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Sodium in PDB 5c41: Crystal Structure of Human Ribokinase in Complex with Amppcp in P21 Spacegroup and with 4 Protomers

Enzymatic activity of Crystal Structure of Human Ribokinase in Complex with Amppcp in P21 Spacegroup and with 4 Protomers

All present enzymatic activity of Crystal Structure of Human Ribokinase in Complex with Amppcp in P21 Spacegroup and with 4 Protomers:
2.7.1.15;

Protein crystallography data

The structure of Crystal Structure of Human Ribokinase in Complex with Amppcp in P21 Spacegroup and with 4 Protomers, PDB code: 5c41 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) 44.55 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.950, 89.190, 144.400, 90.00, 98.16, 90.00
R / Rfree (%) 17.2 / 20.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Ribokinase in Complex with Amppcp in P21 Spacegroup and with 4 Protomers (pdb code 5c41). 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 in P21 Spacegroup and with 4 Protomers, PDB code: 5c41:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5c41

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Sodium binding site 1 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp in P21 Spacegroup and with 4 Protomers


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 P21 Spacegroup and with 4 Protomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:18.3
occ:1.00
 O A:HOH579 2.3 24.9 1.0
O A:SER301 2.3 16.6 1.0
O A:HOH629 2.4 16.8 1.0
O A:ASP263 2.4 23.1 1.0
O A:ALA304 2.5 24.0 1.0
OG A:SER310 2.8 18.1 1.0
C A:SER301 3.3 16.6 1.0
CB A:SER310 3.4 19.4 1.0
C A:ASP263 3.6 24.3 1.0
C A:ALA304 3.7 25.7 1.0
CA A:VAL302 3.9 18.9 1.0
N A:VAL302 4.0 16.7 1.0
O A:THR265 4.0 20.3 1.0
CB A:ASP263 4.3 30.3 1.0
CA A:SER301 4.3 15.6 1.0
C A:VAL302 4.3 20.6 1.0
N A:ALA304 4.3 23.3 1.0
CB A:SER301 4.4 15.0 1.0
CA A:ASP263 4.4 28.0 1.0
OG A:SER301 4.4 16.4 1.0
CG A:ASP263 4.5 31.9 1.0
C A:ALA305 4.5 29.0 1.0
N A:THR307 4.5 26.9 1.0
N A:THR264 4.5 23.5 1.0
O A:VAL302 4.6 21.7 1.0
CA A:ALA304 4.6 24.8 1.0
N A:GLY306 4.6 30.8 1.0
N A:THR265 4.6 22.0 1.0
N A:ALA305 4.7 27.9 1.0
CA A:THR264 4.7 22.1 1.0
C A:THR264 4.7 21.1 1.0
CA A:ALA305 4.7 29.5 1.0
N A:ASP263 4.8 27.4 1.0
OD1 A:ASP263 4.8 31.8 1.0
CA A:SER310 4.9 19.1 1.0
O A:ALA305 4.9 28.0 1.0
O A:THR307 4.9 19.4 1.0
OD2 A:ASP263 5.0 37.4 1.0
CA A:THR307 5.0 25.8 1.0
N A:GLN303 5.0 21.0 1.0

Sodium binding site 2 out of 8 in 5c41

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Sodium binding site 2 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp in P21 Spacegroup and with 4 Protomers


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 P21 Spacegroup and with 4 Protomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:21.7
occ:1.00
 O A:HOH569 2.4 12.1 1.0
O A:HOH530 2.4 14.5 1.0
O A:HOH513 2.4 16.9 1.0
O A:HOH501 2.5 7.0 0.5
O A:HOH615 2.5 19.9 1.0
O2B A:ACP401 2.5 17.1 0.5
O A:HOH655 2.6 25.9 1.0
PB A:ACP401 3.9 18.3 0.5
CA A:GLY268 3.9 15.4 1.0
NZ A:LYS54 4.1 19.7 1.0
ND2 A:ASN199 4.1 18.3 1.0
OE2 A:GLU202 4.2 20.5 1.0
O2G A:ACP401 4.2 18.3 0.5
C A:GLY268 4.3 14.4 1.0
O A:HOH734 4.3 29.9 1.0
OD1 A:ASP269 4.3 14.6 1.0
O1B A:ACP401 4.4 19.0 0.5
ND2 A:ASN177 4.4 14.0 1.0
OD1 A:ASN177 4.4 12.7 1.0
O A:HOH522 4.5 24.1 1.0
N A:ASP269 4.5 14.1 1.0
O1B A:ACP401 4.5 17.4 0.5
OE1 A:GLU202 4.5 18.4 1.0
CB A:ALA179 4.5 15.8 1.0
O3A A:ACP401 4.6 17.5 0.5
O2B A:ACP401 4.7 17.8 0.5
N A:GLY268 4.8 15.3 1.0
O1A A:ACP401 4.8 15.4 0.5
CD A:GLU202 4.8 19.3 1.0
O A:GLY268 4.8 13.7 1.0
CG A:ASN177 4.8 13.0 1.0
PB A:ACP401 5.0 19.6 0.5
CG A:ASP269 5.0 14.8 1.0

Sodium binding site 3 out of 8 in 5c41

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Sodium binding site 3 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp in P21 Spacegroup and with 4 Protomers


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 P21 Spacegroup and with 4 Protomers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:17.2
occ:1.00
 O B:SER301 2.4 16.9 1.0
O B:HOH624 2.4 17.6 1.0
O B:ALA304 2.4 22.0 1.0
O B:ASP263 2.5 20.0 1.0
O B:GLY306 2.6 24.7 1.0
OG B:SER310 2.8 18.6 1.0
CB B:SER310 3.3 20.1 1.0
C B:SER301 3.4 17.4 1.0
C B:ALA304 3.6 23.7 1.0
C B:ASP263 3.7 21.8 1.0
C B:GLY306 3.8 26.7 1.0
CA B:VAL302 4.0 18.9 1.0
N B:VAL302 4.1 17.9 1.0
O B:THR265 4.1 18.8 1.0
CB B:ASP263 4.2 24.7 1.0
N B:ALA304 4.3 22.5 1.0
CA B:SER301 4.3 16.7 1.0
C B:VAL302 4.4 20.6 1.0
C B:ALA305 4.4 27.4 1.0
CA B:ASP263 4.4 23.4 1.0
N B:GLY306 4.4 28.0 1.0
CB B:SER301 4.4 16.1 1.0
CG B:ASP263 4.5 25.8 1.0
CA B:ALA304 4.5 23.8 1.0
OG B:SER301 4.6 15.8 1.0
N B:ALA305 4.6 25.1 1.0
O B:VAL302 4.6 20.8 1.0
CA B:ALA305 4.7 26.8 1.0
N B:THR264 4.7 22.0 1.0
O B:ALA305 4.7 28.6 1.0
N B:THR307 4.7 24.7 1.0
N B:ASP263 4.8 23.3 1.0
CA B:GLY306 4.8 27.6 1.0
CA B:SER310 4.8 20.3 1.0
CA B:THR307 4.8 22.7 1.0
O B:THR307 4.8 20.4 1.0
OD1 B:ASP263 4.8 26.2 1.0
CA B:THR264 4.8 21.1 1.0
N B:THR265 4.8 20.6 1.0
C B:THR264 4.9 20.3 1.0
OD2 B:ASP263 4.9 28.0 1.0

Sodium binding site 4 out of 8 in 5c41

Go back to Sodium Binding Sites List in 5c41
Sodium binding site 4 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp in P21 Spacegroup and with 4 Protomers


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 P21 Spacegroup and with 4 Protomers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:23.9
occ:1.00
 O B:HOH542 2.2 21.6 1.0
O B:HOH612 2.3 13.9 1.0
O B:HOH523 2.4 18.9 1.0
O B:HOH536 2.4 17.2 1.0
O B:HOH641 2.5 31.5 1.0
O B:HOH663 2.6 18.7 1.0
CA B:GLY268 3.9 15.4 1.0
O B:HOH543 4.1 28.2 1.0
O B:HOH683 4.2 22.6 1.0
NZ B:LYS54 4.2 18.5 1.0
OE2 B:GLU202 4.2 22.2 1.0
OD1 B:ASP269 4.2 17.6 1.0
C B:GLY268 4.2 15.1 1.0
ND2 B:ASN199 4.2 22.6 1.0
ND2 B:ASN177 4.4 17.6 1.0
O1B B:ACP401 4.4 19.9 1.0
OD1 B:ASN177 4.5 16.4 1.0
N B:ASP269 4.5 15.3 1.0
OE1 B:GLU202 4.5 20.3 1.0
O2B B:ACP401 4.6 24.3 1.0
CB B:ALA179 4.6 17.1 1.0
O B:HOH540 4.6 25.2 1.0
N B:GLY268 4.7 15.9 1.0
O1A B:ACP401 4.7 22.8 1.0
O B:GLY268 4.8 14.4 1.0
CD B:GLU202 4.8 21.9 1.0
CG B:ASN177 4.9 16.3 1.0
CG B:ASP269 4.9 16.7 1.0
PB B:ACP401 4.9 23.6 1.0

Sodium binding site 5 out of 8 in 5c41

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Sodium binding site 5 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp in P21 Spacegroup and with 4 Protomers


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 in P21 Spacegroup and with 4 Protomers within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:23.4
occ:1.00
 O C:HOH502 2.2 14.4 0.5
O C:SER301 2.4 22.1 1.0
O C:ALA304 2.4 34.0 1.0
O C:HOH629 2.5 19.1 1.0
O C:ASP263 2.6 30.1 1.0
OG C:SER310 2.7 24.4 1.0
O C:GLY306 2.9 31.0 0.5
CB C:SER310 3.2 25.6 1.0
C C:SER301 3.4 21.8 1.0
C C:ALA304 3.6 36.4 1.0
C C:ASP263 3.8 31.2 1.0
CA C:VAL302 4.0 23.7 1.0
C C:GLY306 4.0 32.0 0.5
O C:THR265 4.0 24.0 1.0
N C:VAL302 4.1 21.9 1.0
N C:THR307 4.2 33.5 0.5
CB C:ASP263 4.2 35.3 1.0
N C:ALA304 4.3 33.3 1.0
CA C:SER301 4.3 20.5 1.0
C C:VAL302 4.4 26.9 1.0
CG C:ASP263 4.4 35.4 1.0
N C:GLY306 4.4 37.3 0.5
C C:ALA305 4.4 38.8 1.0
CB C:SER301 4.4 19.7 1.0
CA C:THR307 4.5 30.0 0.5
CA C:ASP263 4.5 34.1 1.0
N C:GLY306 4.5 39.3 0.5
CA C:ALA304 4.5 35.7 1.0
N C:ALA305 4.6 38.7 1.0
OG C:SER301 4.6 19.2 1.0
CA C:ALA305 4.6 40.0 1.0
O C:THR307 4.7 27.7 0.5
O C:VAL302 4.7 27.7 1.0
O C:THR307 4.7 26.6 0.5
O C:ALA305 4.7 40.6 1.0
CA C:THR307 4.7 28.0 0.5
CA C:SER310 4.8 25.9 1.0
OD2 C:ASP263 4.8 39.6 1.0
N C:THR264 4.8 30.3 1.0
OD1 C:ASP263 4.8 33.0 1.0
N C:ASP263 4.8 34.3 1.0
CA C:GLY306 4.9 35.5 0.5
N C:THR307 4.9 30.1 0.5
N C:THR265 5.0 28.2 1.0
N C:GLN303 5.0 28.2 1.0

Sodium binding site 6 out of 8 in 5c41

Go back to Sodium Binding Sites List in 5c41
Sodium binding site 6 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp in P21 Spacegroup and with 4 Protomers


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 in P21 Spacegroup and with 4 Protomers within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:22.6
occ:1.00
 O C:HOH520 2.2 24.8 1.0
O C:HOH574 2.3 16.3 1.0
O1B C:ACP401 2.4 22.9 1.0
O C:HOH519 2.4 18.7 1.0
O C:HOH710 2.7 29.1 1.0
O C:HOH685 2.8 39.9 1.0
NZ C:LYS54 3.9 22.9 1.0
PB C:ACP401 3.9 31.2 1.0
CA C:GLY268 4.0 15.9 1.0
O C:HOH617 4.0 35.5 1.0
OE2 C:GLU202 4.1 21.3 1.0
O3G C:ACP401 4.2 34.0 1.0
ND2 C:ASN199 4.3 19.6 1.0
OD1 C:ASP269 4.3 16.7 1.0
C C:GLY268 4.3 15.2 1.0
OD1 C:ASN177 4.3 14.5 1.0
O2B C:ACP401 4.3 25.5 1.0
ND2 C:ASN177 4.3 13.7 1.0
CB C:ALA179 4.4 17.6 1.0
OE1 C:GLU202 4.4 18.9 1.0
N C:ASP269 4.5 15.6 1.0
O C:HOH512 4.6 27.0 1.0
O3A C:ACP401 4.7 25.2 1.0
CD C:GLU202 4.7 19.8 1.0
N C:GLY268 4.7 17.0 1.0
CG C:ASN177 4.8 13.4 1.0
O C:GLY268 4.9 13.7 1.0
C3B C:ACP401 5.0 31.9 1.0

Sodium binding site 7 out of 8 in 5c41

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Sodium binding site 7 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp in P21 Spacegroup and with 4 Protomers


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 in P21 Spacegroup and with 4 Protomers within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:35.3
occ:1.00
 O D:ASP263 2.4 45.5 1.0
O D:HOH594 2.4 34.9 1.0
O D:SER301 2.4 35.8 1.0
O D:ALA304 2.4 42.6 1.0
O D:HOH581 2.5 33.6 1.0
OG D:SER310 2.9 30.8 1.0
C D:SER301 3.3 34.8 1.0
CB D:SER310 3.4 31.4 1.0
C D:ASP263 3.5 48.3 1.0
C D:ALA304 3.6 44.4 1.0
CA D:VAL302 3.8 39.2 1.0
N D:VAL302 4.0 36.1 1.0
O D:THR265 4.0 38.2 1.0
CB D:ASP263 4.1 52.5 1.0
N D:ALA304 4.3 43.4 1.0
C D:VAL302 4.3 41.8 1.0
CA D:SER301 4.3 32.3 1.0
CA D:ASP263 4.3 52.1 1.0
CB D:SER301 4.4 30.8 1.0
CG D:ASP263 4.5 52.7 1.0
O D:VAL302 4.5 44.4 1.0
C D:ALA305 4.5 46.0 1.0
CA D:ALA304 4.5 44.2 1.0
N D:THR264 4.5 48.6 1.0
OG D:SER301 4.5 31.8 1.0
N D:THR307 4.6 42.0 1.0
N D:ALA305 4.6 46.8 1.0
N D:GLY306 4.6 46.6 1.0
CA D:ALA305 4.7 48.0 1.0
N D:THR265 4.7 44.6 1.0
CA D:THR264 4.7 46.6 1.0
N D:ASP263 4.7 52.7 1.0
C D:THR264 4.7 44.5 1.0
OD1 D:ASP263 4.7 52.9 1.0
O D:ALA305 4.8 44.2 1.0
OD2 D:ASP263 4.9 53.6 1.0
CA D:SER310 4.9 30.0 1.0
N D:GLN303 4.9 41.6 1.0

Sodium binding site 8 out of 8 in 5c41

Go back to Sodium Binding Sites List in 5c41
Sodium binding site 8 out of 8 in the Crystal Structure of Human Ribokinase in Complex with Amppcp in P21 Spacegroup and with 4 Protomers


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 in P21 Spacegroup and with 4 Protomers within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na404

b:42.9
occ:1.00
 O D:HOH524 2.1 38.6 1.0
O D:HOH511 2.3 30.7 1.0
O D:HOH552 2.3 41.8 1.0
O D:HOH521 2.4 27.2 1.0
O D:HOH611 2.6 46.6 1.0
O D:HOH577 2.7 38.3 1.0
NZ D:LYS54 3.9 33.5 1.0
OE2 D:GLU202 4.1 47.5 1.0
ND2 D:ASN199 4.1 49.0 1.0
CA D:GLY268 4.2 32.7 1.0
O D:HOH609 4.2 42.7 1.0
O2B D:ACP401 4.3 48.4 1.0
ND2 D:ASN177 4.3 34.7 1.0
OD1 D:ASP269 4.4 31.1 1.0
OD1 D:ASN177 4.4 32.5 1.0
OE1 D:GLU202 4.4 47.0 1.0
CB D:ALA179 4.4 35.7 1.0
O D:HOH510 4.5 34.4 1.0
C D:GLY268 4.5 30.6 1.0
O1B D:ACP401 4.5 42.6 1.0
CD D:GLU202 4.7 48.3 1.0
N D:ASP269 4.7 30.1 1.0
O D:HOH509 4.7 37.4 1.0
CG D:ASN177 4.8 32.9 1.0
O2A D:ACP401 4.9 42.3 1.0
O D:GLY268 5.0 29.4 1.0
PB D:ACP401 5.0 50.1 1.0
N D:GLY268 5.0 33.6 1.0
CG D:ASN199 5.0 50.3 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 P21 Spacegroup and with 4 Protomers To Be Published.
Page generated: Tue Dec 15 10:37:34 2020

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