Atomistry » Potassium » PDB 4toh-4wol » 4udi
Atomistry »
  Potassium »
    PDB 4toh-4wol »
      4udi »

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

Go back to Potassium Binding Sites List in 4udi
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

Go back to Potassium Binding Sites List in 4udi
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

Go back to Potassium Binding Sites List in 4udi
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

Go back to Potassium Binding Sites List in 4udi
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

Go back to Potassium Binding Sites List in 4udi
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

Go back to Potassium Binding Sites List in 4udi
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy