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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

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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: Tue Dec 15 11:08:01 2020

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