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

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy