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Chlorine in PDB 6axw: Structure of the I124A Mutant of the Hiv-1 Capsid Protein

Protein crystallography data

The structure of Structure of the I124A Mutant of the Hiv-1 Capsid Protein, PDB code: 6axw was solved by A.T.Gres, K.A.Kirby, S.G.Sarafianos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.95 / 2.40
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 92.611, 92.611, 57.954, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 23.6

Other elements in 6axw:

The structure of Structure of the I124A Mutant of the Hiv-1 Capsid Protein also contains other interesting chemical elements:

Iodine (I) 9 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein (pdb code 6axw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein, PDB code: 6axw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 6axw

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Chlorine binding site 1 out of 10 in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl310

b:41.9
occ:1.00
 O A:GLY60 2.8 39.2 1.0
O A:HOH531 3.0 49.1 1.0
O A:HOH475 3.1 33.5 1.0
CD2 A:HIS62 3.6 41.8 1.0
CG A:GLU28 3.8 50.0 1.0
NE2 A:HIS62 3.9 43.6 1.0
C A:GLY60 4.0 38.0 1.0
CG1 A:VAL27 4.0 39.4 1.0
CA A:GLU28 4.2 46.0 1.0
N A:GLU28 4.3 42.1 1.0
CG1 A:VAL59 4.4 32.6 1.0
C A:VAL27 4.5 40.0 1.0
N A:GLY60 4.6 35.4 1.0
CB A:GLU28 4.6 47.9 1.0
O A:HOH414 4.6 39.9 1.0
O A:VAL27 4.7 40.4 1.0
CB A:VAL27 4.8 38.5 1.0
CA A:GLY61 4.8 38.8 1.0
CG A:HIS62 4.8 41.1 1.0
N A:GLY61 4.8 38.8 1.0
CA A:GLY60 4.9 36.8 1.0

Chlorine binding site 2 out of 10 in 6axw

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Chlorine binding site 2 out of 10 in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl311

b:50.9
occ:1.00
 O A:HOH453 2.9 31.7 1.0
NH2 A:ARG173 3.5 40.0 1.0
O A:HOH525 3.9 59.2 1.0
CG A:PRO38 4.2 38.4 1.0
NE A:ARG173 4.3 37.6 1.0
CZ A:ARG173 4.4 38.4 1.0
CD A:PRO38 4.4 37.2 1.0
CB A:PRO38 4.6 38.2 1.0

Chlorine binding site 3 out of 10 in 6axw

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Chlorine binding site 3 out of 10 in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl312

b:54.5
occ:1.00
 N A:ARG97 3.4 58.2 1.0
CD A:ARG97 3.7 57.0 1.0
CG A:ARG97 3.8 56.1 1.0
CB A:ARG97 3.9 57.6 1.0
CA A:MET96 4.1 62.5 1.0
C A:MET96 4.2 58.9 1.0
CA A:ARG97 4.3 58.5 1.0
O A:GLN95 4.3 62.2 1.0
CE A:MET96 4.3 65.5 1.0
NE A:ARG97 4.3 55.4 1.0
OE2 A:GLU113 4.5 54.8 1.0
CG2 A:ILE91 4.5 52.7 1.0
SD A:MET96 4.6 69.5 1.0
CG1 A:ILE91 4.7 52.0 1.0
CB A:MET96 4.9 63.5 1.0
CB A:ILE91 5.0 53.5 1.0
O A:HOH533 5.0 48.2 1.0

Chlorine binding site 4 out of 10 in 6axw

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Chlorine binding site 4 out of 10 in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl313

b:56.6
occ:1.00
 O A:HOH449 3.4 36.5 1.0
CL A:CL315 3.4 53.9 0.8
CD1 A:ILE153 4.0 43.6 1.0
CG2 A:THR148 4.1 55.2 1.0
O A:ASP152 4.1 47.1 1.0
NH1 A:ARG167 4.3 41.7 1.0
C A:ASP152 4.7 44.9 1.0
CB A:ASP152 4.7 46.6 1.0
CB A:THR148 4.8 51.6 1.0

Chlorine binding site 5 out of 10 in 6axw

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Chlorine binding site 5 out of 10 in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl314

b:59.1
occ:0.95
 CL A:CL315 3.3 53.9 0.8
CD A:LYS170 3.6 46.4 1.0
O A:ARG167 3.8 37.6 1.0
CE A:LYS170 3.8 50.6 1.0
CB A:ARG167 3.8 37.4 1.0
CA A:ARG167 3.8 36.0 1.0
OG1 A:THR171 3.8 39.5 1.0
CG A:ARG167 3.9 39.1 1.0
CG A:LYS170 4.0 43.6 1.0
CB A:LYS170 4.2 40.5 1.0
C A:ARG167 4.3 36.0 1.0
O A:HOH521 4.4 39.2 1.0
CD A:ARG167 4.5 40.4 1.0
N A:THR171 4.8 37.3 1.0
OG1 A:THR148 5.0 55.0 1.0

Chlorine binding site 6 out of 10 in 6axw

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Chlorine binding site 6 out of 10 in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl315

b:53.9
occ:0.80
 NH1 A:ARG167 3.2 41.7 1.0
CL A:CL314 3.3 59.1 0.9
CL A:CL313 3.4 56.6 1.0
CD A:ARG167 3.8 40.4 1.0
CD1 A:ILE153 3.8 43.6 1.0
CZ A:ARG167 4.3 40.7 1.0
CG2 A:THR148 4.3 55.2 1.0
CG A:ARG167 4.4 39.1 1.0
CB A:ARG167 4.4 37.4 1.0
NE A:ARG167 4.5 40.2 1.0
O A:HOH449 4.7 36.5 1.0
OG1 A:THR171 4.9 39.5 1.0

Chlorine binding site 7 out of 10 in 6axw

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Chlorine binding site 7 out of 10 in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of the I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl316

b:63.5
occ:0.92
 O A:HOH511 2.9 58.6 1.0
N A:GLU128 3.3 45.5 1.0
CE A:MET118 3.5 55.9 1.0
N A:GLY127 3.5 44.3 1.0
CA A:PRO125 3.6 47.8 1.0
C A:PRO125 3.6 45.8 1.0
CA A:GLY127 3.7 43.2 1.0
CG A:MET118 3.8 55.3 1.0
CG A:GLU128 3.8 59.3 1.0
O A:PRO125 3.8 43.7 1.0
CB A:PRO125 3.8 49.5 1.0
C A:GLY127 4.0 43.2 1.0
N A:VAL126 4.1 44.8 1.0
CB A:GLU128 4.1 54.1 1.0
SD A:MET118 4.2 55.9 1.0
CA A:GLU128 4.3 47.3 1.0
C A:VAL126 4.5 44.0 1.0
CB A:MET118 4.6 57.6 1.0
CA A:VAL126 4.9 44.0 1.0
CD A:GLU128 5.0 63.6 1.0
OE2 A:GLU128 5.0 65.8 1.0
N A:PRO125 5.0 49.6 1.0

Chlorine binding site 8 out of 10 in 6axw

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Chlorine binding site 8 out of 10 in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of the I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl317

b:89.8
occ:1.00
 O A:HOH494 3.0 42.1 1.0
CD2 A:TYR145 3.6 57.9 1.0
CB A:ALA31 3.8 49.8 1.0
CE2 A:TYR145 4.0 59.6 1.0
CE1 A:HIS62 4.3 43.9 1.0
ND1 A:HIS62 4.4 43.2 1.0
CD2 A:PHE32 4.5 42.5 1.0
CG A:TYR145 4.6 55.7 1.0
O A:HOH544 4.7 56.4 1.0
N A:PHE32 4.8 47.0 1.0
CB A:TYR145 4.9 52.6 1.0

Chlorine binding site 9 out of 10 in 6axw

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Chlorine binding site 9 out of 10 in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of the I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl318

b:91.0
occ:1.00
 O A:HOH546 3.8 48.0 1.0
O A:HOH505 3.9 57.1 1.0
CB A:MET96 3.9 63.5 1.0
CD1 A:TRP117 4.1 55.2 1.0
O A:MET96 4.2 57.5 1.0
CB A:ALA124 4.3 51.2 1.0
NE1 A:TRP117 4.6 55.7 1.0
O A:ARG97 4.6 60.0 1.0
C A:MET96 4.7 58.9 1.0
CG A:MET96 4.7 65.9 1.0
ND1 A:HIS120 4.8 74.4 1.0
CA A:MET96 4.8 62.5 1.0
CG A:HIS120 4.8 72.3 1.0
N A:MET96 5.0 63.0 1.0
CE1 A:HIS120 5.0 75.0 1.0

Chlorine binding site 10 out of 10 in 6axw

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Chlorine binding site 10 out of 10 in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of the I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl319

b:79.2
occ:1.00
 O A:HOH443 3.0 61.6 1.0
CD A:LYS203 4.0 58.0 1.0
CG A:LYS203 4.1 55.3 1.0
CE A:LYS199 4.3 56.0 1.0
CG1 A:VAL191 4.3 41.8 1.0
CA A:GLN192 4.3 49.6 1.0
N A:GLN192 4.5 45.2 1.0
CE A:LYS203 4.5 61.3 1.0
CB A:GLN192 4.6 54.6 1.0
CG A:GLN192 4.8 60.7 1.0
C A:VAL191 4.9 41.3 1.0
CB A:VAL191 4.9 41.2 1.0
NZ A:LYS199 4.9 59.4 1.0

Reference:

M.Novikova, L.J.Adams, J.Fontana, A.T.Gres, M.Balasubramaniam, D.C.Winkler, S.B.Kudchodkar, F.Soheilian, S.G.Sarafianos, A.C.Steven, E.O.Freed. Identification of A Structural Element in Hiv-1 Gag Required For Virus Particle Assembly and Maturation. Mbio V. 9 2018.
ISSN: ESSN 2150-7511
PubMed: 30327442
DOI: 10.1128/MBIO.01567-18
Page generated: Fri Jul 26 22:22:46 2024

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