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Chlorine in PDB 5m1y: The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This

Enzymatic activity of The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This

All present enzymatic activity of The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This:
3.2.1.17;

Protein crystallography data

The structure of The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This, PDB code: 5m1y was solved by J.R.Helliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 27.251, 62.537, 58.981, 90.00, 90.92, 90.00
R / Rfree (%) 21.6 / 26.2

Other elements in 5m1y:

The structure of The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This also contains other interesting chemical elements:

Iodine (I) 26 atoms
Platinum (Pt) 3 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This (pdb code 5m1y). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This, PDB code: 5m1y:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5m1y

Go back to Chlorine Binding Sites List in 5m1y
Chlorine binding site 1 out of 3 in the The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl217

b:17.6
occ:1.00
PT A:PT201 2.3 10.1 0.8
HZ2 A:LYS96 3.5 21.0 1.0
I A:IOD203 3.5 14.8 0.9
I A:IOD204 3.6 10.6 0.9
HZ1 A:LYS96 3.8 21.0 1.0
NZ A:LYS96 4.0 17.5 1.0
HD21 A:ASN93 4.1 18.6 1.0
HZ3 A:LYS96 4.2 21.0 1.0
HA A:HIS15 4.3 15.3 1.0
ND1 A:HIS15 4.4 12.1 1.0
HB3 A:HIS15 4.7 14.0 1.0
O A:HIS15 4.8 14.7 1.0
ND2 A:ASN93 4.8 15.5 1.0

Chlorine binding site 2 out of 3 in 5m1y

Go back to Chlorine Binding Sites List in 5m1y
Chlorine binding site 2 out of 3 in the The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl218

b:21.7
occ:1.00
PT A:PT202 2.2 11.7 0.6
HG2 A:ARG128 2.5 21.9 1.0
HE A:ARG128 2.6 23.3 1.0
H A:ARG128 2.8 22.8 1.0
HD2 A:ARG128 3.1 22.1 1.0
NE A:ARG128 3.2 19.4 1.0
HB3 A:CYS6 3.3 16.1 1.0
CG A:ARG128 3.3 18.3 1.0
I A:IOD205 3.3 6.8 0.6
CD A:ARG128 3.4 18.4 1.0
I A:IOD207 3.7 16.8 0.6
N A:ARG128 3.7 19.0 1.0
HA A:CYS127 3.8 21.8 1.0
HG3 A:ARG128 3.9 21.9 1.0
O A:ARG128 3.9 19.9 1.0
HB2 A:CYS6 3.9 16.1 1.0
CB A:CYS6 4.0 13.4 1.0
CB A:ARG128 4.3 19.6 1.0
HD3 A:ARG128 4.3 22.1 1.0
CA A:ARG128 4.4 19.8 1.0
CZ A:ARG128 4.4 16.0 1.0
HH21 A:ARG128 4.4 24.1 1.0
HB3 A:CYS127 4.4 21.1 1.0
C A:ARG128 4.5 19.8 1.0
HB2 A:ALA10 4.5 16.0 1.0
O A:CYS6 4.6 13.2 1.0
CA A:CYS127 4.6 18.1 1.0
HB3 A:ARG128 4.6 23.5 1.0
C A:CYS127 4.7 17.6 1.0
I A:IOD206 4.8 20.6 0.7
HG A:LEU129 4.8 18.7 1.0
C A:CYS6 4.8 15.2 1.0
NH2 A:ARG128 4.8 20.1 1.0
CB A:CYS127 5.0 17.6 1.0

Chlorine binding site 3 out of 3 in 5m1y

Go back to Chlorine Binding Sites List in 5m1y
Chlorine binding site 3 out of 3 in the The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl212

b:21.9
occ:1.00
NA B:NA213 2.5 16.5 1.0
PT B:PT201 2.6 28.2 0.7
HZ2 B:LYS96 2.8 22.9 1.0
HZ1 B:LYS96 2.8 22.9 1.0
NZ B:LYS96 3.1 19.1 1.0
HZ3 B:LYS96 3.3 22.9 1.0
I B:IOD203 3.3 24.8 0.8
O B:HIS15 3.7 17.1 1.0
HA B:HIS15 3.8 22.6 1.0
C B:HIS15 4.3 18.6 1.0
HB3 B:HIS15 4.3 22.2 1.0
I B:IOD202 4.3 34.7 0.7
CA B:HIS15 4.4 18.8 1.0
CE B:LYS96 4.5 16.5 1.0
HE3 B:LYS96 4.7 19.8 1.0
ND1 B:HIS15 4.8 18.5 1.0
CB B:HIS15 4.8 18.5 1.0

Reference:

J.R.Helliwell, S.W.M.Tanley. The Case of 1LKR Held at the Pdb and Its Variable Amino Acid Occupancies; Re Refinement of 4OW9 to Correct This Zenodo 2016.
DOI: 10.5281/ZENODO.160328
Page generated: Wed Oct 28 12:50:00 2020

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