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Manganese in PDB 4ixx: Crystal Structure of S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis

Enzymatic activity of Crystal Structure of S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis

All present enzymatic activity of Crystal Structure of S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis:
2.5.1.54;

Protein crystallography data

The structure of Crystal Structure of S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis, PDB code: 4ixx was solved by P.J.Cross, A.L.Pietersma, T.M.Allison, S.M.Wilson-Coutts, F.C.Cochrane, E.J.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.59 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.064, 132.432, 75.028, 90.00, 95.72, 90.00
R / Rfree (%) 19.1 / 22.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis (pdb code 4ixx). 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 S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis, PDB code: 4ixx:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4ixx

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Manganese binding site 1 out of 4 in the Crystal Structure of S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis


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 S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:35.0
occ:1.00
 OD2 A:ASP324 2.1 26.7 1.0
OE2 A:GLU304 2.2 26.4 1.0
NE2 A:HIS270 2.3 29.2 1.0
SG A:CYS63 2.7 24.4 1.0
O A:HOH501 3.1 30.5 1.0
CD A:GLU304 3.2 28.5 1.0
CG A:ASP324 3.2 26.5 1.0
CE1 A:HIS270 3.2 29.3 1.0
CD2 A:HIS270 3.3 29.1 1.0
OE1 A:GLU304 3.4 28.6 1.0
CB A:ASP324 3.7 27.6 1.0
NZ A:LYS99 3.7 37.2 1.0
CB A:CYS63 3.8 26.1 1.0
OD1 A:ASP324 4.2 24.6 1.0
NH2 A:ARG94 4.2 28.9 1.0
CA A:CYS63 4.3 26.5 1.0
ND1 A:HIS270 4.3 29.2 1.0
CG A:HIS270 4.4 28.8 1.0
CE A:LYS99 4.5 36.8 1.0
CG A:GLU304 4.5 28.9 1.0
O A:HOH529 4.7 29.1 1.0
O A:CYS63 4.7 25.8 1.0
CA A:ASP324 4.9 28.4 1.0
N A:ASP324 4.9 28.6 1.0
O1 A:SO4403 4.9 36.6 0.5
C A:CYS63 4.9 26.9 1.0

Manganese binding site 2 out of 4 in 4ixx

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Manganese binding site 2 out of 4 in the Crystal Structure of S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis


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 S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:59.5
occ:1.00
 OE2 B:GLU304 1.8 40.1 1.0
OD2 B:ASP324 1.8 45.4 1.0
NE2 B:HIS270 2.4 47.9 1.0
SG B:CYS63 2.6 40.5 1.0
CG B:ASP324 2.9 48.9 1.0
CD B:GLU304 2.9 45.3 1.0
CE1 B:HIS270 3.3 46.6 1.0
CD2 B:HIS270 3.4 48.2 1.0
CB B:ASP324 3.5 49.5 1.0
OE1 B:GLU304 3.5 48.9 1.0
O B:HOH501 3.6 39.9 1.0
CB B:CYS63 3.7 41.1 1.0
NZ B:LYS99 3.7 87.8 1.0
OD1 B:ASP324 4.0 50.0 1.0
NH1 B:ARG94 4.0 52.5 1.0
CG B:GLU304 4.2 44.3 1.0
CA B:CYS63 4.3 39.7 1.0
ND1 B:HIS270 4.5 47.7 1.0
CE B:LYS99 4.5 88.2 1.0
CG B:HIS270 4.5 49.6 1.0
O B:CYS63 4.7 41.0 1.0
CA B:ASP324 4.8 52.7 1.0
N B:ASP324 4.8 54.0 1.0
C B:CYS63 4.9 40.1 1.0
CZ B:ARG94 4.9 49.1 1.0

Manganese binding site 3 out of 4 in 4ixx

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Manganese binding site 3 out of 4 in the Crystal Structure of S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis


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 S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:48.6
occ:1.00
 OD2 C:ASP324 1.8 54.8 1.0
OE2 C:GLU304 2.0 38.5 1.0
NE2 C:HIS270 2.3 44.6 1.0
SG C:CYS63 2.6 42.5 1.0
CD C:GLU304 2.9 41.1 1.0
CG C:ASP324 2.9 55.9 1.0
OE1 C:GLU304 3.1 44.4 1.0
CE1 C:HIS270 3.2 43.2 1.0
CD2 C:HIS270 3.3 46.6 1.0
CB C:ASP324 3.7 55.4 1.0
CB C:CYS63 3.7 42.7 1.0
OD1 C:ASP324 3.9 55.5 1.0
NZ C:LYS99 3.9 84.4 1.0
O C:HOH501 3.9 47.3 1.0
NH2 C:ARG94 4.2 41.0 1.0
CG C:GLU304 4.2 38.9 1.0
CA C:CYS63 4.2 40.8 1.0
ND1 C:HIS270 4.4 44.7 1.0
CG C:HIS270 4.5 45.8 1.0
O3 C:SO4403 4.6 35.9 0.5
O C:CYS63 4.7 43.3 1.0
CE C:LYS99 4.7 85.2 1.0
CA C:ASP324 4.8 57.5 1.0
C C:CYS63 4.8 41.5 1.0
N C:ASP324 4.8 60.3 1.0

Manganese binding site 4 out of 4 in 4ixx

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Manganese binding site 4 out of 4 in the Crystal Structure of S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis


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 S213G Variant DAH7PS Without Tyr Bound From Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:40.4
occ:1.00
 OE2 D:GLU304 1.8 40.4 1.0
OD2 D:ASP324 1.8 33.3 1.0
NE2 D:HIS270 2.3 38.8 1.0
SG D:CYS63 2.6 34.2 1.0
CG D:ASP324 2.9 34.2 1.0
CD D:GLU304 3.0 38.4 1.0
CE1 D:HIS270 3.2 38.3 1.0
O D:HOH501 3.3 28.8 1.0
CD2 D:HIS270 3.3 40.2 1.0
OE1 D:GLU304 3.5 41.0 1.0
NZ D:LYS99 3.7 32.0 1.0
CB D:CYS63 3.7 34.1 1.0
CB D:ASP324 3.8 35.3 1.0
OD1 D:ASP324 3.9 33.1 1.0
NH2 D:ARG94 4.1 39.4 1.0
CG D:GLU304 4.2 36.3 1.0
CA D:CYS63 4.3 32.7 1.0
ND1 D:HIS270 4.4 40.2 1.0
CG D:HIS270 4.4 41.3 1.0
CE D:LYS99 4.5 33.7 1.0
O D:CYS63 4.6 33.1 1.0
O2 D:SO4403 4.7 41.5 0.5
C D:CYS63 4.8 32.6 1.0
N D:ASP324 4.9 36.5 1.0
CA D:ASP324 4.9 37.0 1.0

Reference:

P.J.Cross, A.L.Pietersma, T.M.Allison, S.M.Wilson-Coutts, F.C.Cochrane, E.J.Parker. Neisseria Meningitidis Expresses A Single 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase That Is Inhibited Primarily By Phenylalanine. Protein Sci. V. 22 1087 2013.
ISSN: ISSN 0961-8368
PubMed: 23754471
DOI: 10.1002/PRO.2293
Page generated: Sat Oct 5 19:56:01 2024

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