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Iodine 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:

Platinum (Pt) 3 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Iodine 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 Iodine atom.
In total 26 binding sites of Iodine 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 Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 26 in 5m1y

Go back to Iodine Binding Sites List in 5m1y
Iodine binding site 1 out of 26 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 Iodine with other atoms in the I 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:I203

b:14.8
occ:0.89
PT A:PT201 2.6 10.1 0.8
ND1 A:HIS15 3.2 12.1 1.0
HA A:HIS15 3.2 15.3 1.0
CL A:CL217 3.5 17.6 1.0
HE1 A:HIS15 3.6 16.6 1.0
HG2 A:ARG14 3.7 19.4 1.0
CE1 A:HIS15 3.7 13.8 1.0
O A:ARG14 4.0 14.5 1.0
CA A:HIS15 4.2 12.8 1.0
CG A:HIS15 4.2 13.9 1.0
C A:ARG14 4.5 13.0 1.0
CG A:ARG14 4.6 16.1 1.0
N A:HIS15 4.6 13.1 1.0
HG3 A:ARG14 4.7 19.4 1.0
CB A:HIS15 4.7 11.7 1.0
NE2 A:HIS15 4.8 14.8 1.0
HB3 A:HIS15 4.9 14.0 1.0

Iodine binding site 2 out of 26 in 5m1y

Go back to Iodine Binding Sites List in 5m1y
Iodine binding site 2 out of 26 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 Iodine with other atoms in the I 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:I204

b:10.6
occ:0.86
PT A:PT201 2.5 10.1 0.8
HB3 A:HIS15 3.0 14.0 1.0
OD1 A:ASN93 3.2 17.8 1.0
ND1 A:HIS15 3.2 12.1 1.0
HZ2 A:LYS96 3.2 21.0 1.0
HG23 A:THR89 3.2 18.0 1.0
HG12 A:VAL92 3.4 14.5 1.0
HD21 A:ASN93 3.4 18.6 1.0
CG A:ASN93 3.4 17.5 1.0
HB A:VAL92 3.4 13.8 1.0
ND2 A:ASN93 3.5 15.5 1.0
CL A:CL217 3.6 17.6 1.0
CG A:HIS15 3.6 13.9 1.0
HG11 A:VAL92 3.7 14.5 1.0
CB A:HIS15 3.7 11.7 1.0
HZ1 A:LYS96 3.8 21.0 1.0
CG1 A:VAL92 3.9 12.1 1.0
NZ A:LYS96 3.9 17.5 1.0
H A:ASN93 3.9 16.6 1.0
HE3 A:LYS96 3.9 17.0 1.0
HA A:ASN93 3.9 16.0 1.0
HA A:THR89 3.9 18.6 1.0
O A:THR89 4.0 14.1 1.0
CE1 A:HIS15 4.0 13.8 1.0
N A:ASN93 4.0 13.8 1.0
HG22 A:THR89 4.1 18.0 1.0
HD22 A:ASN93 4.1 18.6 1.0
CG2 A:THR89 4.1 15.0 1.0
CB A:VAL92 4.1 11.5 1.0
CA A:ASN93 4.3 13.3 1.0
HE1 A:HIS15 4.3 16.6 1.0
CB A:ASN93 4.4 14.3 1.0
HA A:HIS15 4.4 15.3 1.0
HB2 A:HIS15 4.4 14.0 1.0
CE A:LYS96 4.4 14.2 1.0
O A:HIS15 4.5 14.7 1.0
C A:VAL92 4.5 12.5 1.0
CD2 A:HIS15 4.5 14.1 1.0
HD2 A:LYS96 4.6 17.2 1.0
HB2 A:ASN93 4.6 17.2 1.0
CA A:HIS15 4.6 12.8 1.0
HZ3 A:LYS96 4.6 21.0 1.0
CA A:THR89 4.7 15.5 1.0
HG21 A:THR89 4.7 18.0 1.0
NE2 A:HIS15 4.7 14.8 1.0
HG13 A:VAL92 4.8 14.5 1.0
C A:THR89 4.8 14.6 1.0
CA A:VAL92 5.0 12.1 1.0
CB A:THR89 5.0 16.4 1.0

Iodine binding site 3 out of 26 in 5m1y

Go back to Iodine Binding Sites List in 5m1y
Iodine binding site 3 out of 26 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 Iodine with other atoms in the I 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
A:I205

b:6.8
occ:0.60
PT A:PT202 2.7 11.7 0.6
HH21 A:ARG128 3.1 24.1 1.0
HB2 A:CYS6 3.2 16.1 1.0
HE A:ARG128 3.2 23.3 1.0
CL A:CL218 3.3 21.7 1.0
NH2 A:ARG128 3.6 20.1 1.0
NE A:ARG128 3.7 19.4 1.0
I A:IOD206 3.8 20.6 0.7
HB3 A:CYS6 3.9 16.1 1.0
CB A:CYS6 3.9 13.4 1.0
CZ A:ARG128 4.0 16.0 1.0
HH22 A:ARG128 4.2 24.1 1.0
HA A:CYS127 4.3 21.8 1.0
SG A:CYS6 4.4 15.1 1.0
HD2 A:ARG128 4.5 22.1 1.0
O A:GLY126 4.5 20.0 1.0
CD A:ARG128 4.7 18.4 1.0
H A:ARG128 4.7 22.8 1.0

Iodine binding site 4 out of 26 in 5m1y

Go back to Iodine Binding Sites List in 5m1y
Iodine binding site 4 out of 26 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 Iodine with other atoms in the I binding site number 4 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:I206

b:20.6
occ:0.74
PT A:PT202 2.5 11.7 0.6
I A:IOD207 3.5 16.8 0.6
HB2 A:GLU7 3.6 18.4 1.0
I A:IOD205 3.8 6.8 0.6
HA A:GLU7 4.4 18.5 1.0
HG3 A:GLU7 4.4 16.2 1.0
CB A:GLU7 4.4 15.3 1.0
H A:GLU7 4.5 16.0 1.0
HB2 A:CYS6 4.7 16.1 1.0
N A:GLU7 4.7 13.3 1.0
CA A:GLU7 4.7 15.4 1.0
CL A:CL218 4.8 21.7 1.0
CG A:GLU7 5.0 13.5 1.0

Iodine binding site 5 out of 26 in 5m1y

Go back to Iodine Binding Sites List in 5m1y
Iodine binding site 5 out of 26 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 Iodine with other atoms in the I binding site number 5 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:I207

b:16.8
occ:0.62
PT A:PT202 2.6 11.7 0.6
HA A:GLU7 3.4 18.5 1.0
I A:IOD206 3.5 20.6 0.7
CL A:CL218 3.7 21.7 1.0
HG3 A:GLU7 4.1 16.2 1.0
HB2 A:ALA10 4.1 16.0 1.0
HB3 A:ALA10 4.2 16.0 1.0
CA A:GLU7 4.3 15.4 1.0
HB2 A:GLU7 4.5 18.4 1.0
CB A:ALA10 4.5 13.3 1.0
HB1 A:ALA10 4.6 16.0 1.0
CB A:GLU7 4.8 15.3 1.0
O A:CYS6 4.8 13.2 1.0
CG A:GLU7 4.8 13.5 1.0
N A:GLU7 4.8 13.3 1.0

Iodine binding site 6 out of 26 in 5m1y

Go back to Iodine Binding Sites List in 5m1y
Iodine binding site 6 out of 26 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 Iodine with other atoms in the I binding site number 6 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:I208

b:22.0
occ:0.66
HZ3 A:LYS96 3.2 21.0 1.0
HE2 A:TYR20 3.5 14.1 1.0
HA3 A:GLY16 3.7 17.3 1.0
HD2 A:TYR20 3.8 16.2 1.0
HZ1 A:LYS96 3.9 21.0 1.0
NZ A:LYS96 3.9 17.5 1.0
CE2 A:TYR20 4.2 11.8 1.0
HE2 A:LYS96 4.2 17.0 1.0
CD2 A:TYR20 4.4 13.5 1.0
O A:GLY16 4.5 9.9 1.0
O A:HIS15 4.5 14.7 1.0
HZ2 A:LYS96 4.6 21.0 1.0
CE A:LYS96 4.6 14.2 1.0
CA A:GLY16 4.7 14.4 1.0
HD3 A:LYS96 4.7 17.2 1.0
C A:GLY16 5.0 11.3 1.0

Iodine binding site 7 out of 26 in 5m1y

Go back to Iodine Binding Sites List in 5m1y
Iodine binding site 7 out of 26 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 Iodine with other atoms in the I binding site number 7 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:I209

b:13.5
occ:0.74
HD21 A:ASN74 2.9 19.7 1.0
HD3 A:PRO79 3.2 19.2 1.0
HD22 A:ASN74 3.4 19.7 1.0
ND2 A:ASN74 3.5 16.4 1.0
HA A:ILE78 3.7 18.7 1.0
N A:PRO79 3.9 16.6 1.0
N A:ILE78 3.9 17.2 1.0
CD A:PRO79 3.9 16.0 1.0
C A:ILE78 4.0 16.5 1.0
H A:ILE78 4.0 20.6 1.0
CA A:ILE78 4.1 15.6 1.0
HA A:PRO79 4.4 18.7 1.0
C A:ASN77 4.4 16.0 1.0
OD1 A:ASN77 4.4 20.0 1.0
O A:ILE78 4.5 15.1 1.0
HD2 A:PRO79 4.5 19.2 1.0
HB3 A:PRO79 4.5 18.4 1.0
HA A:ASN77 4.6 21.1 1.0
CA A:PRO79 4.7 15.6 1.0
O A:ASN77 4.7 14.8 1.0
CG A:ASN74 4.7 18.7 1.0
HB3 A:ASN65 4.8 25.3 1.0
CB A:PRO79 5.0 15.3 1.0

Iodine binding site 8 out of 26 in 5m1y

Go back to Iodine Binding Sites List in 5m1y
Iodine binding site 8 out of 26 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 Iodine with other atoms in the I binding site number 8 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:I210

b:10.3
occ:0.63
HA A:ARG21 2.9 13.6 1.0
HD2 A:ARG21 3.6 14.9 1.0
CA A:ARG21 3.7 11.4 1.0
H A:GLY22 3.8 14.0 1.0
N A:GLY22 3.9 11.7 1.0
C A:ARG21 3.9 11.7 1.0
H A:ARG21 4.0 12.7 1.0
N A:ARG21 4.3 10.6 1.0
CD A:ARG21 4.6 12.4 1.0
HA3 A:GLY22 4.6 13.5 1.0
HA2 A:GLY22 4.7 13.5 1.0
O A:ARG21 4.7 9.0 1.0
CA A:GLY22 4.7 11.3 1.0
CB A:ARG21 4.9 11.5 1.0

Iodine binding site 9 out of 26 in 5m1y

Go back to Iodine Binding Sites List in 5m1y
Iodine binding site 9 out of 26 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 Iodine with other atoms in the I binding site number 9 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:I211

b:9.1
occ:0.82
HD3 A:ARG5 2.9 14.6 1.0
HZ3 A:LYS33 3.2 18.6 1.0
HE2 A:PHE38 3.3 15.0 1.0
HE A:ARG5 3.4 15.3 1.0
HZ3 A:TRP123 3.4 15.7 1.0
HB2 A:ARG5 3.6 16.2 1.0
HE2 A:LYS33 3.7 15.7 1.0
CD A:ARG5 3.7 12.2 1.0
H21 A:DMS215 3.8 17.2 1.0
NZ A:LYS33 3.9 15.5 1.0
NE A:ARG5 3.9 12.8 1.0
HD3 A:LYS33 4.0 13.5 1.0
HZ1 A:LYS33 4.1 18.6 1.0
CE2 A:PHE38 4.1 12.5 1.0
HZ A:PHE38 4.1 14.3 1.0
H23 A:DMS215 4.2 17.2 1.0
CE A:LYS33 4.2 13.1 1.0
CZ3 A:TRP123 4.2 13.1 1.0
HD2 A:ARG5 4.4 14.6 1.0
CB A:ARG5 4.4 13.5 1.0
C2 A:DMS215 4.4 14.3 1.0
CZ A:PHE38 4.5 11.9 1.0
CG A:ARG5 4.5 13.6 1.0
HG3 A:ARG5 4.6 16.3 1.0
CD A:LYS33 4.6 11.3 1.0
HE3 A:TRP123 4.6 13.1 1.0
HZ2 A:LYS33 4.7 18.6 1.0
HB3 A:ARG5 4.8 16.2 1.0
HG2 A:LYS33 4.8 14.3 1.0
CE3 A:TRP123 4.9 10.9 1.0

Iodine binding site 10 out of 26 in 5m1y

Go back to Iodine Binding Sites List in 5m1y
Iodine binding site 10 out of 26 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 Iodine with other atoms in the I binding site number 10 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:I212

b:7.6
occ:0.48
H A:GLY26 2.7 12.3 1.0
HB2 A:SER24 2.9 13.5 1.0
HA A:GLN121 3.0 13.1 1.0
HD13 A:ILE124 3.0 18.8 1.0
HG A:SER24 3.1 14.6 1.0
OE1 A:GLN121 3.2 15.7 1.0
HD11 A:ILE124 3.2 18.8 1.0
HA3 A:GLY26 3.3 10.8 1.0
OG A:SER24 3.4 12.2 1.0
HG23 A:VAL120 3.4 11.6 1.0
N A:GLY26 3.5 10.3 1.0
CD1 A:ILE124 3.5 15.6 1.0
CB A:SER24 3.6 11.3 1.0
HG12 A:ILE124 3.7 18.3 1.0
CA A:GLY26 3.9 9.0 1.0
CA A:GLN121 3.9 10.9 1.0
CD A:GLN121 4.0 14.6 1.0
HB3 A:SER24 4.2 13.5 1.0
CG1 A:ILE124 4.2 15.2 1.0
N A:GLN121 4.2 12.0 1.0
H A:LEU25 4.2 14.2 1.0
HB2 A:GLN121 4.2 18.5 1.0
HG21 A:ILE124 4.3 15.3 1.0
HB3 A:LEU25 4.3 12.7 1.0
N A:LEU25 4.3 11.8 1.0
CG2 A:VAL120 4.3 9.7 1.0
HA2 A:GLY26 4.4 10.8 1.0
HD12 A:ILE124 4.4 18.8 1.0
C A:SER24 4.4 10.2 1.0
HG21 A:VAL120 4.4 11.6 1.0
HG23 A:ILE124 4.5 15.3 1.0
O A:VAL120 4.5 10.9 1.0
C A:VAL120 4.5 12.2 1.0
CB A:GLN121 4.5 15.4 1.0
H A:GLN121 4.5 14.4 1.0
HE22 A:GLN121 4.6 16.2 1.0
C A:LEU25 4.6 9.1 1.0
CA A:SER24 4.6 10.2 1.0
NE2 A:GLN121 4.7 13.5 1.0
H A:ASN27 4.7 11.4 1.0
CG2 A:ILE124 4.8 12.8 1.0
HB A:VAL120 4.8 13.5 1.0
HG13 A:ILE124 4.9 18.3 1.0
CA A:LEU25 4.9 11.0 1.0
CG A:GLN121 4.9 13.7 1.0
HG22 A:VAL120 4.9 11.6 1.0
C A:GLN121 4.9 14.1 1.0
O A:SER24 4.9 10.5 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: Sun Dec 13 19:40:11 2020

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