CB A:ASP333 3.6 38.3 1.0
CA A:CYS126 4.0 26.8 1.0
ND1 A:HIS296 4.0 31.0 1.0
CG A:GLU322 4.1 28.9 1.0
OD1 A:ASP333 4.1 46.9 1.0
CG A:HIS296 4.2 25.6 1.0
CH3 A:ACT363 4.4 46.6 1.0
CG2 A:THR295 4.5 21.3 1.0
NH2 A:ARG150 4.6 44.0 0.6
CB A:GLU322 4.8 22.8 1.0
N A:CYS126 4.9 25.9 1.0

Manganese binding site 2 out of 4 in 3nvt

Go back to Manganese Binding Sites List in 3nvt
Manganese binding site 2 out of 4 in the 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn362

b:29.1
occ:0.40
 MN A:MN362 0.0 29.1 0.4
MN A:MN362 1.4 18.7 0.6
NE2 A:HIS296 2.0 29.3 1.0
SG A:CYS126 2.2 30.8 1.0
OE2 A:GLU322 2.3 38.4 1.0
CE1 A:HIS296 2.5 32.1 1.0
CD A:GLU322 3.0 33.0 1.0
OE1 A:GLU322 3.0 33.7 1.0
O A:HOH695 3.1 67.4 1.0
OD2 A:ASP333 3.2 44.4 1.0
CH3 A:ACT363 3.2 46.6 1.0
CB A:CYS126 3.3 27.8 1.0
CD2 A:HIS296 3.3 28.4 1.0
NH2 A:ARG150 3.7 44.0 0.6
CA A:CYS126 3.7 26.8 1.0
ND1 A:HIS296 3.8 31.0 1.0
C A:ACT363 3.8 46.4 1.0
NZ A:LYS155 3.9 33.6 1.0
CG A:HIS296 4.2 25.6 1.0
NH2 A:ARG150 4.2 24.7 0.4
CG A:ASP333 4.2 44.6 1.0
OXT A:ACT363 4.2 47.2 1.0
CG A:GLU322 4.4 28.9 1.0
O A:CYS126 4.4 26.6 1.0
C A:CYS126 4.5 27.6 1.0
O A:ACT363 4.5 46.4 1.0
CZ A:ARG150 4.6 26.3 0.4
O A:HOH697 4.7 99.3 1.0
CB A:ASP333 4.8 38.3 1.0
NH1 A:ARG150 4.8 25.3 0.4
CZ A:ARG150 4.8 42.8 0.6
N A:CYS126 4.9 25.9 1.0
CE A:LYS155 4.9 34.9 1.0

Manganese binding site 3 out of 4 in 3nvt

Go back to Manganese Binding Sites List in 3nvt
Manganese binding site 3 out of 4 in the 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn362

b:18.5
occ:0.70
 MN B:MN362 0.0 18.5 0.7
MN B:MN362 1.3 22.4 0.3
OE1 B:GLU322 2.0 25.5 1.0
OD2 B:ASP333 2.1 34.2 1.0
NE2 B:HIS296 2.1 27.8 1.0
SG B:CYS126 2.4 23.0 1.0
OE2 B:GLU322 2.5 28.4 1.0
CD B:GLU322 2.6 26.0 1.0
CE1 B:HIS296 2.9 29.7 1.0
CB B:CYS126 3.1 20.2 1.0
CG B:ASP333 3.1 33.8 1.0
CD2 B:HIS296 3.2 26.2 1.0
CB B:ASP333 3.6 27.4 1.0
CA B:CYS126 4.0 20.3 1.0
ND1 B:HIS296 4.0 28.7 1.0
CG B:GLU322 4.1 22.4 1.0
OD1 B:ASP333 4.1 36.5 1.0
CG B:HIS296 4.2 23.8 1.0
NH2 B:ARG150 4.5 36.1 0.5
CG2 B:THR295 4.7 18.1 1.0
CB B:GLU322 4.9 18.6 1.0
N B:CYS126 4.9 19.5 1.0

Manganese binding site 4 out of 4 in 3nvt

Go back to Manganese Binding Sites List in 3nvt
Manganese binding site 4 out of 4 in the 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 1.95 Angstrom Crystal Structure of A Bifunctional 3-Deoxy-7- Phosphoheptulonate Synthase/Chorismate Mutase (Aroa) From Listeria Monocytogenes Egd-E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn362

b:22.4
occ:0.30
 MN B:MN362 0.0 22.4 0.3
MN B:MN362 1.3 18.5 0.7
NE2 B:HIS296 2.1 27.8 1.0
OE2 B:GLU322 2.1 28.4 1.0
SG B:CYS126 2.2 23.0 1.0
CE1 B:HIS296 2.5 29.7 1.0
CD B:GLU322 2.8 26.0 1.0
OE1 B:GLU322 2.8 25.5 1.0
CB B:CYS126 3.1 20.2 1.0
OD2 B:ASP333 3.3 34.2 1.0
CD2 B:HIS296 3.4 26.2 1.0
NH2 B:ARG150 3.6 36.1 0.5
CA B:CYS126 3.6 20.3 1.0
ND1 B:HIS296 3.8 28.7 1.0
NZ B:LYS155 4.0 25.7 1.0
NH2 B:ARG150 4.1 22.0 0.5
O B:HOH526 4.2 28.2 1.0
CG B:GLU322 4.2 22.4 1.0
CG B:HIS296 4.2 23.8 1.0
CG B:ASP333 4.3 33.8 1.0
C B:CYS126 4.4 21.0 1.0
O B:CYS126 4.5 20.5 1.0
CZ B:ARG150 4.5 23.9 0.5
CZ B:ARG150 4.7 33.9 0.5
N B:CYS126 4.7 19.5 1.0
CB B:ASP333 4.8 27.4 1.0
NH1 B:ARG150 4.8 24.1 0.5
CE B:LYS155 5.0 26.9 1.0

Reference:

S.H.Light, A.S.Halavaty, G.Minasov, L.Shuvalova, W.F.Anderson. Structural Analysis of A 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase with An N-Terminal Chorismate Mutase-Like Regulatory Domain. Protein Sci. V. 21 887 2012.
ISSN: ISSN 0961-8368
PubMed: 22505283
DOI: 10.1002/PRO.2075
Page generated: Sat Oct 5 17:21:27 2024

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