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Sodium in PDB 6wk0: Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose

Enzymatic activity of Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose

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

Protein crystallography data

The structure of Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose, PDB code: 6wk0 was solved by J.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.43 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.02, 89.35, 144.7, 90, 98.61, 90
R / Rfree (%) 19.7 / 23.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose (pdb code 6wk0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose, PDB code: 6wk0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 6wk0

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Sodium binding site 1 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose


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 and Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:26.6
occ:1.00
 O A:SER301 2.2 24.3 1.0
O A:HOH559 2.3 37.1 1.0
O A:ASP263 2.4 34.6 1.0
O A:HOH690 2.4 26.7 1.0
O A:ALA304 2.4 31.6 1.0
OG A:SER310 2.9 25.0 1.0
C A:SER301 3.2 25.9 1.0
CB A:SER310 3.3 26.7 1.0
C A:ASP263 3.6 35.6 1.0
C A:ALA304 3.7 34.9 1.0
CA A:VAL302 3.8 26.8 1.0
N A:VAL302 3.9 25.7 1.0
O A:THR265 4.0 28.6 1.0
CB A:ASP263 4.2 41.3 1.0
CA A:SER301 4.2 26.2 1.0
C A:VAL302 4.3 28.7 1.0
N A:ALA304 4.3 31.4 1.0
CA A:ASP263 4.4 39.1 1.0
CB A:SER301 4.4 24.7 1.0
OD1 A:ASP263 4.5 42.5 1.0
OG A:SER301 4.5 27.1 1.0
CG A:ASP263 4.5 41.7 1.0
N A:THR264 4.5 34.1 1.0
O A:VAL302 4.6 28.8 1.0
C A:ALA305 4.6 38.0 1.0
CA A:ALA304 4.6 33.3 1.0
N A:THR265 4.6 32.2 1.0
N A:THR307 4.6 35.6 1.0
N A:GLY306 4.6 39.3 1.0
N A:ALA305 4.7 36.5 1.0
CA A:THR264 4.7 32.6 1.0
C A:THR264 4.7 31.4 1.0
CA A:ALA305 4.7 38.5 1.0
N A:ASP263 4.8 39.4 1.0
CA A:SER310 4.8 27.5 1.0
N A:GLN303 4.8 28.4 1.0
O A:ALA305 4.9 35.8 1.0
O A:THR307 5.0 29.2 1.0

Sodium binding site 2 out of 8 in 6wk0

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Sodium binding site 2 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose


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 and Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:29.7
occ:1.00
 O A:HOH601 2.3 23.5 1.0
O A:HOH620 2.4 21.2 1.0
O A:HOH539 2.5 21.5 1.0
O1B A:ACP401 2.5 27.1 1.0
O A:HOH768 2.5 23.5 1.0
O A:HOH566 2.6 41.0 1.0
NZ A:LYS54 3.9 27.0 1.0
CA A:GLY268 3.9 24.1 1.0
PB A:ACP401 4.0 36.1 1.0
O3G A:ACP401 4.1 40.3 1.0
OE2 A:GLU202 4.2 27.6 1.0
ND2 A:ASN199 4.2 25.5 1.0
OD1 A:ASP269 4.3 21.7 1.0
C A:GLY268 4.3 22.0 1.0
O A:HOH695 4.3 39.0 1.0
OD1 A:ASN177 4.4 21.3 1.0
ND2 A:ASN177 4.4 19.0 1.0
O A:HOH537 4.5 29.1 1.0
N A:ASP269 4.5 21.9 1.0
CB A:ALA179 4.5 25.7 1.0
O2B A:ACP401 4.6 28.3 1.0
OE1 A:GLU202 4.6 22.8 1.0
N A:GLY268 4.7 23.6 1.0
O3A A:ACP401 4.7 34.4 1.0
CG A:ASN177 4.8 19.8 1.0
CD A:GLU202 4.8 25.3 1.0
O A:GLY268 4.9 22.3 1.0
CG A:ASP269 5.0 21.9 1.0

Sodium binding site 3 out of 8 in 6wk0

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Sodium binding site 3 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose


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 and Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:26.2
occ:1.00
 O B:SER301 2.4 26.4 1.0
O B:ASP263 2.5 31.7 1.0
O B:HOH647 2.5 29.4 1.0
O B:ALA304 2.5 31.4 1.0
OG B:SER310 2.7 26.0 1.0
O B:GLY306 2.7 33.3 1.0
CB B:SER310 3.2 28.7 1.0
C B:SER301 3.4 27.1 1.0
C B:ASP263 3.7 32.0 1.0
C B:ALA304 3.8 33.5 1.0
O B:THR265 3.9 25.0 1.0
C B:GLY306 3.9 32.3 1.0
CA B:VAL302 4.0 28.3 1.0
N B:VAL302 4.1 26.5 1.0
CB B:ASP263 4.2 35.3 1.0
C B:ALA305 4.4 36.6 1.0
N B:GLY306 4.4 36.1 1.0
CA B:SER301 4.4 25.7 1.0
C B:VAL302 4.4 30.5 1.0
CA B:ASP263 4.4 34.7 1.0
CG B:ASP263 4.5 36.4 1.0
N B:ALA304 4.5 32.1 1.0
CB B:SER301 4.5 25.2 1.0
O B:ALA305 4.5 36.2 1.0
OG B:SER301 4.6 24.7 1.0
OD1 B:ASP263 4.6 36.4 1.0
N B:ALA305 4.7 34.3 1.0
N B:THR264 4.7 30.3 1.0
CA B:ALA304 4.7 33.9 1.0
CA B:SER310 4.7 29.7 1.0
O B:THR307 4.7 30.0 1.0
CA B:GLY306 4.7 35.8 1.0
O B:VAL302 4.7 31.9 1.0
N B:THR265 4.8 27.6 1.0
CA B:THR264 4.8 29.5 1.0
CA B:ALA305 4.8 35.9 1.0
C B:THR264 4.8 28.6 1.0
N B:THR307 4.9 32.2 1.0
N B:ASP263 4.9 35.3 1.0

Sodium binding site 4 out of 8 in 6wk0

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Sodium binding site 4 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose


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 and Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:48.9
occ:1.00
 O B:HOH532 2.1 33.3 1.0
O B:HOH501 2.1 33.8 1.0
O B:HOH583 2.2 30.8 1.0
O B:HOH577 2.5 24.8 1.0
O B:HOH679 2.5 63.0 1.0
O B:HOH576 2.6 23.6 1.0
O1B B:ACP402 3.0 37.8 0.5
O B:HOH502 3.5 27.5 0.5
NZ B:LYS54 3.9 29.9 1.0
OE2 B:GLU202 4.1 30.8 1.0
OD1 B:ASP269 4.1 26.1 1.0
CA B:GLY268 4.1 23.5 1.0
O2B B:ACP402 4.2 31.1 0.5
ND2 B:ASN199 4.2 31.0 1.0
PB B:ACP402 4.3 38.6 0.5
OD1 B:ASN177 4.3 27.0 1.0
O5 B:RIB401 4.3 23.2 1.0
C B:GLY268 4.4 23.7 1.0
O2B B:ACP402 4.4 32.9 0.5
ND2 B:ASN177 4.4 25.2 1.0
O3G B:ACP402 4.4 36.4 0.5
CB B:ALA179 4.4 25.8 1.0
O B:HOH681 4.4 35.5 1.0
N B:ASP269 4.5 24.0 1.0
OE1 B:GLU202 4.5 28.4 1.0
O1B B:ACP402 4.7 33.5 0.5
CD B:GLU202 4.7 29.7 1.0
CG B:ASN177 4.8 26.4 1.0
CG B:ASP269 4.8 24.9 1.0
N B:GLY268 4.8 24.6 1.0
CE B:LYS54 4.9 27.2 1.0
O2A B:ACP402 4.9 30.0 0.5
O B:GLY268 4.9 24.6 1.0
CD B:LYS54 4.9 26.7 1.0

Sodium binding site 5 out of 8 in 6wk0

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Sodium binding site 5 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:30.9
occ:1.00
 O C:SER301 2.5 31.0 1.0
O C:ASP263 2.5 35.8 1.0
O C:GLY306 2.5 38.9 1.0
O C:HOH607 2.5 28.4 1.0
O C:ALA304 2.6 46.1 1.0
OG C:SER310 2.8 33.0 1.0
CB C:SER310 3.3 35.8 1.0
C C:SER301 3.4 30.6 1.0
C C:ASP263 3.7 36.7 1.0
C C:GLY306 3.8 40.9 1.0
O C:THR265 3.8 32.0 1.0
C C:ALA304 3.9 47.2 1.0
CA C:VAL302 4.1 33.0 1.0
N C:VAL302 4.1 31.5 1.0
CB C:ASP263 4.1 42.1 1.0
CG C:ASP263 4.3 41.8 1.0
CA C:SER301 4.3 30.4 1.0
N C:GLY306 4.4 46.0 1.0
CA C:ASP263 4.4 40.5 1.0
C C:ALA305 4.4 48.0 1.0
CB C:SER301 4.5 29.9 1.0
C C:VAL302 4.5 36.7 1.0
OG C:SER301 4.5 30.0 1.0
N C:ALA304 4.6 44.9 1.0
OD2 C:ASP263 4.6 42.6 1.0
CA C:GLY306 4.7 44.0 1.0
OD1 C:ASP263 4.7 39.2 1.0
O C:ALA305 4.7 46.6 1.0
N C:THR264 4.7 36.6 1.0
O C:THR307 4.7 35.8 1.0
O C:VAL302 4.7 37.4 1.0
N C:THR307 4.8 39.3 1.0
N C:ALA305 4.8 49.9 1.0
CA C:ALA304 4.8 45.9 1.0
CA C:THR307 4.8 37.7 1.0
CA C:SER310 4.8 35.5 1.0
CA C:ALA305 4.8 50.3 1.0
N C:THR265 4.8 35.2 1.0
N C:ASP263 4.9 40.6 1.0
CA C:THR264 4.9 34.9 1.0
C C:THR265 5.0 31.5 1.0
C C:THR264 5.0 34.1 1.0

Sodium binding site 6 out of 8 in 6wk0

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Sodium binding site 6 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na404

b:34.8
occ:1.00
 O C:HOH559 2.2 27.4 1.0
O C:HOH524 2.4 31.1 1.0
O C:HOH525 2.5 23.2 1.0
O1B C:ACP402 2.5 38.9 1.0
O C:HOH616 2.6 29.0 1.0
PB C:ACP402 3.9 43.3 1.0
NZ C:LYS54 3.9 32.5 1.0
O C:HOH642 3.9 42.5 1.0
CA C:GLY268 4.0 26.2 1.0
O2G C:ACP402 4.0 45.9 1.0
OE2 C:GLU202 4.1 33.1 1.0
O2B C:ACP402 4.1 37.3 1.0
ND2 C:ASN199 4.2 28.9 1.0
OD1 C:ASP269 4.3 27.6 1.0
OD1 C:ASN177 4.3 22.6 1.0
C C:GLY268 4.3 25.6 1.0
CB C:ALA179 4.4 27.1 1.0
ND2 C:ASN177 4.4 20.8 1.0
OE1 C:GLU202 4.5 29.4 1.0
N C:ASP269 4.5 26.0 1.0
N C:GLY268 4.7 27.4 1.0
O5 C:RIB401 4.7 27.5 1.0
CD C:GLU202 4.7 30.7 1.0
O3A C:ACP402 4.8 35.8 1.0
CE C:LYS54 4.8 31.4 1.0
CG C:ASN177 4.8 22.1 1.0
O D:HOH526 4.9 56.4 1.0
CG C:ASP269 5.0 28.4 1.0
O C:GLY268 5.0 24.7 1.0

Sodium binding site 7 out of 8 in 6wk0

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Sodium binding site 7 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:55.3
occ:1.00
 O D:HOH531 2.3 47.9 1.0
O D:HOH553 2.3 46.8 1.0
O D:SER301 2.4 52.0 1.0
O D:ASP263 2.4 61.6 1.0
O D:ALA304 2.6 57.9 1.0
OG D:SER310 2.8 52.7 1.0
C D:SER301 3.2 49.3 1.0
CB D:SER310 3.3 50.9 1.0
C D:ASP263 3.6 64.5 1.0
O D:THR265 3.7 49.9 1.0
CA D:VAL302 3.9 52.8 1.0
C D:ALA304 3.9 57.6 1.0
N D:VAL302 3.9 50.6 1.0
CA D:SER301 4.2 47.1 1.0
CB D:ASP263 4.2 67.0 1.0
C D:VAL302 4.3 54.9 1.0
OG D:SER301 4.4 47.5 1.0
CB D:SER301 4.4 46.0 1.0
CA D:ASP263 4.4 67.4 1.0
N D:THR307 4.5 54.8 1.0
N D:ALA304 4.5 56.0 1.0
CG D:ASP263 4.5 67.2 1.0
N D:THR264 4.5 63.9 1.0
N D:THR265 4.6 56.8 1.0
C D:THR264 4.6 58.2 1.0
O D:VAL302 4.6 56.2 1.0
OD1 D:ASP263 4.6 68.3 1.0
CA D:THR264 4.7 61.9 1.0
N D:GLY306 4.7 58.7 1.0
C D:ALA305 4.7 59.5 1.0
CA D:ALA304 4.8 56.5 1.0
C D:THR265 4.8 52.0 1.0
N D:ALA305 4.8 60.1 1.0
CA D:SER310 4.8 48.6 1.0
N D:ASP263 4.9 68.0 1.0
CA D:ALA305 4.9 61.0 1.0
CA D:THR307 4.9 52.1 1.0
O D:THR307 4.9 50.2 1.0
N D:GLN303 5.0 55.8 1.0
OD2 D:ASP263 5.0 70.2 1.0

Sodium binding site 8 out of 8 in 6wk0

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Sodium binding site 8 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Human Ribokinase in Complex with Amppcp and Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:54.5
occ:1.00
 O D:HOH575 2.2 37.2 1.0
O D:HOH540 2.2 49.7 1.0
O1B D:ACP401 2.5 66.8 1.0
O D:HOH564 2.6 57.8 1.0
CA D:GLY268 3.9 48.3 1.0
O1G D:ACP401 3.9 79.4 1.0
PB D:ACP401 3.9 75.0 1.0
ND2 D:ASN199 3.9 66.0 1.0
NZ D:LYS54 4.0 49.7 1.0
OE2 D:GLU202 4.2 69.5 1.0
C D:GLY268 4.4 45.8 1.0
OE1 D:GLU202 4.5 71.2 1.0
ND2 D:ASN177 4.5 50.6 1.0
OD1 D:ASN177 4.6 48.0 1.0
O2B D:ACP401 4.6 54.7 1.0
OD1 D:ASP269 4.6 43.9 1.0
N D:GLY268 4.7 49.0 1.0
N D:ASP269 4.7 44.6 1.0
O D:HOH511 4.7 49.5 1.0
O1A D:ACP401 4.7 71.3 1.0
CB D:ALA179 4.7 55.9 1.0
C3B D:ACP401 4.7 75.5 1.0
CD D:GLU202 4.8 72.0 1.0
CG D:ASN199 4.9 68.9 1.0
O D:GLY268 4.9 44.4 1.0
PG D:ACP401 5.0 86.5 1.0
CB D:ASN199 5.0 67.5 1.0

Reference:

J.Park, J.Park. N/A N/A.
Page generated: Tue Oct 8 14:38:38 2024

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