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Potassium in PDB 4udk: Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, Beta-D-Mannopyranose and Inorganic Phosphate

Protein crystallography data

The structure of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, Beta-D-Mannopyranose and Inorganic Phosphate, PDB code: 4udk 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) 108.17 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.737, 140.886, 168.831, 90.00, 90.00, 90.00
R / Rfree (%) 15.823 / 19.22

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, Beta-D-Mannopyranose and Inorganic Phosphate (pdb code 4udk). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, Beta-D-Mannopyranose and Inorganic Phosphate, PDB code: 4udk:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 4udk

Go back to Potassium Binding Sites List in 4udk
Potassium binding site 1 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, 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 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, Beta-D-Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K333

b:56.7
occ:1.00
 O A:HOH493 2.6 25.0 1.0
O A:TRP255 2.7 18.7 1.0
O A:HOH536 2.8 24.2 1.0
O A:VAL197 3.0 14.7 1.0
O A:HIS196 3.0 14.3 1.0
O A:HOH494 3.1 28.6 1.0
O A:HOH546 3.5 27.2 1.0
C A:VAL197 3.8 15.9 1.0
C A:TRP255 3.9 18.5 1.0
CA A:VAL197 4.0 14.9 1.0
C A:HIS196 4.0 14.1 1.0
N A:VAL197 4.4 14.3 1.0
ND1 A:HIS196 4.4 15.4 1.0
CA A:LYS256 4.5 17.1 1.0
CD1 A:TRP255 4.6 22.4 1.0
N A:LYS256 4.6 17.1 1.0
CG2 A:VAL257 4.7 17.6 1.0
N A:VAL257 4.7 16.4 1.0
CB A:TRP255 4.8 19.5 1.0
CA A:TRP255 4.9 17.0 1.0
N A:MET198 4.9 16.3 1.0

Potassium binding site 2 out of 6 in 4udk

Go back to Potassium Binding Sites List in 4udk
Potassium binding site 2 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, 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 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, Beta-D-Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K333

b:58.3
occ:1.00
 O B:TRP255 2.7 17.6 1.0
O B:HOH536 2.7 29.5 1.0
O B:HOH493 2.7 26.4 1.0
O B:VAL197 2.8 14.7 1.0
O B:HIS196 2.9 14.1 1.0
O B:HOH494 3.2 27.3 1.0
C B:VAL197 3.5 16.0 1.0
CA B:VAL197 3.6 15.3 1.0
C B:TRP255 3.8 18.0 1.0
C B:HIS196 3.8 14.9 1.0
O B:HOH546 3.9 35.3 1.0
N B:VAL197 4.2 14.3 1.0
CA B:LYS256 4.4 18.6 1.0
ND1 B:HIS196 4.5 16.8 1.0
N B:VAL257 4.5 19.2 1.0
CG2 B:VAL257 4.5 20.8 1.0
N B:LYS256 4.6 17.7 1.0
N B:MET198 4.7 15.3 1.0
CA B:TRP255 4.8 18.0 1.0
CB B:TRP255 4.8 19.6 1.0
CD1 B:TRP255 4.9 21.3 1.0
CB B:VAL197 4.9 14.1 1.0
C B:LYS256 5.0 19.7 1.0

Potassium binding site 3 out of 6 in 4udk

Go back to Potassium Binding Sites List in 4udk
Potassium binding site 3 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, 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 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, Beta-D-Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K333

b:54.3
occ:1.00
 O C:TRP255 2.7 18.4 1.0
O C:HOH536 2.7 25.1 1.0
O C:HOH493 2.9 22.4 1.0
O C:VAL197 3.0 14.6 1.0
O C:HIS196 3.0 13.5 1.0
O C:HOH494 3.1 29.2 1.0
C C:VAL197 3.7 14.4 1.0
O C:HOH546 3.8 32.5 1.0
C C:TRP255 3.8 17.5 1.0
CA C:VAL197 3.8 13.2 1.0
C C:HIS196 4.0 13.1 1.0
CA C:LYS256 4.3 17.4 1.0
N C:VAL197 4.4 12.2 1.0
N C:VAL257 4.5 17.6 1.0
N C:LYS256 4.5 16.7 1.0
ND1 C:HIS196 4.6 15.3 1.0
CG2 C:VAL257 4.7 18.2 1.0
CD1 C:TRP255 4.8 17.2 1.0
CA C:TRP255 4.9 16.4 1.0
CB C:TRP255 4.9 17.5 1.0
C C:LYS256 4.9 16.8 1.0
N C:MET198 4.9 13.8 1.0

Potassium binding site 4 out of 6 in 4udk

Go back to Potassium Binding Sites List in 4udk
Potassium binding site 4 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, 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 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, Beta-D-Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K333

b:59.2
occ:1.00
 O D:HOH536 2.6 30.3 1.0
O D:TRP255 2.7 20.6 1.0
O D:HOH493 2.9 28.1 1.0
O D:VAL197 3.1 17.3 1.0
O D:HOH494 3.2 25.7 1.0
O D:HIS196 3.2 16.0 1.0
O D:HOH546 3.7 35.8 1.0
C D:TRP255 3.8 20.7 1.0
C D:VAL197 3.9 16.9 1.0
CA D:VAL197 4.1 15.9 1.0
C D:HIS196 4.2 15.4 1.0
CA D:LYS256 4.3 21.0 1.0
N D:LYS256 4.5 20.1 1.0
N D:VAL257 4.5 21.4 1.0
N D:VAL197 4.6 14.9 1.0
ND1 D:HIS196 4.6 18.9 1.0
CD1 D:TRP255 4.7 22.5 1.0
CG2 D:VAL257 4.7 20.7 1.0
CA D:TRP255 4.9 21.7 1.0
CB D:TRP255 4.9 21.8 1.0
C D:LYS256 4.9 20.9 1.0

Potassium binding site 5 out of 6 in 4udk

Go back to Potassium Binding Sites List in 4udk
Potassium binding site 5 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, 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 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, Beta-D-Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K333

b:49.7
occ:1.00
 O E:TRP255 2.6 19.6 1.0
O E:HOH536 2.7 24.3 1.0
O E:HOH493 2.9 25.7 1.0
O E:VAL197 2.9 16.2 1.0
O E:HIS196 3.0 14.7 1.0
O E:HOH494 3.2 24.1 1.0
O E:HOH619 3.6 32.3 1.0
C E:TRP255 3.7 19.5 1.0
C E:VAL197 3.8 16.2 1.0
CA E:VAL197 3.9 15.6 1.0
C E:HIS196 4.0 14.4 1.0
CA E:LYS256 4.3 19.9 1.0
N E:VAL197 4.4 14.9 1.0
N E:LYS256 4.4 18.8 1.0
N E:VAL257 4.5 19.6 1.0
ND1 E:HIS196 4.6 16.0 1.0
CD1 E:TRP255 4.6 20.2 1.0
CG2 E:VAL257 4.7 20.0 1.0
CA E:TRP255 4.7 19.1 1.0
CB E:TRP255 4.7 18.9 1.0
C E:LYS256 5.0 20.7 1.0
N E:MET198 5.0 15.5 1.0

Potassium binding site 6 out of 6 in 4udk

Go back to Potassium Binding Sites List in 4udk
Potassium binding site 6 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, 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 1.76 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) in Complex with N-Acetyl-D-Glucosamine, Beta-D-Mannopyranose and Inorganic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K333

b:62.4
occ:1.00
 O F:TRP255 2.7 21.0 1.0
O F:HOH536 2.7 27.4 1.0
O F:HOH493 2.8 27.8 1.0
O F:VAL197 2.9 17.2 1.0
O F:HIS196 3.1 17.3 1.0
O F:HOH494 3.3 30.3 1.0
C F:VAL197 3.7 17.4 1.0
O F:HOH546 3.7 38.0 1.0
C F:TRP255 3.9 20.9 1.0
CA F:VAL197 3.9 17.5 1.0
C F:HIS196 4.0 17.1 1.0
CA F:LYS256 4.4 22.8 1.0
N F:VAL197 4.4 16.1 1.0
N F:VAL257 4.5 21.6 1.0
ND1 F:HIS196 4.6 19.4 1.0
CG2 F:VAL257 4.6 22.9 1.0
N F:LYS256 4.6 20.3 1.0
CD1 F:TRP255 4.7 20.6 1.0
CB F:TRP255 4.8 21.0 1.0
CA F:TRP255 4.8 20.2 1.0
N F:MET198 4.9 17.9 1.0
C F:LYS256 5.0 22.4 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 12:15:05 2024

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