Atomistry » Sodium » PDB 5j2d-5jim » 5jen
Atomistry »
  Sodium »
    PDB 5j2d-5jim »
      5jen »

Sodium in PDB 5jen: Crystal Structure of the Anti-Sigma Factor Rsiv Bound to Lysozyme

Enzymatic activity of Crystal Structure of the Anti-Sigma Factor Rsiv Bound to Lysozyme

All present enzymatic activity of Crystal Structure of the Anti-Sigma Factor Rsiv Bound to Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of the Anti-Sigma Factor Rsiv Bound to Lysozyme, PDB code: 5jen was solved by L.Gakhar, K.B.Williams, C.D.Ellermeir, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.17 / 2.30
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.213, 130.326, 136.712, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23.7

Other elements in 5jen:

The structure of Crystal Structure of the Anti-Sigma Factor Rsiv Bound to Lysozyme also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Anti-Sigma Factor Rsiv Bound to Lysozyme (pdb code 5jen). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of the Anti-Sigma Factor Rsiv Bound to Lysozyme, PDB code: 5jen:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5jen

Go back to Sodium Binding Sites List in 5jen
Sodium binding site 1 out of 6 in the Crystal Structure of the Anti-Sigma Factor Rsiv Bound to Lysozyme


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 the Anti-Sigma Factor Rsiv Bound to Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na400

b:33.1
occ:1.00
O A:HOH607 2.2 39.3 1.0
OG1 A:THR239 2.3 24.3 1.0
O A:HOH538 2.4 29.9 1.0
O A:HOH571 2.4 29.5 1.0
O A:HOH584 2.6 27.5 1.0
O A:HOH506 2.8 33.6 1.0
HB A:THR239 3.3 31.7 1.0
CB A:THR239 3.3 26.4 1.0
H A:THR239 3.5 29.7 1.0
O A:HOH512 3.7 32.4 1.0
O A:HOH631 3.7 41.9 1.0
O A:HOH587 3.8 34.5 1.0
OD2 A:ASP253 3.9 27.4 1.0
HG2 A:ARG174 4.1 48.8 1.0
N A:THR239 4.1 24.8 1.0
HG21 A:THR239 4.2 31.1 1.0
OD1 A:ASP253 4.3 30.9 1.0
CA A:THR239 4.3 18.8 1.0
CG2 A:THR239 4.3 25.9 1.0
CG A:ASP253 4.3 29.7 1.0
HA A:THR239 4.6 22.6 1.0
O A:SER173 4.6 24.1 1.0
O A:HOH529 4.7 21.7 1.0
HG23 A:THR239 4.7 31.1 1.0
HE21 A:GLN238 4.7 31.9 1.0
H A:ASP253 4.8 30.5 1.0
HE22 A:GLN238 4.8 31.9 1.0
OE1 A:GLU256 4.8 28.4 1.0
O A:HOH583 4.8 18.5 1.0
O A:SER251 4.8 24.0 1.0
NE2 A:GLN238 4.8 26.6 1.0
HA A:ARG174 4.9 44.0 1.0
CG A:ARG174 5.0 40.7 1.0
HA A:GLN238 5.0 31.9 1.0

Sodium binding site 2 out of 6 in 5jen

Go back to Sodium Binding Sites List in 5jen
Sodium binding site 2 out of 6 in the Crystal Structure of the Anti-Sigma Factor Rsiv Bound to Lysozyme


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 the Anti-Sigma Factor Rsiv Bound to Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:25.9
occ:1.00
O A:HOH504 2.3 23.3 1.0
O A:SER169 2.4 22.6 1.0
OD2 B:ASP52 2.5 37.2 1.0
O B:HOH311 2.5 21.8 1.0
OH A:TYR255 2.5 25.4 1.0
OG A:SER168 2.7 29.7 1.0
HG A:SER168 3.1 35.6 1.0
H A:SER169 3.3 29.9 1.0
CG B:ASP52 3.4 26.1 1.0
C A:SER169 3.5 23.8 1.0
CZ A:TYR255 3.5 26.6 1.0
N A:SER169 3.6 24.9 1.0
HD22 B:ASN44 3.7 32.7 1.0
HE2 A:TYR255 3.7 32.1 1.0
HB3 A:SER168 3.7 33.7 1.0
HB3 B:GLN57 3.8 23.2 1.0
CB A:SER168 3.8 28.1 1.0
OE1 B:GLU35 3.8 29.8 1.0
HB3 A:SER169 3.8 35.7 1.0
CA A:SER169 4.0 28.8 1.0
HA3 A:GLY260 4.0 35.4 1.0
CE2 A:TYR255 4.0 26.8 1.0
OD1 B:ASP52 4.0 25.8 1.0
OE1 A:GLU254 4.2 29.2 1.0
C A:SER168 4.2 32.1 1.0
HB3 B:ASP52 4.3 36.6 1.0
CB B:ASP52 4.4 30.5 1.0
ND2 B:ASN44 4.4 27.3 1.0
CB A:SER169 4.4 29.8 1.0
HB2 B:ASP52 4.4 36.6 1.0
HA A:TYR170 4.5 33.0 1.0
HB2 A:SER168 4.5 33.7 1.0
CA A:SER168 4.5 29.3 1.0
CB B:GLN57 4.5 19.3 1.0
O A:GLY260 4.6 22.6 1.0
CE1 A:TYR255 4.6 25.3 1.0
HD21 B:ASN44 4.6 32.7 1.0
HB2 B:GLN57 4.6 23.2 1.0
HG3 B:GLN57 4.6 28.9 1.0
N A:TYR170 4.6 24.6 1.0
O B:HOH302 4.6 27.5 1.0
OE1 B:GLN57 4.7 25.0 1.0
HE1 A:TYR255 4.7 30.3 1.0
HA A:SER168 4.7 35.1 1.0
C A:GLY260 4.7 23.0 1.0
CA A:GLY260 4.7 29.5 1.0
CD B:GLU35 4.8 26.7 1.0
HD21 B:ASN46 4.8 44.8 1.0
HA A:SER169 4.9 34.6 1.0
HA2 A:GLY260 4.9 35.4 1.0
OE2 B:GLU35 4.9 35.9 1.0
O B:GLN57 5.0 26.9 1.0
CD A:GLU254 5.0 39.1 1.0

Sodium binding site 3 out of 6 in 5jen

Go back to Sodium Binding Sites List in 5jen
Sodium binding site 3 out of 6 in the Crystal Structure of the Anti-Sigma Factor Rsiv Bound to Lysozyme


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 the Anti-Sigma Factor Rsiv Bound to Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na200

b:37.1
occ:1.00
O B:CYS64 2.3 30.7 1.0
OG B:SER72 2.4 34.9 1.0
O B:SER60 2.5 29.7 1.0
O B:HOH318 2.5 39.7 1.0
O B:HOH341 2.5 40.4 1.0
O B:ARG73 2.6 44.9 1.0
HA B:ASN65 2.8 47.5 1.0
HB2 B:SER72 3.1 46.5 1.0
CB B:SER72 3.3 38.8 1.0
C B:CYS64 3.3 30.2 1.0
HB2 B:SER60 3.4 33.3 1.0
C B:SER60 3.6 31.5 1.0
CA B:ASN65 3.7 39.6 1.0
C B:ARG73 3.7 43.3 1.0
H B:CYS64 3.8 38.3 1.0
HB2 B:ASN74 3.8 49.9 1.0
H B:ASP66 3.9 37.7 1.0
HA B:SER60 3.9 33.0 1.0
HB3 B:SER72 3.9 46.5 1.0
N B:ASN65 3.9 32.2 1.0
HB B:THR69 4.0 48.2 1.0
HA B:ASN74 4.0 53.6 1.0
CA B:SER60 4.1 27.5 1.0
HB2 B:ASN65 4.2 48.5 1.0
N B:ARG73 4.2 40.2 1.0
CB B:SER60 4.2 27.7 1.0
C B:SER72 4.2 38.0 1.0
H B:ARG73 4.3 48.2 1.0
N B:CYS64 4.4 31.9 1.0
CA B:SER72 4.4 36.0 1.0
CB B:ASN65 4.5 40.4 1.0
CA B:CYS64 4.5 28.4 1.0
N B:ASP66 4.5 31.4 1.0
CA B:ASN74 4.6 44.7 1.0
CB B:ASN74 4.6 41.5 1.0
N B:ASN74 4.6 41.3 1.0
CA B:ARG73 4.6 39.2 1.0
C B:ASN65 4.7 35.2 1.0
HA B:ARG61 4.7 41.8 1.0
O B:SER72 4.7 45.9 1.0
N B:ARG61 4.7 25.3 1.0
OD1 B:ASN65 4.7 49.1 1.0
HB3 B:SER60 4.7 33.3 1.0
C B:ARG61 4.7 39.1 1.0
O B:ARG61 4.8 36.9 1.0
H B:ASN65 4.8 38.6 1.0
CB B:THR69 4.9 40.2 1.0
H B:TRP63 4.9 44.9 1.0
CL B:CL201 4.9 42.1 1.0
CA B:ARG61 5.0 34.8 1.0
HA B:ARG73 5.0 47.1 1.0

Sodium binding site 4 out of 6 in 5jen

Go back to Sodium Binding Sites List in 5jen
Sodium binding site 4 out of 6 in the Crystal Structure of the Anti-Sigma Factor Rsiv Bound to Lysozyme


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 the Anti-Sigma Factor Rsiv Bound to Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na400

b:37.8
occ:1.00
OG1 C:THR239 2.3 21.1 1.0
O C:HOH545 2.4 28.4 1.0
O C:HOH613 2.4 24.6 1.0
O C:HOH583 2.6 35.9 1.0
O C:HOH615 2.6 41.2 1.0
O C:HOH586 2.6 27.7 1.0
H C:THR239 3.3 31.3 1.0
O C:HOH506 3.3 41.0 1.0
HB C:THR239 3.3 28.2 1.0
CB C:THR239 3.4 23.5 1.0
N C:THR239 4.0 26.1 1.0
OD2 C:ASP253 4.0 23.1 1.0
O C:HOH608 4.1 24.8 1.0
OD1 C:ASP253 4.1 25.6 1.0
CA C:THR239 4.3 21.3 1.0
CG C:ASP253 4.3 23.0 1.0
O C:HOH648 4.3 46.9 1.0
HG21 C:THR239 4.4 24.5 1.0
HE22 C:GLN238 4.4 30.2 1.0
O C:HOH598 4.4 27.9 1.0
HE21 C:GLN238 4.4 30.2 1.0
CG2 C:THR239 4.5 20.4 1.0
NE2 C:GLN238 4.5 25.1 1.0
OE1 C:GLU256 4.6 29.8 1.0
HG2 C:ARG174 4.6 45.5 1.0
HA C:THR239 4.6 25.6 1.0
O C:SER173 4.7 23.6 1.0
O C:SER251 4.7 26.8 1.0
O C:HOH511 4.7 20.7 1.0
H C:ASP253 4.7 29.5 1.0
O C:HOH606 4.8 18.5 1.0
HG23 C:THR239 4.8 24.5 1.0
HA C:GLN238 4.8 29.4 1.0
HA C:PHE252 5.0 26.9 1.0

Sodium binding site 5 out of 6 in 5jen

Go back to Sodium Binding Sites List in 5jen
Sodium binding site 5 out of 6 in the Crystal Structure of the Anti-Sigma Factor Rsiv Bound to Lysozyme


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 the Anti-Sigma Factor Rsiv Bound to Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:22.1
occ:1.00
O C:SER169 2.3 26.7 1.0
OG C:SER168 2.4 25.5 1.0
OH C:TYR255 2.4 17.8 1.0
OD2 D:ASP52 2.5 25.9 1.0
O D:HOH336 2.5 19.8 1.0
O C:HOH507 2.5 18.0 1.0
HG C:SER169 3.1 49.5 1.0
HB3 C:SER168 3.3 34.5 1.0
H C:SER169 3.3 31.2 1.0
CB C:SER168 3.4 28.7 1.0
C C:SER169 3.4 25.1 1.0
CG D:ASP52 3.4 24.5 1.0
CZ C:TYR255 3.5 24.3 1.0
OG C:SER169 3.5 41.2 1.0
N C:SER169 3.5 26.0 1.0
HE2 C:TYR255 3.6 26.8 1.0
HD22 D:ASN44 3.7 30.6 1.0
HB3 D:GLN57 3.8 28.3 1.0
CE2 C:TYR255 3.9 22.3 1.0
OD1 D:ASP52 4.0 26.1 1.0
CA C:SER169 4.0 28.7 1.0
OE1 D:GLU35 4.0 20.2 1.0
HA3 C:GLY260 4.1 27.5 1.0
HB2 C:SER168 4.1 34.5 1.0
C C:SER168 4.1 31.8 1.0
OE1 C:GLU254 4.2 26.4 1.0
CA C:SER168 4.3 29.7 1.0
HB3 D:ASP52 4.3 25.9 1.0
HA C:TYR170 4.4 32.7 1.0
CB D:ASP52 4.4 21.6 1.0
CB C:SER169 4.4 29.9 1.0
ND2 D:ASN44 4.4 25.5 1.0
HB2 D:ASP52 4.5 25.9 1.0
HA C:SER168 4.5 35.6 1.0
N C:TYR170 4.5 24.9 1.0
HD21 D:ASN44 4.5 30.6 1.0
CE1 C:TYR255 4.5 21.6 1.0
O C:GLY260 4.6 19.1 1.0
CB D:GLN57 4.7 23.6 1.0
HE1 C:TYR255 4.7 26.0 1.0
HB2 D:GLN57 4.7 28.3 1.0
CA C:GLY260 4.8 22.9 1.0
O D:HOH305 4.8 34.1 1.0
HG3 D:GLN57 4.8 23.1 1.0
O D:GLN57 4.8 21.1 1.0
HA2 C:GLY260 4.8 27.5 1.0
HA C:SER169 4.9 34.5 1.0
C C:GLY260 4.9 15.4 1.0
OE1 D:GLN57 4.9 20.9 1.0
CA C:TYR170 5.0 27.3 1.0
O C:SER168 5.0 26.8 1.0
CD D:GLU35 5.0 22.6 1.0

Sodium binding site 6 out of 6 in 5jen

Go back to Sodium Binding Sites List in 5jen
Sodium binding site 6 out of 6 in the Crystal Structure of the Anti-Sigma Factor Rsiv Bound to Lysozyme


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 the Anti-Sigma Factor Rsiv Bound to Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na200

b:36.0
occ:1.00
O D:ARG73 2.2 38.2 1.0
O D:CYS64 2.3 32.5 1.0
O D:HOH344 2.4 42.0 1.0
O D:SER60 2.5 29.6 1.0
O D:HOH337 2.5 32.4 1.0
OG D:SER72 2.5 39.1 1.0
HB2 D:SER72 2.6 50.1 1.0
HA D:ASN65 3.0 50.1 1.0
CB D:SER72 3.1 41.8 1.0
C D:ARG73 3.4 47.9 1.0
C D:CYS64 3.4 30.6 1.0
C D:SER60 3.6 36.5 1.0
HB3 D:SER72 3.8 50.1 1.0
HB2 D:SER60 3.8 41.9 1.0
H D:CYS64 3.8 41.7 1.0
N D:ARG73 3.9 39.3 1.0
CA D:ASN65 3.9 41.8 1.0
HB2 D:ASN74 3.9 44.8 1.0
HA D:ASN74 3.9 46.6 1.0
C D:SER72 3.9 48.5 1.0
H D:ARG73 4.0 47.2 1.0
N D:ASN65 4.1 37.8 1.0
HB D:THR69 4.1 45.9 1.0
HA D:SER60 4.1 42.1 1.0
CA D:SER72 4.1 45.4 1.0
H D:ASP66 4.2 42.7 1.0
CA D:ARG73 4.3 40.2 1.0
HA D:ARG61 4.3 40.6 1.0
N D:ASN74 4.3 34.1 1.0
CA D:SER60 4.3 35.0 1.0
N D:CYS64 4.3 34.7 1.0
O D:ARG61 4.4 34.0 1.0
HB2 D:ASN65 4.5 49.7 1.0
CA D:ASN74 4.5 38.8 1.0
C D:ARG61 4.5 35.7 1.0
O D:SER72 4.5 45.2 1.0
CA D:CYS64 4.5 32.7 1.0
CB D:SER60 4.5 34.9 1.0
N D:ARG61 4.6 33.2 1.0
HA D:SER72 4.6 54.4 1.0
CB D:ASN74 4.6 37.3 1.0
CA D:ARG61 4.7 33.8 1.0
HA D:ARG73 4.7 48.2 1.0
CB D:ASN65 4.7 41.4 1.0
OD1 D:ASN65 4.7 43.3 1.0
CL D:CL201 4.8 50.7 1.0
H D:TRP63 4.8 39.1 1.0
N D:TRP62 4.8 25.1 1.0
N D:ASP66 4.8 35.6 1.0
H D:ASN65 4.9 45.4 1.0
C D:ASN65 4.9 36.1 1.0
HG21 D:THR69 5.0 38.9 1.0
N D:TRP63 5.0 32.6 1.0
C D:TRP62 5.0 37.0 1.0
O D:THR69 5.0 47.1 1.0
HA D:CYS64 5.0 39.3 1.0
CB D:THR69 5.0 38.3 1.0

Reference:

J.L.Hastie, K.B.Williams, L.Gakhar, J.C.Houtman, C.D.Ellermeier. The Anti-Sigma Factor Rsiv Is A Receptor For Lysozyme: the Crystal Structure of Rsiv-Lysozyme Complex To Be Published.
Page generated: Mon Oct 7 21:52:55 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy