Atomistry » Manganese » PDB 5kg5-5lyw » 5ksr
Atomistry »
  Manganese »
    PDB 5kg5-5lyw »
      5ksr »

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: Sun Oct 6 01:46:07 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy