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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Fri Jul 26 09:18:05 2024

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