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Sodium in PDB 5c3z: Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup

Enzymatic activity of Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup

All present enzymatic activity of Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup:
2.7.1.15;

Protein crystallography data

The structure of Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup, PDB code: 5c3z was solved by J.Park, J.Chakrabarti, B.Singh, R.S.Gupta, M.S.Junop, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.557, 72.943, 91.864, 90.00, 114.81, 90.00
R / Rfree (%) 14.9 / 18.8

Other elements in 5c3z:

The structure of Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup (pdb code 5c3z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup, PDB code: 5c3z:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5c3z

Go back to Sodium Binding Sites List in 5c3z
Sodium binding site 1 out of 4 in the Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:31.2
occ:1.00
 O A:HOH501 2.1 25.4 0.5
O A:SER301 2.5 23.9 1.0
O A:ASP263 2.5 28.0 1.0
O A:HOH658 2.5 29.6 1.0
O A:ALA304 2.6 28.0 1.0
OG A:SER310 2.9 27.2 1.0
O A:GLY306 3.0 35.0 0.5
CB A:SER310 3.3 27.9 1.0
C A:SER301 3.5 23.3 1.0
C A:ASP263 3.6 29.5 1.0
C A:ALA304 3.8 32.3 1.0
O A:THR265 3.8 28.2 1.0
CA A:VAL302 4.0 24.1 1.0
CB A:ASP263 4.1 37.8 1.0
N A:VAL302 4.1 24.5 1.0
C A:GLY306 4.2 34.6 0.5
CG A:ASP263 4.4 46.4 1.0
C A:VAL302 4.4 27.8 1.0
CA A:ASP263 4.4 34.8 1.0
CA A:SER301 4.4 25.2 1.0
N A:ALA304 4.5 30.2 1.0
CB A:SER301 4.5 26.2 1.0
N A:THR307 4.5 31.5 0.5
C A:ALA305 4.5 38.6 1.0
O A:VAL302 4.5 27.0 1.0
N A:GLY306 4.6 38.7 0.5
N A:THR264 4.6 28.8 1.0
N A:THR265 4.6 29.1 1.0
OD2 A:ASP263 4.6 57.9 1.0
CA A:ALA304 4.6 32.6 1.0
OG A:SER301 4.7 26.6 1.0
CA A:THR264 4.7 27.7 1.0
C A:THR264 4.7 28.0 1.0
N A:ALA305 4.7 35.0 1.0
CA A:ALA305 4.7 38.0 1.0
N A:GLY306 4.7 38.6 0.5
O A:ALA305 4.8 39.0 1.0
N A:ASP263 4.8 33.6 1.0
C A:THR265 4.8 28.6 1.0
CA A:SER310 4.8 28.0 1.0
OD1 A:ASP263 4.9 49.3 1.0
O A:THR307 4.9 28.6 0.5
O A:THR307 4.9 28.3 0.5
CA A:THR307 4.9 33.4 0.5

Sodium binding site 2 out of 4 in 5c3z

Go back to Sodium Binding Sites List in 5c3z
Sodium binding site 2 out of 4 in the Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:44.9
occ:1.00
 O A:HOH518 2.3 41.3 1.0
O A:HOH535 2.3 35.2 1.0
O A:HOH558 2.3 34.9 1.0
O A:HOH507 2.4 29.1 1.0
O A:HOH673 2.7 45.3 1.0
O A:HOH651 3.7 40.9 1.0
CA A:GLY268 4.0 23.5 1.0
NZ A:LYS54 4.0 32.8 1.0
OE2 A:GLU202 4.0 34.2 1.0
ND2 A:ASN199 4.2 31.8 1.0
OD1 A:ASP269 4.2 26.9 1.0
OE1 A:GLU202 4.3 32.8 1.0
ND2 A:ASN177 4.3 23.9 1.0
C A:GLY268 4.3 22.7 1.0
O A:HOH705 4.4 36.4 1.0
OD1 A:ASN177 4.4 24.5 1.0
O2B A:ACP401 4.5 31.7 1.0
O A:HOH562 4.5 47.5 1.0
N A:ASP269 4.5 21.2 1.0
CB A:ALA179 4.5 25.6 1.0
O1B A:ACP401 4.6 37.2 1.0
CD A:GLU202 4.7 31.6 1.0
O1A A:ACP401 4.7 35.9 1.0
O A:HOH506 4.7 38.6 1.0
CG A:ASN177 4.8 23.8 1.0
N A:GLY268 4.8 23.4 1.0
O A:GLY268 4.9 22.2 1.0
CG A:ASN199 4.9 31.1 1.0
PB A:ACP401 5.0 36.2 1.0
CG A:ASP269 5.0 26.5 1.0

Sodium binding site 3 out of 4 in 5c3z

Go back to Sodium Binding Sites List in 5c3z
Sodium binding site 3 out of 4 in the Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:39.4
occ:1.00
 O B:HOH621 2.1 48.1 1.0
O B:ASP263 2.4 37.5 1.0
O B:SER301 2.4 35.9 1.0
O B:HOH631 2.5 37.7 1.0
O B:ALA304 2.5 39.3 1.0
OG B:SER310 3.1 38.1 1.0
C B:SER301 3.4 36.5 1.0
CB B:SER310 3.5 39.6 1.0
C B:ASP263 3.5 40.7 1.0
O B:THR265 3.7 36.1 1.0
C B:ALA304 3.8 46.6 1.0
CA B:VAL302 3.8 36.8 1.0
CB B:ASP263 4.0 51.3 1.0
N B:VAL302 4.0 35.6 1.0
C B:VAL302 4.2 38.3 1.0
CG B:ASP263 4.3 55.3 1.0
CA B:ASP263 4.3 45.0 1.0
N B:ALA304 4.4 43.3 1.0
O B:VAL302 4.4 38.9 1.0
CA B:SER301 4.4 33.9 1.0
OD2 B:ASP263 4.5 66.3 1.0
N B:THR307 4.5 41.6 1.0
N B:THR264 4.5 39.4 1.0
CB B:SER301 4.6 32.8 1.0
N B:THR265 4.6 36.8 1.0
C B:ALA305 4.6 48.0 1.0
CA B:ALA304 4.6 47.0 1.0
CA B:THR264 4.6 38.4 1.0
C B:THR264 4.7 36.2 1.0
OG B:SER301 4.7 32.6 1.0
N B:ASP263 4.7 47.9 1.0
N B:ALA305 4.7 47.7 1.0
CA B:ALA305 4.7 48.0 1.0
N B:GLY306 4.7 45.7 1.0
C B:THR265 4.8 34.8 1.0
O B:ALA305 4.9 46.4 1.0
N B:GLN303 4.9 40.9 1.0
OD1 B:ASP263 4.9 52.5 1.0
CA B:THR307 5.0 42.0 1.0
CB B:VAL302 5.0 36.6 1.0

Sodium binding site 4 out of 4 in 5c3z

Go back to Sodium Binding Sites List in 5c3z
Sodium binding site 4 out of 4 in the Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:41.1
occ:1.00
 O B:HOH554 2.3 31.0 1.0
O B:HOH521 2.3 35.9 1.0
O B:HOH506 2.4 26.6 1.0
O B:HOH510 2.5 35.0 1.0
O B:HOH637 2.5 45.5 1.0
O B:HOH579 2.5 43.4 1.0
CA B:GLY268 4.0 27.2 1.0
NZ B:LYS54 4.0 31.9 1.0
O B:HOH654 4.2 41.5 1.0
C B:GLY268 4.2 26.9 1.0
OE2 B:GLU202 4.2 37.9 1.0
OD1 B:ASP269 4.2 30.0 1.0
O B:HOH660 4.2 34.9 1.0
ND2 B:ASN177 4.3 27.6 1.0
OD1 B:ASN177 4.3 26.4 1.0
ND2 B:ASN199 4.4 33.3 1.0
O B:HOH667 4.4 56.8 1.0
O B:HOH624 4.4 45.9 1.0
OE1 B:GLU202 4.4 35.4 1.0
CB B:ALA179 4.4 27.2 1.0
N B:ASP269 4.5 26.2 1.0
O2B B:ACP401 4.6 37.4 1.0
O1B B:ACP401 4.6 31.0 1.0
O2A B:ACP401 4.7 36.8 1.0
O B:GLY268 4.7 25.7 1.0
CG B:ASN177 4.8 25.3 1.0
CD B:GLU202 4.8 38.8 1.0
N B:GLY268 4.9 26.6 1.0

Reference:

J.Park, J.Chakrabarti, B.Singh, R.S.Gupta, M.S.Junop. Crystal Structure of Human Ribokinase in Complex with Amppcp in C2 Spacegroup To Be Published.
Page generated: Mon Oct 7 20:12:32 2024

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