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Chlorine in PDB 4nx4: Re-Refinement of Cap-1 Hiv-Ca Complex

Protein crystallography data

The structure of Re-Refinement of Cap-1 Hiv-Ca Complex, PDB code: 4nx4 was solved by P.T.Lang, J.M.Holton, J.S.Fraser, T.Alber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.15 / 1.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 42.187, 62.777, 106.286, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 19.1

Other elements in 4nx4:

The structure of Re-Refinement of Cap-1 Hiv-Ca Complex also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Re-Refinement of Cap-1 Hiv-Ca Complex (pdb code 4nx4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Re-Refinement of Cap-1 Hiv-Ca Complex, PDB code: 4nx4:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4nx4

Go back to Chlorine Binding Sites List in 4nx4
Chlorine binding site 1 out of 3 in the Re-Refinement of Cap-1 Hiv-Ca Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Re-Refinement of Cap-1 Hiv-Ca Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:23.0
occ:0.57
H C:LEU111 2.3 20.2 1.0
HE22 C:GLN50 2.4 34.6 1.0
O C:HOH363 3.0 51.5 1.0
HA C:THR110 3.1 20.3 1.0
N C:LEU111 3.1 16.8 1.0
NE2 C:GLN50 3.2 28.8 1.0
HB2 C:LEU111 3.3 22.5 1.0
HB3 C:LEU111 3.5 22.5 1.0
HB C:THR110 3.5 23.1 1.0
O C:HOH382 3.5 27.8 1.0
HE21 C:GLN50 3.6 34.6 1.0
CB C:LEU111 3.8 18.8 1.0
CA C:THR110 3.8 16.9 1.0
C C:THR110 3.9 15.5 1.0
CA C:LEU111 4.0 16.6 1.0
CB C:THR110 4.1 19.2 1.0
CD C:GLN50 4.2 26.9 1.0
HG22 C:THR110 4.3 24.9 1.0
OE1 C:GLN50 4.3 30.6 1.0
HA C:LEU111 4.5 20.0 1.0
H C:GLN112 4.6 21.7 1.0
CG2 C:THR110 4.8 20.8 1.0
O C:SER109 4.9 17.8 1.0

Chlorine binding site 2 out of 3 in 4nx4

Go back to Chlorine Binding Sites List in 4nx4
Chlorine binding site 2 out of 3 in the Re-Refinement of Cap-1 Hiv-Ca Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Re-Refinement of Cap-1 Hiv-Ca Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl204

b:61.3
occ:0.42
CL1 C:JPR204 0.0 61.3 0.4
C4 C:JPR204 1.7 61.0 0.4
CL1 C:JPR204 1.8 59.6 0.5
H11 C:JPR204 2.0 73.3 0.5
C4 C:JPR204 2.2 60.3 0.5
C2 C:JPR204 2.5 60.7 0.5
C1 C:JPR204 2.6 61.1 0.5
C6 C:JPR204 2.6 61.1 0.4
H6 C:JPR204 2.7 73.3 0.4
C2 C:JPR204 2.8 60.9 0.4
H13A C:JPR204 2.8 73.3 0.5
H12 C:JPR204 2.9 73.5 0.4
C1 C:JPR204 3.2 61.3 0.4
H11 C:JPR204 3.2 73.5 0.4
C6 C:JPR204 3.2 60.9 0.5
HD21 C:LEU138 3.3 27.1 1.0
HG21 C:VAL59 3.4 36.4 1.0
H12 C:JPR204 3.5 73.3 0.5
HD22 C:LEU69 3.5 30.8 1.0
H6 C:JPR204 3.6 73.1 0.5
HG23 C:VAL59 3.6 36.4 1.0
C3 C:JPR204 3.7 60.9 0.5
HD23 C:LEU138 3.8 27.1 1.0
HZ2 C:TRP23 3.8 25.8 1.0
CD2 C:LEU138 3.8 22.6 1.0
HD22 C:LEU138 3.8 27.1 1.0
HD23 C:LEU69 3.9 30.8 1.0
CG2 C:VAL59 3.9 30.4 1.0
C7 C:JPR204 4.0 61.3 0.4
C3 C:JPR204 4.1 60.9 0.4
HE2 C:MET66 4.1 50.4 1.0
CD2 C:LEU69 4.1 25.7 1.0
H13A C:JPR204 4.1 73.5 0.4
HE1 C:MET66 4.2 50.4 1.0
HD22 C:LEU56 4.2 29.2 1.0
C7 C:JPR204 4.2 61.2 0.5
H3 C:JPR204 4.3 73.1 0.5
HD21 C:LEU69 4.4 30.8 1.0
HB C:VAL59 4.4 38.3 1.0
C5 C:JPR204 4.4 61.2 0.5
CZ2 C:TRP23 4.5 21.4 1.0
C5 C:JPR204 4.5 61.2 0.4
HG11 C:VAL27 4.6 36.2 1.0
CE C:MET66 4.6 42.0 1.0
HD23 C:LEU56 4.7 29.2 1.0
HH2 C:TRP23 4.7 27.7 1.0
HG22 C:VAL59 4.7 36.4 1.0
HG21 C:VAL27 4.7 35.1 1.0
HG13 C:VAL27 4.8 36.2 1.0
CB C:VAL59 4.8 31.9 1.0
HD13 C:ILE141 4.8 43.2 1.0
CD2 C:LEU56 4.8 24.3 1.0
H3 C:JPR204 4.9 73.0 0.4
HD12 C:ILE141 4.9 43.2 1.0
HG22 C:VAL27 4.9 35.1 1.0
CH2 C:TRP23 5.0 23.1 1.0

Chlorine binding site 3 out of 3 in 4nx4

Go back to Chlorine Binding Sites List in 4nx4
Chlorine binding site 3 out of 3 in the Re-Refinement of Cap-1 Hiv-Ca Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Re-Refinement of Cap-1 Hiv-Ca Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl204

b:59.6
occ:0.49
CL1 C:JPR204 0.0 59.6 0.5
C4 C:JPR204 1.7 60.3 0.5
CL1 C:JPR204 1.8 61.3 0.4
C4 C:JPR204 2.3 61.0 0.4
C6 C:JPR204 2.7 60.9 0.5
HE2 C:MET66 2.7 50.4 1.0
H6 C:JPR204 2.8 73.1 0.5
C2 C:JPR204 2.8 60.7 0.5
C6 C:JPR204 2.8 61.1 0.4
H6 C:JPR204 2.8 73.3 0.4
H13A C:JPR204 2.9 73.3 0.5
C1 C:JPR204 3.1 61.1 0.5
H11 C:JPR204 3.1 73.3 0.5
HE1 C:MET66 3.2 50.4 1.0
C2 C:JPR204 3.3 60.9 0.4
HD23 C:LEU69 3.3 30.8 1.0
CE C:MET66 3.3 42.0 1.0
H12 C:JPR204 3.3 73.5 0.4
HA C:MET66 3.4 43.6 1.0
HD22 C:LEU69 3.5 30.8 1.0
HG23 C:VAL59 3.6 36.4 1.0
HB2 C:MET66 3.7 45.6 1.0
C1 C:JPR204 3.8 61.3 0.4
CD2 C:LEU69 3.8 25.7 1.0
C7 C:JPR204 4.0 61.3 0.4
C7 C:JPR204 4.0 61.2 0.5
C3 C:JPR204 4.1 60.9 0.5
HG21 C:VAL59 4.1 36.4 1.0
H12 C:JPR204 4.1 73.3 0.5
SD C:MET66 4.1 40.5 1.0
CA C:MET66 4.1 36.4 1.0
HE3 C:MET66 4.2 50.4 1.0
O1 C:JPR204 4.2 60.1 0.4
H11 C:JPR204 4.2 73.5 0.4
CG2 C:VAL59 4.3 30.4 1.0
O C:VAL59 4.3 44.7 1.0
HB2 C:HIS62 4.3 42.7 0.1
HB1 C:ALA65 4.3 50.0 1.0
N C:MET66 4.3 35.8 1.0
HB2 C:LEU69 4.3 31.7 1.0
C3 C:JPR204 4.3 60.9 0.4
CB C:MET66 4.3 38.0 1.0
HB3 C:ALA65 4.3 50.0 1.0
HD22 C:LEU56 4.4 29.2 1.0
HD13 C:ILE141 4.4 43.2 1.0
HD21 C:LEU69 4.4 30.8 1.0
HB3 C:LEU69 4.5 31.7 1.0
C5 C:JPR204 4.5 61.2 0.5
C C:ALA65 4.6 37.7 1.0
H C:MET66 4.6 42.9 1.0
HD21 C:LEU138 4.6 27.1 1.0
C5 C:JPR204 4.6 61.2 0.4
H13A C:JPR204 4.6 73.5 0.4
HB C:VAL59 4.7 38.3 1.0
HD23 C:LEU138 4.7 27.1 1.0
O C:ALA65 4.7 34.3 1.0
CB C:ALA65 4.8 41.7 1.0
CB C:LEU69 4.8 26.4 1.0
HD11 C:ILE141 4.8 43.2 1.0
H3 C:JPR204 4.8 73.1 0.5
CG C:MET66 4.9 40.0 1.0
HD12 C:ILE141 4.9 43.2 1.0
CD1 C:ILE141 4.9 36.0 1.0
O C:HIS62 4.9 36.3 0.1
N1 C:JPR204 4.9 61.2 0.4
CG C:LEU69 5.0 26.1 1.0
HG22 C:VAL59 5.0 36.4 1.0

Reference:

P.T.Lang, J.M.Holton, J.S.Fraser, T.Alber. Protein Structural Ensembles Are Revealed By Redefining X-Ray Electron Density Noise. Proc.Natl.Acad.Sci.Usa V. 111 237 2014.
ISSN: ISSN 0027-8424
PubMed: 24363322
DOI: 10.1073/PNAS.1302823110
Page generated: Sat Dec 12 10:59:28 2020

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