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Potassium in PDB 4udj: Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate

Protein crystallography data

The structure of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate, PDB code: 4udj was solved by S.Ladeveze, G.Cioci, G.Potocki-Veronese, S.Tranier, L.Mourey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 108.13 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.880, 140.840, 168.750, 90.00, 90.00, 90.00
R / Rfree (%) 14.955 / 19.333

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate (pdb code 4udj). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate, PDB code: 4udj:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 1 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate


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 B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K333

b:61.1
occ:1.00
 O A:HOH493 2.7 23.4 1.0
O A:TRP255 2.7 16.2 1.0
O A:HOH536 2.8 26.3 1.0
O A:VAL197 2.9 12.4 1.0
O A:HIS196 3.1 12.5 1.0
O A:HOH494 3.3 25.1 1.0
O A:HOH546 3.5 21.4 1.0
C A:VAL197 3.7 13.4 1.0
CA A:VAL197 3.9 12.6 1.0
C A:TRP255 3.9 16.0 1.0
C A:HIS196 4.0 12.6 1.0
N A:VAL197 4.3 12.6 1.0
ND1 A:HIS196 4.4 15.0 1.0
CA A:LYS256 4.6 16.1 1.0
CG2 A:VAL257 4.6 15.7 1.0
N A:VAL257 4.7 15.0 1.0
N A:LYS256 4.7 15.5 1.0
CD1 A:TRP255 4.8 19.4 1.0
CB A:TRP255 4.8 17.5 1.0
N A:MET198 4.8 13.6 1.0
CA A:TRP255 4.8 16.3 1.0

Potassium binding site 2 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 2 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate


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 B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K606

b:36.4
occ:1.00
 O A:HOH609 2.6 12.5 1.0
OD2 A:ASP277 2.6 13.9 1.0
OG A:SER41 2.7 9.2 1.0
O A:ASP304 2.7 10.4 1.0
CB A:SER41 3.4 9.8 1.0
CG A:ASP277 3.5 14.7 1.0
CB A:ASP277 3.5 13.7 1.0
CE1 A:PHE43 3.6 12.7 0.5
ND2 A:ASN40 3.6 10.1 1.0
NH2 A:ARG65 3.6 12.7 1.0
CE1 A:PHE43 3.7 10.9 0.5
C A:ASP304 3.9 10.6 1.0
CZ A:PHE43 3.9 12.2 0.5
CZ A:PHE43 3.9 10.6 0.5
CZ A:ARG65 4.1 13.0 1.0
CB A:ASP304 4.2 11.6 1.0
CD1 A:PHE43 4.3 12.5 0.5
OD2 A:ASP61 4.3 9.3 1.0
NE A:ARG65 4.3 12.4 1.0
O A:HOH457 4.4 14.1 1.0
CD1 A:PHE43 4.5 10.8 0.5
CB A:ASP61 4.7 9.3 1.0
OD1 A:ASP277 4.7 17.3 1.0
CA A:ASP304 4.7 10.9 1.0
CG A:ASP61 4.8 9.2 1.0
O A:HOH375 4.8 8.2 1.0
NH1 A:ARG65 4.8 12.9 1.0
CA A:SER41 4.9 9.9 1.0
N A:THR305 4.9 10.2 1.0
CG A:ASN40 4.9 10.4 1.0
CE2 A:PHE43 4.9 10.3 0.5
CE2 A:PHE43 4.9 11.9 0.5
CA A:THR305 5.0 10.7 1.0

Potassium binding site 3 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 3 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate


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 B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K607

b:44.6
occ:1.00
 OD2 F:ASP277 2.5 23.8 1.0
O F:HOH587 2.6 21.4 1.0
O F:ASP304 2.7 16.8 1.0
OG F:SER41 2.8 17.7 1.0
CG F:ASP277 3.4 24.5 1.0
CB F:SER41 3.5 18.7 1.0
CB F:ASP277 3.5 21.3 1.0
NH2 F:ARG65 3.5 16.0 1.0
ND2 F:ASN40 3.7 18.4 1.0
CE1 F:PHE43 3.7 16.3 0.5
CE1 F:PHE43 3.7 17.5 0.5
C F:ASP304 3.9 17.4 1.0
CZ F:PHE43 4.0 17.3 0.5
CZ F:ARG65 4.0 15.9 1.0
CZ F:PHE43 4.1 16.0 0.5
CB F:ASP304 4.2 16.4 1.0
O F:HOH457 4.2 20.6 1.0
OD2 F:ASP61 4.3 19.1 1.0
NE F:ARG65 4.3 15.5 1.0
CD1 F:PHE43 4.4 16.1 0.5
CD1 F:PHE43 4.5 17.4 0.5
OD1 F:ASP277 4.6 25.7 1.0
CA F:ASP304 4.7 17.1 1.0
CB F:ASP61 4.8 19.1 1.0
NH1 F:ARG65 4.8 16.0 1.0
O F:HOH375 4.8 13.5 1.0
CG F:ASP61 4.9 18.6 1.0
N F:THR305 4.9 17.9 1.0
CA F:SER41 4.9 18.4 1.0
CA F:THR305 5.0 18.5 1.0
CA F:ASP277 5.0 21.5 1.0
CG F:ASN40 5.0 17.9 1.0

Potassium binding site 4 out of 8 in 4udj

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Potassium binding site 4 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate


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 B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K333

b:61.2
occ:1.00
 O B:TRP255 2.7 16.2 1.0
O B:HOH493 2.8 24.4 1.0
O B:HOH536 2.8 25.8 1.0
O B:HIS196 2.9 12.8 1.0
O B:VAL197 3.0 12.4 1.0
O B:HOH494 3.1 22.7 1.0
C B:VAL197 3.7 12.9 1.0
CA B:VAL197 3.8 12.4 1.0
C B:TRP255 3.8 15.9 1.0
C B:HIS196 3.9 12.6 1.0
O B:HOH546 4.0 36.7 1.0
N B:VAL197 4.3 11.8 1.0
CA B:LYS256 4.3 17.2 1.0
N B:LYS256 4.5 15.8 1.0
ND1 B:HIS196 4.5 14.0 1.0
N B:VAL257 4.5 16.5 1.0
CD1 B:TRP255 4.7 18.2 1.0
CG2 B:VAL257 4.7 18.7 1.0
CA B:TRP255 4.8 15.4 1.0
CB B:TRP255 4.8 16.8 1.0
N B:MET198 4.9 13.7 1.0
C B:LYS256 5.0 17.3 1.0

Potassium binding site 5 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 5 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K333

b:60.7
occ:1.00
 O C:TRP255 2.6 14.8 1.0
O C:HOH536 2.8 24.7 1.0
O C:VAL197 2.9 10.7 1.0
O C:HOH493 2.9 18.1 1.0
O C:HIS196 3.0 10.6 1.0
O C:HOH494 3.4 23.0 1.0
C C:VAL197 3.6 11.4 1.0
O C:HOH546 3.6 27.2 1.0
CA C:VAL197 3.7 10.5 1.0
C C:TRP255 3.8 15.0 1.0
C C:HIS196 3.9 10.5 1.0
N C:VAL197 4.2 10.0 1.0
CA C:LYS256 4.3 14.6 1.0
N C:VAL257 4.5 14.8 1.0
ND1 C:HIS196 4.5 11.9 1.0
N C:LYS256 4.5 13.9 1.0
CG2 C:VAL257 4.6 16.9 1.0
CD1 C:TRP255 4.8 16.0 1.0
CA C:TRP255 4.8 14.3 1.0
N C:MET198 4.8 11.9 1.0
CB C:TRP255 4.9 15.2 1.0
C C:LYS256 4.9 14.5 1.0
CB C:VAL197 5.0 10.6 1.0

Potassium binding site 6 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 6 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K333

b:56.7
occ:1.00
 O D:HOH536 2.5 27.5 1.0
O D:TRP255 2.7 20.1 1.0
O D:HOH493 2.9 25.9 1.0
O D:HIS196 3.2 13.9 1.0
O D:HOH494 3.2 24.5 1.0
O D:VAL197 3.3 15.4 1.0
C D:TRP255 3.9 19.6 1.0
C D:VAL197 4.0 16.0 1.0
CA D:VAL197 4.2 14.8 1.0
C D:HIS196 4.2 14.2 1.0
CA D:LYS256 4.3 19.5 1.0
N D:VAL257 4.5 18.5 1.0
N D:LYS256 4.5 18.7 1.0
CD1 D:TRP255 4.6 20.7 1.0
ND1 D:HIS196 4.6 17.4 1.0
N D:VAL197 4.7 14.0 1.0
CG2 D:VAL257 4.7 18.3 1.0
CB D:TRP255 4.9 21.2 1.0
CA D:TRP255 4.9 20.0 1.0
C D:LYS256 4.9 19.2 1.0

Potassium binding site 7 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 7 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K333

b:57.4
occ:1.00
 O E:TRP255 2.6 18.0 1.0
O E:HOH536 2.6 27.4 1.0
O E:HOH493 3.1 24.0 1.0
O E:VAL197 3.1 13.6 1.0
O E:HOH494 3.1 18.4 1.0
O E:HIS196 3.2 12.1 1.0
C E:TRP255 3.7 18.7 1.0
O E:HOH597 3.8 31.1 1.0
C E:VAL197 3.9 13.6 1.0
CA E:VAL197 4.0 13.1 1.0
C E:HIS196 4.1 12.3 1.0
CA E:LYS256 4.2 18.7 1.0
N E:LYS256 4.4 18.1 1.0
N E:VAL257 4.4 19.2 1.0
CD1 E:TRP255 4.5 19.1 1.0
N E:VAL197 4.5 12.2 1.0
CB E:TRP255 4.7 17.9 1.0
CG2 E:VAL257 4.7 21.3 1.0
CA E:TRP255 4.7 18.5 1.0
ND1 E:HIS196 4.7 14.7 1.0
C E:LYS256 4.8 19.4 1.0

Potassium binding site 8 out of 8 in 4udj

Go back to Potassium Binding Sites List in 4udj
Potassium binding site 8 out of 8 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.60 Angstrom in Complex with Beta-D- Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K333

b:64.1
occ:1.00
 O F:HOH536 2.7 24.4 1.0
O F:TRP255 2.7 19.0 1.0
O F:HOH493 2.7 19.0 1.0
O F:VAL197 3.0 17.1 1.0
O F:HIS196 3.1 14.7 1.0
O F:HOH494 3.3 27.1 1.0
C F:VAL197 3.8 17.5 1.0
C F:TRP255 3.8 19.1 1.0
CA F:VAL197 3.9 16.6 1.0
C F:HIS196 4.1 15.4 1.0
CA F:LYS256 4.3 20.6 1.0
N F:VAL197 4.5 15.0 1.0
N F:LYS256 4.5 19.0 1.0
ND1 F:HIS196 4.5 19.0 1.0
N F:VAL257 4.5 19.8 1.0
CD1 F:TRP255 4.7 17.8 1.0
CG2 F:VAL257 4.7 18.4 1.0
CA F:TRP255 4.8 18.4 1.0
CB F:TRP255 4.9 19.2 1.0
C F:LYS256 4.9 20.4 1.0
N F:MET198 5.0 16.4 1.0

Reference:

S.Ladeveze, G.Cioci, P.Roblin, L.Mourey, S.Tranier, G.Potocki-Veronese. Structural Bases For N-Glycan Processing By Mannoside Phosphorylase Acta Crystallogr.,Sect.D V. 71 1 2015.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004715006604
Page generated: Mon Aug 12 12:14:47 2024

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