Potassium in PDB 7xxk: Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp, PDB code: 7xxk was solved by R.J.Zhou, X.C.Ni, J.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.783, 116.992, 127.039, 90, 90, 90
R / Rfree (%) 17.8 / 23.2

Other elements in 7xxk:

The structure of Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 13 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp (pdb code 7xxk). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp, PDB code: 7xxk:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 7xxk

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Potassium binding site 1 out of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:32.0
occ:1.00
 O B:HOH583 3.3 28.0 1.0
N A:SER312 3.4 20.8 1.0
CB A:SER312 3.6 20.8 1.0
N A:ALA311 3.7 21.8 1.0
CB A:SER310 3.8 23.1 1.0
O A:HOH578 3.8 27.3 1.0
OG A:SER310 3.9 24.4 1.0
OG1 B:THR263 3.9 32.3 1.0
CB A:ALA311 4.1 22.2 1.0
CA A:SER312 4.1 20.1 1.0
CA A:ALA311 4.2 22.0 1.0
C A:ALA311 4.3 21.6 1.0
O B:HOH630 4.3 45.4 1.0
CG2 B:THR296 4.3 30.6 1.0
CG2 B:THR263 4.3 30.5 1.0
C A:SER310 4.4 21.9 1.0
CB B:THR263 4.5 30.2 1.0
CA A:SER310 4.6 21.9 1.0
CA B:THR263 4.7 28.0 1.0
O B:ARG262 4.8 26.1 1.0
OG A:SER312 4.8 22.9 1.0

Potassium binding site 2 out of 9 in 7xxk

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Potassium binding site 2 out of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K405

b:29.8
occ:1.00
 O A:HOH545 2.9 33.4 1.0
OE1 A:GLN303 3.0 31.9 1.0
CB A:ASP348 3.6 23.5 1.0
CD A:GLN303 3.7 29.8 1.0
O A:HOH501 3.7 32.4 1.0
CG A:GLN303 3.8 24.6 1.0
CG A:GLN349 3.9 21.1 1.0
N A:GLN349 4.0 20.0 1.0
CB A:ASN345 4.1 23.6 1.0
C A:ASP348 4.1 19.5 1.0
CB A:GLN303 4.2 20.1 1.0
O A:ASN345 4.4 24.5 1.0
CA A:GLN349 4.4 20.6 1.0
O A:ASP348 4.5 18.7 1.0
CG A:ASN345 4.5 24.7 1.0
CA A:ASP348 4.5 21.1 1.0
O A:HOH594 4.6 38.7 1.0
OD2 A:ASP348 4.6 33.5 1.0
CG A:ASP348 4.7 29.2 1.0
OD1 A:ASN345 4.8 25.9 1.0
CB A:GLN349 4.8 21.0 1.0
NE2 A:GLN303 4.8 29.1 1.0
CD A:GLN349 5.0 22.1 1.0
NE2 A:GLN349 5.0 20.0 1.0

Potassium binding site 3 out of 9 in 7xxk

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Potassium binding site 3 out of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K406

b:24.0
occ:1.00
 O A:HOH642 3.3 36.8 1.0
N A:ARG277 3.3 25.6 1.0
CB A:ARG276 3.7 28.0 1.0
CG2 A:THR271 3.8 29.3 1.0
CG A:ARG277 3.8 25.9 1.0
CA A:ARG276 3.8 25.9 1.0
C A:ARG276 4.0 25.9 1.0
CB A:ARG277 4.2 25.6 1.0
CA A:ARG277 4.3 25.8 1.0
CD1 A:ILE292 4.4 23.9 1.0
O A:ARG277 4.4 27.9 1.0
CG2 C:VAL324 4.6 29.0 1.0
CE2 A:PHE363 4.7 44.5 1.0
CB C:VAL324 4.8 28.6 1.0
CG1 C:VAL324 4.9 29.8 1.0
C A:ARG277 4.9 27.4 1.0
CG A:ARG276 4.9 31.7 1.0
CD A:ARG277 5.0 24.9 1.0
CB A:THR271 5.0 28.1 1.0

Potassium binding site 4 out of 9 in 7xxk

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Potassium binding site 4 out of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K407

b:38.6
occ:1.00
 OE1 A:GLU323 2.3 49.0 1.0
N A:VAL324 3.4 23.9 1.0
CD A:GLU323 3.5 44.2 1.0
CA A:GLU323 3.7 26.1 1.0
CB A:GLU323 3.7 29.6 1.0
O A:VAL324 3.8 25.2 1.0
CG A:GLU323 4.0 36.1 1.0
C A:GLU323 4.0 25.7 1.0
CG2 A:VAL324 4.4 24.7 1.0
CA A:VAL324 4.5 23.6 1.0
OE2 A:GLU323 4.5 44.6 1.0
C A:VAL324 4.6 24.1 1.0
O A:HOH523 4.6 33.7 1.0
O A:MET322 4.7 24.9 1.0
N A:GLU323 4.9 25.5 1.0

Potassium binding site 5 out of 9 in 7xxk

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Potassium binding site 5 out of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K401

b:30.9
occ:1.00
 O A:HOH601 2.9 26.0 1.0
N B:SER312 3.3 18.2 1.0
CB B:SER312 3.5 19.1 1.0
O B:HOH582 3.6 26.8 1.0
N B:ALA311 3.7 18.4 1.0
CB B:SER310 3.8 20.9 1.0
OG1 A:THR263 3.8 28.6 1.0
CG2 A:THR263 3.9 27.3 1.0
CB B:ALA311 4.0 16.8 1.0
OG B:SER310 4.0 20.8 1.0
CA B:SER312 4.0 18.4 1.0
CA B:ALA311 4.1 17.6 1.0
C B:ALA311 4.2 18.1 1.0
CG2 A:THR296 4.2 22.4 1.0
C B:SER310 4.3 18.8 1.0
CB A:THR263 4.4 26.9 1.0
CA B:SER310 4.6 20.0 1.0
OG B:SER312 4.7 20.1 1.0
CA A:THR263 4.8 24.7 1.0
CZ2 A:TRP301 4.9 21.3 1.0
O A:HOH645 4.9 51.4 1.0
NE1 A:TRP301 4.9 21.2 1.0

Potassium binding site 6 out of 9 in 7xxk

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Potassium binding site 6 out of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


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 Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K403

b:27.2
occ:1.00
 O D:HOH595 3.2 24.7 1.0
N C:SER312 3.4 17.2 1.0
CB C:SER312 3.6 19.6 1.0
N C:ALA311 3.7 16.9 1.0
CL C:CL408 3.8 48.9 1.0
CB C:SER310 3.8 19.8 1.0
OG1 D:THR263 3.9 24.2 1.0
CG2 D:THR263 4.0 22.3 1.0
OG C:SER310 4.0 20.9 1.0
CB C:ALA311 4.1 16.5 1.0
CA C:SER312 4.1 17.8 1.0
CG2 D:THR296 4.2 23.6 1.0
CA C:ALA311 4.2 16.9 1.0
C C:ALA311 4.2 16.9 1.0
C C:SER310 4.4 17.7 1.0
CB D:THR263 4.4 22.4 1.0
CA C:SER310 4.6 18.5 1.0
O D:HOH640 4.7 43.5 1.0
CA D:THR263 4.7 20.1 1.0
OG C:SER312 4.9 21.4 1.0
O D:ARG262 5.0 19.2 1.0

Potassium binding site 7 out of 9 in 7xxk

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Potassium binding site 7 out of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K401

b:29.6
occ:1.00
 O C:HOH561 3.2 20.5 1.0
N D:SER312 3.2 19.7 1.0
CB D:SER312 3.5 20.8 1.0
N D:ALA311 3.7 16.9 1.0
O D:HOH576 3.7 23.4 1.0
CB D:SER310 3.9 19.0 1.0
CG2 C:THR263 3.9 23.4 1.0
CA D:SER312 4.0 19.6 1.0
OG1 C:THR263 4.0 23.5 1.0
OG D:SER310 4.1 21.0 1.0
CB D:ALA311 4.1 17.4 1.0
C D:ALA311 4.1 19.5 1.0
CA D:ALA311 4.1 17.6 1.0
CG2 C:THR296 4.2 20.2 1.0
C D:SER310 4.4 17.2 1.0
CB C:THR263 4.5 22.6 1.0
CA D:SER310 4.6 17.5 1.0
O C:HOH609 4.6 36.0 1.0
OG D:SER312 4.8 22.0 1.0
CZ2 C:TRP301 4.8 18.6 1.0
CA C:THR263 4.8 21.1 1.0
NE1 C:TRP301 4.9 18.9 1.0

Potassium binding site 8 out of 9 in 7xxk

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Potassium binding site 8 out of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K402

b:30.8
occ:1.00
 O D:HOH603 3.5 20.8 1.0
NE2 D:GLN303 3.5 22.7 1.0
O D:HOH630 3.6 58.2 1.0
CG D:GLN303 4.0 21.1 1.0
CD D:GLN303 4.3 23.2 1.0
O D:HOH551 4.3 44.4 1.0
O D:HOH561 4.4 30.2 1.0
ND2 D:ASN345 4.6 31.6 1.0

Potassium binding site 9 out of 9 in 7xxk

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Potassium binding site 9 out of 9 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K402

b:28.8
occ:1.00
 O E:HOH569 3.3 24.6 1.0
N F:SER312 3.4 20.2 1.0
CB F:SER312 3.6 21.4 1.0
O F:HOH551 3.6 32.5 1.0
OG1 E:THR263 3.7 29.0 1.0
N F:ALA311 3.7 21.0 1.0
CB F:SER310 3.9 23.7 1.0
CA F:SER312 4.1 20.6 1.0
CB F:ALA311 4.1 20.4 1.0
OG F:SER310 4.1 25.6 1.0
O F:HOH602 4.1 45.6 1.0
CG2 E:THR296 4.2 25.4 1.0
CA F:ALA311 4.2 20.6 1.0
CG2 E:THR263 4.2 28.1 1.0
C F:ALA311 4.3 20.5 1.0
CB E:THR263 4.4 27.5 1.0
C F:SER310 4.4 21.4 1.0
CA F:SER310 4.7 22.4 1.0
CA E:THR263 4.7 25.8 1.0
O E:HOH627 4.8 55.0 1.0
OG F:SER312 4.8 22.7 1.0
O E:HOH621 4.9 37.1 1.0
O E:ARG262 5.0 24.3 1.0

Reference:

R.J.Zhou, X.C.Ni, J.Lei. Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp To Be Published.
Page generated: Wed Apr 5 10:27:34 2023

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