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Manganese in PDB 5ksr: Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).

Enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).

All present enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).:
3.1.3.5;

Protein crystallography data

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger)., PDB code: 5ksr was solved by A.T.P.Machado, E.M.B.Fonseca, M.A.Dos Reis, A.M.Saraiva, C.A.Dos Santos, M.A.De Toledo, I.Polikarpov, A.P.De Souza, R.De Aparicio, J.Iulek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.25 / 1.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 172.336, 84.170, 87.310, 90.00, 96.62, 90.00
R / Rfree (%) 19.6 / 23.8

Other elements in 5ksr:

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). also contains other interesting chemical elements:

Iodine (I) 6 atoms
Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). (pdb code 5ksr). 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-Tb (Tetramer Bigger)., PDB code: 5ksr:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5ksr

Go back to Manganese Binding Sites List in 5ksr
Manganese binding site 1 out of 4 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).


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-Tb (Tetramer Bigger). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:41.8
occ:1.00
 OD1 A:ASP9 2.4 37.1 1.0
OD1 A:ASN92 2.4 21.6 1.0
O A:HOH714 3.2 47.1 1.0
CG A:ASN92 3.4 23.9 1.0
CG A:ASP9 3.4 37.7 1.0
OD2 A:ASP8 3.5 32.1 1.0
ND2 A:ASN92 3.6 22.8 1.0
O A:HOH605 3.7 28.1 1.0
CL A:CL504 3.8 31.3 1.0
CB A:ASP8 3.9 32.7 1.0
OD2 A:ASP9 3.9 37.5 1.0
ND2 A:ASN93 4.0 33.8 1.0
CG A:ASP8 4.1 36.6 1.0
N A:ASP9 4.4 17.5 1.0
O A:HOH690 4.4 20.2 1.0
C A:ASP8 4.5 21.1 1.0
OG1 A:THR106 4.6 16.3 1.0
CB A:ASP9 4.6 32.3 1.0
CA A:ASP9 4.7 24.6 1.0
CB A:ASN92 4.8 15.4 1.0
CA A:ASP8 4.8 19.6 1.0
O A:ASP8 5.0 20.1 1.0
OD1 A:ASP38 5.0 44.4 1.0
CB A:SER40 5.0 60.1 1.0

Manganese binding site 2 out of 4 in 5ksr

Go back to Manganese Binding Sites List in 5ksr
Manganese binding site 2 out of 4 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).


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-Tb (Tetramer Bigger). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:43.6
occ:1.00
 OD1 B:ASN92 2.5 22.9 1.0
OD1 B:ASP9 2.6 40.0 1.0
OD2 B:ASP8 3.3 30.3 1.0
CG B:ASN92 3.4 22.0 1.0
O B:HOH604 3.5 37.1 1.0
CG B:ASP9 3.6 40.8 1.0
ND2 B:ASN92 3.6 22.2 1.0
CL B:CL503 3.7 31.7 1.0
CB B:ASP8 4.0 31.9 1.0
CG B:ASP8 4.1 34.9 1.0
OD2 B:ASP9 4.1 42.6 1.0
ND2 B:ASN93 4.1 37.6 1.0
O B:HOH692 4.3 47.6 1.0
N B:ASP9 4.4 20.5 1.0
O B:HOH685 4.5 24.6 1.0
C B:ASP8 4.5 22.4 1.0
OG1 B:THR106 4.6 16.2 1.0
CB B:ASP9 4.8 35.3 1.0
CA B:ASP9 4.8 25.8 1.0
CB B:ASN92 4.8 19.9 1.0
CA B:ASP8 4.9 20.8 1.0
CB B:SER40 4.9 61.3 1.0
O B:ASP8 4.9 22.9 1.0

Manganese binding site 3 out of 4 in 5ksr

Go back to Manganese Binding Sites List in 5ksr
Manganese binding site 3 out of 4 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).


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-Tb (Tetramer Bigger). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:35.5
occ:1.00
 O C:HOH691 2.4 30.2 1.0
OD1 C:ASP8 2.4 32.8 1.0
OD1 C:ASN92 2.4 21.3 1.0
OD1 C:ASP9 2.5 37.4 1.0
OG C:SER40 3.2 56.8 1.0
CG C:ASP8 3.3 32.6 1.0
CG C:ASN92 3.4 21.6 1.0
CG C:ASP9 3.4 36.1 1.0
OD2 C:ASP8 3.5 29.7 1.0
ND2 C:ASN92 3.7 22.3 1.0
O C:HOH613 3.8 22.1 1.0
CL C:CL504 3.8 37.4 1.0
OD2 C:ASP9 3.9 37.2 1.0
O C:HOH608 4.1 51.0 1.0
O C:HOH661 4.4 23.4 1.0
N C:ASP9 4.5 23.3 1.0
CB C:SER40 4.6 55.9 1.0
O C:HOH630 4.6 50.5 1.0
OD1 C:ASN93 4.6 31.5 1.0
C C:ASP8 4.6 22.7 1.0
OG1 C:THR106 4.6 22.4 1.0
CB C:ASP9 4.6 31.2 1.0
CA C:ASP9 4.7 26.4 1.0
CB C:ASP8 4.7 31.5 1.0
CB C:ASN92 4.8 22.1 1.0
OD1 C:ASP38 4.8 45.9 1.0
O C:ASP8 4.9 23.1 1.0

Manganese binding site 4 out of 4 in 5ksr

Go back to Manganese Binding Sites List in 5ksr
Manganese binding site 4 out of 4 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).


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-Tb (Tetramer Bigger). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:37.4
occ:1.00
 O D:HOH675 2.1 43.3 1.0
O D:HOH697 2.4 33.7 1.0
OD1 D:ASP8 2.4 34.7 1.0
OD1 D:ASP9 2.5 33.3 1.0
OD1 D:ASN92 2.6 21.8 1.0
CG D:ASP8 3.3 33.8 1.0
OD2 D:ASP8 3.5 33.4 1.0
CG D:ASN92 3.5 24.4 1.0
CG D:ASP9 3.6 35.4 1.0
O D:HOH621 3.8 47.8 1.0
ND2 D:ASN92 3.8 24.9 1.0
CL D:CL503 3.8 36.9 1.0
OD2 D:ASP9 4.1 39.9 1.0
O D:HOH603 4.2 41.1 1.0
O D:HOH664 4.4 24.2 1.0
N D:ASP9 4.4 24.2 1.0
OD1 D:ASN93 4.5 35.9 1.0
C D:ASP8 4.5 19.8 1.0
OG1 D:THR106 4.6 20.9 1.0
CA D:ASP9 4.7 27.8 1.0
CB D:ASP8 4.7 28.8 1.0
CB D:ASP9 4.7 33.3 1.0
CB D:SER40 4.8 59.4 1.0
O D:ASP8 4.8 22.4 1.0
OD1 D:ASP38 4.9 42.8 1.0
CB D:ASN92 4.9 23.9 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: Tue Dec 15 04:43:15 2020

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