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Manganese in PDB 5kst: Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).

Enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).

All present enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).:
3.1.3.5;

Protein crystallography data

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp)., PDB code: 5kst was solved by A.T.P.Machado, E.M.B.Fonseca, M.A.Dos Reis, A.M.Saraiva, C.A.Dos Santos, M.A.S.De Toledo, I.Polikarpov, A.P.De Souza, R.Aparicio, J.Iulek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.96 / 2.76
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.001, 78.209, 82.158, 90.00, 96.74, 90.00
R / Rfree (%) 19.7 / 24.8

Other elements in 5kst:

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). also contains other interesting chemical elements:

Iodine (I) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). (pdb code 5kst). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp)., PDB code: 5kst:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5kst

Go back to Manganese Binding Sites List in 5kst
Manganese binding site 1 out of 4 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:39.2
occ:1.00
 OD1 A:ASP9 1.9 37.4 1.0
O2 A:PO4503 2.1 42.3 1.0
OD1 A:ASN92 2.2 41.1 1.0
OG A:SER40 2.4 67.0 1.0
OD1 A:ASP8 2.4 43.7 1.0
OD2 A:ASP8 2.9 43.8 1.0
CG A:ASP8 2.9 43.1 1.0
CG A:ASP9 3.1 37.4 1.0
CG A:ASN92 3.3 40.9 1.0
CB A:SER40 3.3 68.0 1.0
P A:PO4503 3.3 40.9 1.0
O1 A:PO4503 3.6 38.2 1.0
OD2 A:ASP9 3.6 37.7 1.0
OD1 A:ASN93 3.8 48.8 1.0
ND2 A:ASN92 3.8 41.3 1.0
CA A:SER40 4.0 67.8 1.0
N A:ASP9 4.1 35.9 1.0
O4 A:PO4503 4.1 41.9 1.0
OG1 A:THR106 4.2 40.0 1.0
O A:HOH609 4.3 39.4 1.0
CB A:ASP9 4.3 37.2 1.0
CB A:ASP8 4.4 40.7 1.0
CA A:ASP9 4.4 36.8 1.0
O3 A:PO4503 4.4 42.6 1.0
C A:ASP8 4.4 40.9 1.0
CB A:ASN92 4.5 40.4 1.0
OD1 A:ASP38 4.5 51.5 1.0
CG A:ASN93 4.7 48.5 1.0
N A:SER40 4.8 67.8 1.0
O A:ASP8 4.8 41.8 1.0
CA A:ASP8 4.9 39.8 1.0
CA A:ASN92 4.9 41.1 1.0
ND2 A:ASN93 4.9 49.7 1.0
N A:ASN93 5.0 43.4 1.0

Manganese binding site 2 out of 4 in 5kst

Go back to Manganese Binding Sites List in 5kst
Manganese binding site 2 out of 4 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:37.8
occ:1.00
 OD1 B:ASP9 1.9 34.8 1.0
OD1 B:ASN92 2.1 38.6 1.0
O3 B:PO4303 2.2 37.8 1.0
OD1 B:ASP8 2.3 49.4 1.0
OG B:SER40 2.5 81.8 1.0
CG B:ASP8 3.0 48.5 1.0
OD2 B:ASP8 3.0 48.7 1.0
CG B:ASP9 3.0 35.1 1.0
CG B:ASN92 3.2 38.3 1.0
P B:PO4303 3.3 36.6 1.0
O4 B:PO4303 3.4 33.7 1.0
CB B:SER40 3.5 82.1 1.0
OD2 B:ASP9 3.5 35.2 1.0
OD1 B:ASN93 3.7 57.7 1.0
ND2 B:ASN92 3.7 37.9 1.0
O1 B:PO4303 4.0 36.2 1.0
O B:HOH408 4.1 38.4 1.0
OG1 B:THR106 4.1 39.6 1.0
N B:ASP9 4.1 37.0 1.0
CA B:SER40 4.2 83.0 1.0
CB B:ASP9 4.2 35.8 1.0
CA B:ASP9 4.4 36.9 1.0
CB B:ASP8 4.4 47.5 1.0
CB B:ASN92 4.4 39.2 1.0
C B:ASP8 4.4 48.1 1.0
O2 B:PO4303 4.5 36.8 1.0
O B:HOH440 4.5 26.6 1.0
CG B:ASN93 4.6 57.8 1.0
OD1 B:ASP38 4.6 64.7 1.0
O B:HOH402 4.7 32.7 1.0
CA B:ASN92 4.8 40.5 1.0
N B:ASN93 4.8 55.2 1.0
CA B:ASP8 4.9 47.5 1.0
O B:ASP8 4.9 48.9 1.0
ND2 B:ASN93 4.9 59.0 1.0
N B:SER40 4.9 84.5 1.0

Manganese binding site 3 out of 4 in 5kst

Go back to Manganese Binding Sites List in 5kst
Manganese binding site 3 out of 4 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:34.6
occ:1.00
 OD1 C:ASP9 2.0 38.8 1.0
OD1 C:ASN92 2.1 34.4 1.0
O2 C:PO4503 2.1 37.8 1.0
OD1 C:ASP8 2.2 36.4 1.0
OG C:SER40 2.3 50.4 1.0
CG C:ASP8 3.1 34.7 1.0
CG C:ASP9 3.1 39.0 1.0
CG C:ASN92 3.2 35.4 1.0
P C:PO4503 3.4 37.3 1.0
OD2 C:ASP8 3.4 34.0 1.0
CB C:SER40 3.4 51.5 1.0
O4 C:PO4503 3.5 38.7 1.0
OD1 C:ASN93 3.7 42.0 1.0
ND2 C:ASN92 3.7 36.4 1.0
OD2 C:ASP9 3.7 40.7 1.0
O C:HOH620 3.9 28.7 1.0
OG1 C:THR106 4.0 33.5 1.0
O1 C:PO4503 4.0 39.0 1.0
N C:ASP9 4.1 35.2 1.0
CB C:ASP9 4.3 38.2 1.0
CA C:SER40 4.3 51.3 1.0
CA C:ASP9 4.3 36.6 1.0
C C:ASP8 4.4 34.6 1.0
CG C:ASN93 4.4 42.0 1.0
CB C:ASN92 4.5 35.5 1.0
O3 C:PO4503 4.5 37.2 1.0
CB C:ASP8 4.5 33.3 1.0
N C:ASN93 4.6 41.1 1.0
OD1 C:ASP38 4.7 53.5 1.0
O C:ASP8 4.7 35.0 1.0
ND2 C:ASN93 4.7 40.6 1.0
CA C:ASN92 4.8 37.2 1.0
CA C:ASP8 4.9 33.6 1.0
N C:SER40 4.9 50.8 1.0

Manganese binding site 4 out of 4 in 5kst

Go back to Manganese Binding Sites List in 5kst
Manganese binding site 4 out of 4 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp).


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa- Xfsure-Tsamp (Tetramer Smaller - Crystallization with 3'Amp). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn602

b:49.7
occ:1.00
 O3 D:PO4604 1.9 55.0 1.0
OD1 D:ASP8 2.2 45.7 1.0
OD1 D:ASN92 2.2 46.0 1.0
OG D:SER40 2.3 69.7 1.0
OD1 D:ASP9 2.4 51.5 1.0
CG D:ASP8 3.0 43.1 1.0
OD2 D:ASP8 3.1 41.8 1.0
P D:PO4604 3.2 54.0 1.0
CB D:SER40 3.2 69.8 1.0
CG D:ASN92 3.3 46.8 1.0
CG D:ASP9 3.4 51.8 1.0
ND2 D:ASN92 3.7 46.7 1.0
O1 D:PO4604 3.7 53.7 1.0
O2 D:PO4604 3.8 54.6 1.0
OD1 D:ASN93 3.9 45.7 1.0
OG1 D:THR106 3.9 40.2 1.0
OD2 D:ASP9 4.0 53.1 1.0
CA D:SER40 4.1 69.6 1.0
N D:ASP9 4.3 48.2 1.0
O4 D:PO4604 4.3 53.8 1.0
C D:ASP8 4.4 40.2 1.0
CB D:ASP8 4.4 41.0 1.0
CA D:ASP9 4.5 49.2 1.0
CB D:ASP9 4.6 50.7 1.0
CB D:ASN92 4.6 47.9 1.0
CG D:ASN93 4.7 45.2 1.0
O D:ASP8 4.7 39.3 1.0
OD1 D:ASP38 4.7 73.0 1.0
N D:SER40 4.8 70.0 1.0
N D:ASN93 4.9 47.9 1.0
CA D:ASP8 4.9 40.6 1.0
ND2 D:ASN93 4.9 44.5 1.0
CA D:ASN92 5.0 48.0 1.0

Reference:

A.T.P.Machado, E.M.B.Fonseca, M.A.D.Reis, A.M.Saraiva, C.A.D.Santos, M.A.S.De Toledo, I.Polikarpov, A.P.De Souza, R.Aparicio, J.Iulek. Conformational Variability of the Stationary Phase Survival Protein E From Xylella Fastidiosa Revealed By X-Ray Crystallography, Small-Angle X-Ray Scattering Studies, and Normal Mode Analysis. Proteins V. 85 1931 2017.
ISSN: ESSN 1097-0134
PubMed: 28677327
DOI: 10.1002/PROT.25347
Page generated: Sun Oct 6 01:46:15 2024

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