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Chlorine 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
Potassium (K) 9 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 13 binding sites of Chlorine where determined in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp, PDB code: 7xxk:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 13 in 7xxk

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Chlorine binding site 1 out of 13 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl402

b:26.0
occ:1.00
 NE2 B:GLN303 3.3 35.0 1.0
CG B:GLN303 3.5 28.9 1.0
O B:LYS299 3.6 28.4 1.0
CD B:GLN303 3.9 32.8 1.0
CA B:HIS300 3.9 28.3 1.0
CD B:PRO302 4.0 27.7 1.0
CG B:PRO302 4.2 29.5 1.0
CB B:PRO302 4.2 28.9 1.0
ND1 B:HIS300 4.3 35.6 1.0
N B:GLN303 4.4 25.4 1.0
C B:HIS300 4.4 27.9 1.0
O B:HOH609 4.5 38.2 1.0
C B:LYS299 4.5 28.5 1.0
CB B:HIS300 4.6 30.4 1.0
CB B:GLN303 4.6 26.1 1.0
O B:HIS300 4.7 28.1 1.0
N B:PRO302 4.7 28.0 1.0
N B:HIS300 4.7 27.8 1.0
CG B:HIS300 4.9 34.0 1.0
CA B:PRO302 5.0 27.6 1.0

Chlorine binding site 2 out of 13 in 7xxk

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Chlorine binding site 2 out of 13 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl403

b:26.3
occ:1.00
 CE B:LYS355 3.2 37.2 1.0
NZ B:LYS355 3.4 40.4 1.0
CD B:LYS355 3.9 32.6 1.0
O B:HOH556 4.0 37.9 1.0
CG B:LYS355 4.7 28.6 1.0

Chlorine binding site 3 out of 13 in 7xxk

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Chlorine binding site 3 out of 13 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl404

b:41.4
occ:1.00
 N B:THR263 3.4 26.9 1.0
CA B:ARG262 3.6 26.3 1.0
CB B:ARG262 3.8 27.8 1.0
CG B:ARG262 3.9 29.9 1.0
O B:THR263 3.9 28.1 1.0
CE2 B:TYR268 3.9 37.0 1.0
CD2 B:TYR268 4.0 36.6 1.0
C B:ARG262 4.1 26.6 1.0
CA B:THR263 4.4 28.0 1.0
CB B:THR263 4.5 30.2 1.0
C B:THR263 4.6 28.3 1.0
O B:HOH622 4.6 48.1 1.0
O B:HOH607 4.8 46.1 1.0
N B:ARG262 4.8 25.6 1.0
OG1 B:THR263 4.9 32.3 1.0
CD B:ARG262 4.9 31.2 1.0
O B:LYS261 5.0 25.7 1.0

Chlorine binding site 4 out of 13 in 7xxk

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Chlorine binding site 4 out of 13 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
C:Cl404

b:28.7
occ:1.00
 O C:HOH617 2.9 50.2 1.0
N C:THR263 3.4 20.5 1.0
O C:HOH504 3.6 35.9 1.0
CA C:ARG262 3.6 20.2 1.0
CB C:ARG262 3.9 20.0 1.0
CE2 C:TYR268 3.9 21.3 1.0
CD2 C:TYR268 3.9 20.4 1.0
O C:THR263 4.0 21.1 1.0
CD C:LYS257 4.0 50.3 1.0
CG C:ARG262 4.1 21.1 1.0
C C:ARG262 4.1 20.7 1.0
CA C:THR263 4.5 21.1 1.0
C C:THR263 4.6 21.0 1.0
CB C:THR263 4.6 22.6 1.0
O C:HOH629 4.7 55.2 1.0
N C:ARG262 4.8 20.7 1.0
O C:LYS261 4.8 21.9 1.0
CE C:LYS257 4.9 54.4 1.0
OG1 C:THR263 4.9 23.5 1.0
CB C:LYS257 5.0 39.8 1.0

Chlorine binding site 5 out of 13 in 7xxk

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Chlorine binding site 5 out of 13 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
C:Cl405

b:52.8
occ:1.00
 ND2 C:ASN269 3.3 24.6 1.0
OE1 C:GLN272 3.5 41.6 1.0
OD1 C:ASN269 3.9 23.2 1.0
CG C:GLN272 3.9 30.0 1.0
O C:HOH545 4.0 27.7 1.0
CG C:ASN269 4.0 23.3 1.0
CD C:GLN272 4.1 38.1 1.0
CB C:THR271 4.4 21.0 1.0
CG2 C:THR271 4.4 21.2 1.0
OG1 C:THR271 5.0 22.6 1.0

Chlorine binding site 6 out of 13 in 7xxk

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Chlorine binding site 6 out of 13 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl406

b:50.6
occ:1.00
 NH2 C:ARG262 3.4 26.5 1.0
NH1 C:ARG262 3.7 25.2 1.0
NH2 C:ARG259 3.9 39.2 1.0
O C:HOH534 4.0 44.9 1.0
CZ C:ARG262 4.1 26.1 1.0
O C:HOH522 4.1 39.8 1.0
CZ C:ARG259 4.7 38.2 1.0

Chlorine binding site 7 out of 13 in 7xxk

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Chlorine binding site 7 out of 13 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
C:Cl407

b:54.6
occ:1.00
 N C:ARG276 3.4 22.1 1.0
O C:HOH547 3.4 28.8 1.0
O F:HOH594 3.6 62.5 1.0
CA C:GLY275 3.8 21.3 1.0
O F:HOH589 4.0 42.3 1.0
CD F:ARG293 4.1 40.8 1.0
C C:GLY275 4.1 21.6 1.0
O C:HOH508 4.2 29.1 1.0
CB C:ARG276 4.2 26.1 1.0
O C:HOH585 4.3 50.7 1.0
CA C:ARG276 4.4 23.7 1.0
CG C:ARG276 4.6 31.8 1.0
O F:HOH583 4.8 29.8 1.0
CG F:ARG293 4.8 37.1 1.0
O C:ARG276 5.0 24.5 1.0

Chlorine binding site 8 out of 13 in 7xxk

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Chlorine binding site 8 out of 13 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
C:Cl408

b:48.9
occ:1.00
 N C:ALA311 3.0 16.9 1.0
O D:HOH612 3.1 40.9 1.0
CA C:SER310 3.7 18.5 1.0
C C:SER310 3.8 17.7 1.0
CB C:ALA311 3.8 16.5 1.0
K C:K403 3.8 27.2 1.0
CA C:ALA311 4.0 16.9 1.0
CB C:SER310 4.0 19.8 1.0
O C:HOH621 4.1 60.8 1.0
O C:HOH631 4.2 47.7 1.0
O C:HOH570 4.5 50.6 1.0
O C:HOH611 4.7 35.5 1.0
O D:HOH595 4.7 24.7 1.0
O C:SER310 5.0 18.9 1.0

Chlorine binding site 9 out of 13 in 7xxk

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Chlorine binding site 9 out of 13 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
D:Cl403

b:41.0
occ:1.00
 NZ D:LYS256 3.1 54.7 1.0
N D:THR263 3.3 19.3 1.0
O D:HOH598 3.6 33.9 1.0
CA D:ARG262 3.6 19.7 1.0
O D:THR263 3.9 19.0 1.0
CB D:ARG262 3.9 20.3 1.0
C D:ARG262 4.0 19.8 1.0
CE2 D:TYR268 4.1 24.9 1.0
CG D:ARG262 4.2 21.0 1.0
CE D:LYS256 4.3 53.5 1.0
CD2 D:TYR268 4.3 24.0 1.0
CA D:THR263 4.3 20.1 1.0
CB D:THR263 4.4 22.4 1.0
C D:THR263 4.5 19.7 1.0
CB D:LYS257 4.5 41.0 1.0
O D:LYS261 4.7 19.8 1.0
N D:ARG262 4.8 19.2 1.0
OG1 D:THR263 4.8 24.2 1.0
CG D:LYS257 4.9 47.3 1.0

Chlorine binding site 10 out of 13 in 7xxk

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Chlorine binding site 10 out of 13 in the Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Sars-Cov-2 N-Ctd in Complex with Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:44.2
occ:1.00
 O E:HOH607 2.9 44.7 1.0
N E:THR263 3.2 24.9 1.0
CA E:ARG262 3.5 24.3 1.0
CE E:LYS256 3.6 59.7 1.0
CD E:LYS256 3.8 56.3 1.0
C E:ARG262 3.9 24.6 1.0
O E:THR263 3.9 26.9 1.0
CB E:ARG262 4.0 25.1 1.0
CD E:LYS257 4.1 54.4 1.0
CE E:LYS257 4.1 58.9 1.0
CA E:THR263 4.1 25.8 1.0
CG E:LYS257 4.2 48.9 1.0
CG E:ARG262 4.2 27.2 1.0
CB E:THR263 4.2 27.5 1.0
CE2 E:TYR268 4.4 30.8 1.0
C E:THR263 4.4 26.3 1.0
O E:LYS261 4.5 24.3 1.0
CD2 E:TYR268 4.5 30.1 1.0
NZ E:LYS257 4.5 61.5 1.0
CB E:LYS257 4.6 44.4 1.0
N E:ARG262 4.7 23.9 1.0
OG1 E:THR263 4.7 29.0 1.0
O E:HOH615 4.8 57.7 1.0
NZ E:LYS256 5.0 62.0 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: Tue Jul 30 05:53:06 2024

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