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Potassium in PDB 6dwo: Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583

Protein crystallography data

The structure of Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583, PDB code: 6dwo was solved by A.J.Fisher, Y.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.18 / 2.15
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 163.350, 168.990, 258.520, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.9

Other elements in 6dwo:

The structure of Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583 also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583 (pdb code 6dwo). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583, PDB code: 6dwo:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6dwo

Go back to Potassium Binding Sites List in 6dwo
Potassium binding site 1 out of 4 in the Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:29.2
occ:1.00
O A:TYR599 2.7 23.1 1.0
OD1 A:ASN20 2.7 22.2 1.0
O A:HOH923 2.7 29.2 1.0
O A:THR597 2.8 24.5 1.0
O A:HOH1172 3.0 23.0 1.0
O A:HOH1298 3.3 42.0 1.0
C A:TYR599 3.6 24.0 1.0
CG A:ASN20 3.7 24.1 1.0
O A:HOH1297 3.9 33.4 1.0
CB A:ASN20 3.9 22.0 1.0
C A:THR597 4.0 25.9 1.0
O A:HOH1192 4.0 42.7 1.0
CA A:PRO600 4.1 24.6 1.0
CA A:ASN20 4.2 22.6 1.0
N A:PRO600 4.2 24.0 1.0
N A:TYR599 4.2 22.4 1.0
CB A:THR597 4.6 26.4 1.0
CA A:TYR599 4.6 22.6 1.0
CA A:THR597 4.7 23.6 1.0
C A:PRO600 4.7 25.1 1.0
C A:GLY598 4.8 25.5 1.0
O A:HOH1013 4.8 31.8 1.0
O A:SER19 4.9 25.0 1.0
N A:GLY598 4.9 22.6 1.0
ND2 A:ASN20 4.9 23.3 1.0
O A:THR591 4.9 27.8 1.0

Potassium binding site 2 out of 4 in 6dwo

Go back to Potassium Binding Sites List in 6dwo
Potassium binding site 2 out of 4 in the Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1002

b:25.9
occ:1.00
O B:HOH1202 2.7 31.4 1.0
O B:TYR599 2.7 21.7 1.0
OD1 B:ASN20 2.7 24.8 1.0
O B:THR597 2.9 25.3 1.0
O B:HOH1326 2.9 27.4 1.0
O B:HOH1504 3.2 44.0 1.0
O B:HOH1508 3.6 36.5 1.0
C B:TYR599 3.6 24.1 1.0
CG B:ASN20 3.7 23.6 1.0
CB B:ASN20 4.0 23.2 1.0
C B:THR597 4.0 24.0 1.0
O B:HOH1422 4.1 43.5 1.0
CA B:PRO600 4.1 23.3 1.0
N B:PRO600 4.2 23.1 1.0
CA B:ASN20 4.2 22.6 1.0
N B:TYR599 4.3 25.9 1.0
CA B:TYR599 4.6 22.3 1.0
CB B:THR597 4.6 25.3 1.0
O B:HOH1344 4.7 33.0 1.0
C B:PRO600 4.7 22.2 1.0
CA B:THR597 4.8 23.3 1.0
C B:GLY598 4.8 26.1 1.0
O B:THR591 4.9 28.9 1.0
O B:SER19 4.9 22.3 1.0
ND2 B:ASN20 4.9 21.0 1.0
N B:GLY598 4.9 23.2 1.0

Potassium binding site 3 out of 4 in 6dwo

Go back to Potassium Binding Sites List in 6dwo
Potassium binding site 3 out of 4 in the Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1002

b:29.8
occ:1.00
O C:HOH1169 2.6 43.1 1.0
O C:TYR599 2.6 22.6 1.0
OD1 C:ASN20 2.7 28.8 1.0
O C:THR597 2.9 23.8 1.0
O C:HOH1449 2.9 45.0 1.0
O C:HOH1297 3.0 32.8 1.0
C C:TYR599 3.6 24.3 1.0
CG C:ASN20 3.7 25.2 1.0
CB C:ASN20 3.9 21.6 1.0
C C:THR597 4.0 21.2 1.0
O C:HOH1365 4.0 42.5 1.0
CA C:PRO600 4.1 25.5 1.0
CA C:ASN20 4.2 22.6 1.0
N C:PRO600 4.2 23.8 1.0
N C:TYR599 4.2 23.5 1.0
CA C:TYR599 4.5 24.4 1.0
CB C:THR597 4.6 26.7 1.0
CA C:THR597 4.7 22.8 1.0
C C:GLY598 4.7 26.2 1.0
C C:PRO600 4.8 28.3 1.0
O C:SER19 4.8 23.9 1.0
O C:HOH1226 4.8 38.9 1.0
ND2 C:ASN20 4.9 23.0 1.0
N C:GLY598 4.9 24.6 1.0
O C:THR591 4.9 35.3 1.0

Potassium binding site 4 out of 4 in 6dwo

Go back to Potassium Binding Sites List in 6dwo
Potassium binding site 4 out of 4 in the Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Alpha-1-2-Mannosidase From Enterococcus Faecalis V583 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1002

b:29.9
occ:1.00
O D:TYR599 2.7 20.6 1.0
O D:HOH1108 2.7 36.3 1.0
OD1 D:ASN20 2.7 30.0 1.0
O D:THR597 2.8 27.3 1.0
O D:HOH1165 3.3 24.1 1.0
O D:HOH1457 3.3 43.9 1.0
C D:TYR599 3.6 23.2 1.0
CG D:ASN20 3.7 27.2 1.0
O D:HOH1259 3.9 37.5 1.0
C D:THR597 3.9 26.6 1.0
O D:HOH1449 3.9 39.6 1.0
CB D:ASN20 4.0 24.4 1.0
O D:HOH1446 4.0 47.1 1.0
CA D:PRO600 4.2 26.0 1.0
N D:TYR599 4.2 24.2 1.0
CA D:ASN20 4.2 25.9 1.0
N D:PRO600 4.2 25.0 1.0
CB D:THR597 4.5 25.7 1.0
CA D:TYR599 4.5 23.4 1.0
CA D:THR597 4.7 25.6 1.0
C D:GLY598 4.7 25.7 1.0
C D:PRO600 4.8 27.1 1.0
N D:GLY598 4.8 25.1 1.0
O D:HOH1177 4.8 38.2 1.0
O D:THR591 4.9 28.4 1.0
O D:SER19 4.9 24.8 1.0
ND2 D:ASN20 4.9 26.1 1.0
OG1 D:THR597 5.0 25.4 1.0

Reference:

Y.Li, R.Li, H.Yu, X.Sheng, J.Wang, A.J.Fisher, X.Chen. Enterococcus Faecalis Alpha 1-2-Mannosidase (Efman-I): An Efficient Catalyst For Glycoprotein N-Glycan Modification. Febs Lett. 2019.
ISSN: ISSN 0014-5793
PubMed: 31552675
DOI: 10.1002/1873-3468.13618
Page generated: Mon Dec 14 00:35:11 2020

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