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Potassium in PDB 4udi: Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)

Protein crystallography data

The structure of Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP), PDB code: 4udi 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) 110.20 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.116, 141.206, 176.245, 90.00, 90.00, 90.00
R / Rfree (%) 15.537 / 18.993

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) (pdb code 4udi). 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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP), PDB code: 4udi:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 4udi

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Potassium binding site 1 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)


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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K333

b:50.8
occ:1.00
 O A:HOH582 2.3 33.8 1.0
O A:HOH493 2.4 28.2 1.0
O A:HOH536 2.5 29.2 1.0
O A:TRP255 2.6 26.3 1.0
O A:HIS196 2.7 23.1 1.0
O A:VAL197 2.7 21.0 1.0
O A:HOH494 3.2 40.7 1.0
C A:VAL197 3.4 21.5 1.0
CA A:VAL197 3.5 21.2 1.0
C A:HIS196 3.7 22.5 1.0
C A:TRP255 3.7 26.8 1.0
O A:HOH546 4.0 45.3 1.0
N A:VAL197 4.0 20.9 1.0
ND1 A:HIS196 4.3 25.1 1.0
CA A:LYS256 4.4 26.1 1.0
N A:LYS256 4.5 25.6 1.0
N A:MET198 4.6 21.3 1.0
N A:VAL257 4.6 24.4 1.0
CB A:TRP255 4.6 28.0 1.0
CD1 A:TRP255 4.7 31.1 1.0
CA A:TRP255 4.7 26.0 1.0
CG2 A:VAL257 4.7 24.1 1.0
CB A:VAL197 4.8 21.0 1.0
CA A:HIS196 4.9 23.5 1.0

Potassium binding site 2 out of 6 in 4udi

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Potassium binding site 2 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)


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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K333

b:48.1
occ:1.00
 O B:HOH536 2.4 30.7 1.0
O B:TRP255 2.5 25.4 1.0
O B:VAL197 2.6 20.2 1.0
O B:HOH493 2.6 25.7 1.0
O B:HIS196 2.8 21.5 1.0
C B:VAL197 3.4 21.1 1.0
O B:HOH494 3.5 35.6 1.0
CA B:VAL197 3.6 20.6 1.0
C B:TRP255 3.7 26.2 1.0
C B:HIS196 3.8 21.0 1.0
N B:VAL197 4.1 20.0 1.0
O B:HOH546 4.3 45.9 1.0
ND1 B:HIS196 4.4 24.0 1.0
N B:VAL257 4.4 25.4 1.0
CA B:LYS256 4.4 25.9 1.0
N B:LYS256 4.5 24.4 1.0
CG2 B:VAL257 4.5 25.7 1.0
N B:MET198 4.5 20.3 1.0
CA B:TRP255 4.7 25.4 1.0
CB B:TRP255 4.8 27.9 1.0
CB B:VAL197 4.9 20.2 1.0
CD1 B:TRP255 4.9 30.0 1.0
C B:LYS256 4.9 25.9 1.0
CG1 B:VAL197 5.0 21.0 1.0

Potassium binding site 3 out of 6 in 4udi

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Potassium binding site 3 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)


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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K333

b:50.9
occ:1.00
 O C:HOH536 2.4 37.2 1.0
O C:TRP255 2.4 30.1 1.0
O C:HOH493 2.6 28.2 1.0
O C:VAL197 2.7 22.9 1.0
O C:HIS196 2.7 24.3 1.0
O C:HOH494 3.4 42.8 1.0
C C:VAL197 3.5 23.6 1.0
CA C:VAL197 3.6 22.2 1.0
C C:TRP255 3.6 29.8 1.0
C C:HIS196 3.7 23.4 1.0
O C:HOH546 3.9 42.8 1.0
N C:VAL197 4.1 21.9 1.0
CA C:LYS256 4.3 28.1 1.0
ND1 C:HIS196 4.3 27.0 1.0
N C:LYS256 4.4 27.5 1.0
N C:VAL257 4.4 26.6 1.0
CA C:TRP255 4.6 27.5 1.0
CG2 C:VAL257 4.6 26.6 1.0
N C:MET198 4.7 23.1 1.0
CB C:TRP255 4.7 28.5 1.0
CD1 C:TRP255 4.8 31.8 1.0
CB C:VAL197 4.9 21.3 1.0
C C:LYS256 4.9 28.2 1.0
CA C:HIS196 5.0 24.0 1.0

Potassium binding site 4 out of 6 in 4udi

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Potassium binding site 4 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)


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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K333

b:60.3
occ:1.00
 O D:HOH536 2.4 36.8 1.0
O D:TRP255 2.5 33.1 1.0
O D:HOH493 2.7 33.9 1.0
O D:VAL197 2.8 28.3 1.0
O D:HIS196 2.9 26.2 1.0
O D:HOH494 3.4 41.5 1.0
C D:VAL197 3.6 27.6 1.0
C D:TRP255 3.7 34.6 1.0
CA D:VAL197 3.7 27.0 1.0
C D:HIS196 3.9 25.9 1.0
O D:HOH546 4.1 50.5 1.0
CA D:LYS256 4.2 35.2 1.0
O D:HOH540 4.2 48.1 1.0
N D:VAL197 4.3 25.6 1.0
N D:VAL257 4.3 32.4 1.0
N D:LYS256 4.4 34.0 1.0
ND1 D:HIS196 4.5 26.9 1.0
CG2 D:VAL257 4.6 32.0 1.0
CA D:TRP255 4.7 34.1 1.0
CB D:TRP255 4.7 34.0 1.0
N D:MET198 4.8 27.6 1.0
C D:LYS256 4.8 35.0 1.0
CD1 D:TRP255 4.8 34.6 1.0

Potassium binding site 5 out of 6 in 4udi

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Potassium binding site 5 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)


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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K333

b:61.8
occ:1.00
 O E:TRP255 2.5 36.5 1.0
O E:HOH536 2.5 37.3 1.0
O E:HOH493 2.6 32.1 1.0
O E:VAL197 2.8 29.2 1.0
O E:HIS196 2.9 29.6 1.0
O E:HOH494 3.4 39.8 1.0
C E:TRP255 3.6 37.4 1.0
C E:VAL197 3.6 29.3 1.0
CA E:VAL197 3.8 27.8 1.0
C E:HIS196 3.9 28.5 1.0
CA E:LYS256 4.2 36.8 1.0
N E:VAL197 4.3 27.4 1.0
N E:LYS256 4.3 36.6 1.0
N E:VAL257 4.4 36.2 1.0
ND1 E:HIS196 4.5 28.9 1.0
CG2 E:VAL257 4.6 36.9 1.0
CA E:TRP255 4.6 35.9 1.0
CB E:TRP255 4.7 37.4 1.0
CD1 E:TRP255 4.7 38.0 1.0
N E:MET198 4.8 29.6 1.0
C E:LYS256 4.9 37.5 1.0

Potassium binding site 6 out of 6 in 4udi

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Potassium binding site 6 out of 6 in the Crystal Structure of B-1,4-Mannopyranosyl-Chitobiose Phosphorylase at 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP)


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 1.85 Angstrom From Unknown Human Gut Bacteria (UHGB_MP) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K333

b:63.4
occ:1.00
 O F:TRP255 2.4 36.2 1.0
O F:HOH536 2.5 37.9 1.0
O F:VAL197 2.7 27.8 1.0
O F:HOH493 2.7 31.2 1.0
O F:HIS196 2.8 27.4 1.0
O F:HOH494 3.4 41.7 1.0
C F:VAL197 3.5 29.1 1.0
C F:TRP255 3.5 36.8 1.0
CA F:VAL197 3.6 27.9 1.0
C F:HIS196 3.8 26.1 1.0
O F:HOH546 4.0 48.4 1.0
N F:VAL197 4.2 24.7 1.0
CA F:LYS256 4.2 36.0 1.0
N F:LYS256 4.3 33.4 1.0
N F:VAL257 4.3 33.5 1.0
ND1 F:HIS196 4.5 29.9 1.0
CA F:TRP255 4.5 34.7 1.0
CG2 F:VAL257 4.6 31.4 1.0
CB F:TRP255 4.6 35.8 1.0
N F:MET198 4.7 28.0 1.0
CD1 F:TRP255 4.7 35.5 1.0
C F:LYS256 4.8 36.3 1.0
CB F:VAL197 4.9 28.1 1.0
CG1 F:VAL197 5.0 29.8 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 12:14:35 2024

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