Atomistry » Chlorine » PDB 5ibc-5ilm » 5ifm
Atomistry »
  Chlorine »
    PDB 5ibc-5ilm »
      5ifm »

Chlorine in PDB 5ifm: Human Nono (P54NRB) Homodimer

Protein crystallography data

The structure of Human Nono (P54NRB) Homodimer, PDB code: 5ifm was solved by G.J.Knott, C.S.Bond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.15 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.150, 407.177, 68.961, 90.00, 97.75, 90.00
R / Rfree (%) 19.7 / 23.4

Other elements in 5ifm:

The structure of Human Nono (P54NRB) Homodimer also contains other interesting chemical elements:

Potassium (K) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human Nono (P54NRB) Homodimer (pdb code 5ifm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Human Nono (P54NRB) Homodimer, PDB code: 5ifm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 5ifm

Go back to Chlorine Binding Sites List in 5ifm
Chlorine binding site 1 out of 10 in the Human Nono (P54NRB) Homodimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Nono (P54NRB) Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:48.0
occ:1.00
 NH1 A:ARG140 2.7 51.0 1.0
N E:GLN245 3.5 40.9 1.0
NE2 E:GLN245 3.5 36.8 1.0
CB E:ASN244 3.8 35.5 1.0
CG E:GLN245 3.8 34.3 1.0
CG A:ARG142 4.0 46.2 1.0
CA E:ASN244 4.0 38.1 1.0
CZ A:ARG140 4.0 63.0 1.0
CB E:GLN245 4.1 44.5 1.0
CD E:GLN245 4.2 48.5 1.0
CB A:ARG142 4.2 38.2 1.0
C E:ASN244 4.3 42.8 1.0
CA E:GLN245 4.4 42.8 1.0
NH2 A:ARG140 4.6 54.4 1.0
CD A:ARG142 4.8 42.6 1.0
CD2 A:PHE77 4.8 37.0 1.0
CG E:ASN244 4.9 45.1 1.0
CE2 A:PHE77 5.0 37.8 1.0
NE A:ARG140 5.0 58.1 1.0

Chlorine binding site 2 out of 10 in 5ifm

Go back to Chlorine Binding Sites List in 5ifm
Chlorine binding site 2 out of 10 in the Human Nono (P54NRB) Homodimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Nono (P54NRB) Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:56.6
occ:1.00
 NH1 C:ARG140 3.0 44.5 1.0
NE2 G:GLN245 3.4 30.8 1.0
N G:GLN245 3.6 36.7 1.0
CB G:ASN244 3.7 28.8 1.0
CG C:ARG142 3.9 29.6 1.0
CG G:GLN245 3.9 32.8 1.0
CA G:ASN244 4.0 34.9 1.0
O D:HOH522 4.0 40.1 1.0
CB C:ARG142 4.1 28.1 1.0
CD G:GLN245 4.1 49.5 1.0
CB G:GLN245 4.2 39.3 1.0
C G:ASN244 4.3 38.8 1.0
CZ C:ARG140 4.4 62.9 1.0
CD2 C:PHE77 4.5 37.7 1.0
CA G:GLN245 4.5 37.6 1.0
CE2 C:PHE77 4.7 39.2 1.0
CG G:ASN244 4.9 45.3 1.0
CD C:ARG142 4.9 20.5 1.0

Chlorine binding site 3 out of 10 in 5ifm

Go back to Chlorine Binding Sites List in 5ifm
Chlorine binding site 3 out of 10 in the Human Nono (P54NRB) Homodimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Nono (P54NRB) Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:59.7
occ:1.00
 NH1 G:ARG140 2.8 43.9 1.0
N C:GLN245 3.4 30.7 1.0
CB C:ASN244 3.6 21.5 1.0
NE2 C:GLN245 3.7 26.6 1.0
CA C:ASN244 3.8 30.0 1.0
CG G:ARG142 3.9 24.1 1.0
CG C:GLN245 4.0 39.5 1.0
C C:ASN244 4.1 33.7 1.0
O H:HOH501 4.1 32.9 1.0
CB C:GLN245 4.1 33.5 1.0
CB G:ARG142 4.1 18.3 1.0
CZ G:ARG140 4.1 53.5 1.0
CD2 G:PHE77 4.3 34.5 1.0
CA C:GLN245 4.3 31.6 1.0
CD C:GLN245 4.4 49.8 1.0
CE2 G:PHE77 4.5 38.0 1.0
CD G:ARG140 4.7 47.1 1.0
CG C:ASN244 4.8 34.2 1.0
NE G:ARG140 4.9 49.7 1.0
CD G:ARG142 4.9 31.1 1.0

Chlorine binding site 4 out of 10 in 5ifm

Go back to Chlorine Binding Sites List in 5ifm
Chlorine binding site 4 out of 10 in the Human Nono (P54NRB) Homodimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human Nono (P54NRB) Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:90.6
occ:1.00
 NH1 D:ARG142 2.7 57.0 1.0
CB D:GLU234 3.3 46.0 1.0
O D:HOH527 3.3 34.5 1.0
NH2 D:ARG140 3.3 53.2 1.0
CG D:GLU234 3.6 59.7 1.0
CZ D:ARG142 3.9 58.3 1.0
CG D:PRO237 4.3 42.1 1.0
CZ D:ARG140 4.3 78.7 1.0
O D:GLY235 4.4 37.0 1.0
CD D:PRO237 4.4 38.3 1.0
CA D:GLU234 4.4 44.0 1.0
CD1 D:LEU240 4.5 51.4 1.0
C D:GLU234 4.5 38.8 1.0
NE D:ARG140 4.5 74.5 1.0
O D:GLU234 4.6 35.2 1.0
NH2 D:ARG142 4.7 55.0 1.0
NE D:ARG142 4.8 48.3 1.0
OD2 D:ASP231 4.8 61.1 1.0
CD D:ARG142 4.8 32.1 1.0
N D:GLY235 5.0 32.1 1.0
CD D:GLU234 5.0 71.8 1.0

Chlorine binding site 5 out of 10 in 5ifm

Go back to Chlorine Binding Sites List in 5ifm
Chlorine binding site 5 out of 10 in the Human Nono (P54NRB) Homodimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Human Nono (P54NRB) Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:52.3
occ:1.00
 NH1 E:ARG140 2.7 52.8 1.0
N A:GLN245 3.7 41.8 1.0
NE2 A:GLN245 3.7 24.4 1.0
CB A:ASN244 3.8 42.7 1.0
CG E:ARG142 3.9 30.7 1.0
CZ E:ARG140 4.0 70.8 1.0
CG A:GLN245 4.0 39.6 1.0
CA A:ASN244 4.1 42.4 1.0
CB E:ARG142 4.2 27.3 1.0
CB A:GLN245 4.3 42.9 1.0
CD A:GLN245 4.4 49.4 1.0
C A:ASN244 4.4 47.6 1.0
CA A:GLN245 4.6 40.6 1.0
NH2 E:ARG140 4.6 54.2 1.0
CD2 E:PHE77 4.6 31.5 1.0
CD E:ARG142 4.8 32.8 1.0
CE2 E:PHE77 4.8 34.2 1.0
NE E:ARG140 4.9 68.8 1.0
CG A:ASN244 5.0 52.2 1.0

Chlorine binding site 6 out of 10 in 5ifm

Go back to Chlorine Binding Sites List in 5ifm
Chlorine binding site 6 out of 10 in the Human Nono (P54NRB) Homodimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Human Nono (P54NRB) Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl401

b:64.3
occ:1.00
 NH2 F:ARG140 2.9 80.5 1.0
NE2 I:GLN245 3.6 40.4 1.0
N I:GLN245 3.9 46.3 1.0
CZ F:ARG140 3.9 0.2 1.0
CB I:ASN244 3.9 42.2 1.0
O E:HOH501 4.0 37.2 1.0
CG I:GLN245 4.1 43.7 1.0
NE F:ARG140 4.2 80.7 1.0
CG F:ARG142 4.2 36.5 1.0
CD I:GLN245 4.3 53.0 1.0
CB I:GLN245 4.4 47.6 1.0
CA I:ASN244 4.4 46.4 1.0
CB F:ARG142 4.5 28.6 1.0
C I:ASN244 4.7 50.3 1.0
CA I:GLN245 4.8 46.1 1.0
CD F:ARG142 4.9 48.7 1.0

Chlorine binding site 7 out of 10 in 5ifm

Go back to Chlorine Binding Sites List in 5ifm
Chlorine binding site 7 out of 10 in the Human Nono (P54NRB) Homodimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Human Nono (P54NRB) Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl402

b:79.1
occ:1.00
 NH1 I:ARG140 2.8 96.0 1.0
NE2 F:GLN245 3.5 68.4 1.0
N F:GLN245 3.6 64.5 1.0
CG I:ARG142 3.7 67.9 1.0
CG F:GLN245 3.7 74.5 1.0
CB F:ASN244 3.9 59.0 1.0
CB I:ARG142 4.0 63.6 1.0
CD F:GLN245 4.1 87.1 1.0
CB F:GLN245 4.1 68.5 1.0
CZ I:ARG140 4.1 0.7 1.0
CA F:ASN244 4.2 62.1 1.0
C F:ASN244 4.4 66.3 1.0
CA F:GLN245 4.5 65.4 1.0
CD I:ARG142 4.6 72.4 1.0
CD2 I:PHE77 4.6 68.6 1.0
NH2 I:ARG140 4.8 82.3 1.0
CE2 I:PHE77 4.8 71.3 1.0
NE I:ARG140 5.0 0.5 1.0

Chlorine binding site 8 out of 10 in 5ifm

Go back to Chlorine Binding Sites List in 5ifm
Chlorine binding site 8 out of 10 in the Human Nono (P54NRB) Homodimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Human Nono (P54NRB) Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl401

b:70.5
occ:1.00
 CB G:GLU234 3.2 45.3 1.0
NZ G:LYS126 3.5 60.9 1.0
CE G:LYS126 3.6 44.3 1.0
CG G:GLU234 4.0 51.9 1.0
CA G:GLU234 4.0 45.6 1.0
N G:GLU234 4.0 47.6 1.0
CD G:ARG142 4.0 31.1 1.0
NE G:ARG142 4.0 35.4 1.0
CZ G:ARG142 4.2 45.6 1.0
NH1 G:ARG142 4.3 31.5 1.0
CB G:GLU233 4.6 58.0 1.0
OD1 G:ASP231 4.7 74.4 1.0
C G:GLU233 4.7 55.2 1.0
NH2 G:ARG142 4.9 36.7 1.0
CD G:GLU234 5.0 69.5 1.0
CD G:LYS126 5.0 32.4 1.0

Chlorine binding site 9 out of 10 in 5ifm

Go back to Chlorine Binding Sites List in 5ifm
Chlorine binding site 9 out of 10 in the Human Nono (P54NRB) Homodimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Human Nono (P54NRB) Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl401

b:64.0
occ:1.00
 NH1 K:ARG140 2.9 42.9 1.0
N H:GLN245 3.5 54.8 1.0
NE2 H:GLN245 3.5 53.1 1.0
CG H:GLN245 3.5 57.1 1.0
CB H:ASN244 3.8 49.4 1.0
CG K:ARG142 4.0 48.5 1.0
CB H:GLN245 4.0 57.4 1.0
CD H:GLN245 4.0 74.1 1.0
CA H:ASN244 4.1 51.0 1.0
CZ K:ARG140 4.2 69.4 1.0
CB K:ARG142 4.2 45.2 1.0
C H:ASN244 4.2 56.1 1.0
CA H:GLN245 4.3 55.2 1.0
CD2 K:PHE77 4.7 57.5 1.0
CE2 K:PHE77 4.8 60.7 1.0
CD K:ARG142 4.8 60.8 1.0
NH2 K:ARG140 4.9 58.8 1.0
CG H:ASN244 5.0 78.5 1.0

Chlorine binding site 10 out of 10 in 5ifm

Go back to Chlorine Binding Sites List in 5ifm
Chlorine binding site 10 out of 10 in the Human Nono (P54NRB) Homodimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Human Nono (P54NRB) Homodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl401

b:73.5
occ:1.00
 NH1 L:ARG75 2.9 71.3 1.0
OG L:SER147 3.2 66.4 1.0
CB L:SER147 3.7 56.0 1.0
OE1 L:GLN72 3.8 54.1 1.0
CD L:GLN72 4.1 51.6 1.0
CZ L:ARG75 4.1 84.4 1.0
NE2 L:GLN72 4.2 36.2 1.0
NH2 L:ARG75 4.5 67.0 1.0
NH1 L:ARG115 4.8 43.8 1.0
CG L:GLN72 5.0 44.1 1.0

Reference:

G.J.Knott, S.Panjikar, A.Thorn, A.H.Fox, M.R.Conte, M.Lee, C.S.Bond. A Crystallographic Study of Human Nono (P54(Nrb)): Overcoming Pathological Problems with Purification, Data Collection and Noncrystallographic Symmetry. Acta Crystallogr D Struct V. 72 761 2016BIOL.
PubMed: 27303796
DOI: 10.1107/S2059798316005830
Page generated: Sat Dec 12 11:50:39 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy