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

Platinum Binding Sites:

The binding sites of Platinum 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 Platinum atom.
In total 3 binding sites of Platinum 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 Platinum binding site number: 1; 2; 3;

Platinum binding site 1 out of 3 in 5m1y

Go back to Platinum Binding Sites List in 5m1y
Platinum 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 Platinum with other atoms in the Pt 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:Pt201

b:10.1
occ:0.80
 ND1 A:HIS15 2.1 12.1 1.0
CL A:CL217 2.3 17.6 1.0
I A:IOD204 2.5 10.6 0.9
I A:IOD203 2.6 14.8 0.9
HA A:HIS15 2.9 15.3 1.0
CE1 A:HIS15 3.0 13.8 1.0
CG A:HIS15 3.1 13.9 1.0
HB3 A:HIS15 3.1 14.0 1.0
HE1 A:HIS15 3.2 16.6 1.0
CB A:HIS15 3.4 11.7 1.0
CA A:HIS15 3.6 12.8 1.0
HG23 A:THR89 3.8 18.0 1.0
HZ1 A:LYS96 4.1 21.0 1.0
HZ2 A:LYS96 4.1 21.0 1.0
NE2 A:HIS15 4.2 14.8 1.0
CD2 A:HIS15 4.2 14.1 1.0
O A:HIS15 4.3 14.7 1.0
HB2 A:HIS15 4.4 14.0 1.0
C A:HIS15 4.4 12.8 1.0
NZ A:LYS96 4.6 17.5 1.0
N A:HIS15 4.7 13.1 1.0
CG2 A:THR89 4.8 15.0 1.0
HD21 A:ASN93 4.9 18.6 1.0
HG21 A:THR89 5.0 18.0 1.0
HG11 A:VAL92 5.0 14.5 1.0
OD1 A:ASN93 5.0 17.8 1.0

Platinum binding site 2 out of 3 in 5m1y

Go back to Platinum Binding Sites List in 5m1y
Platinum 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 Platinum with other atoms in the Pt 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:Pt202

b:11.7
occ:0.57
 CL A:CL218 2.2 21.7 1.0
I A:IOD206 2.5 20.6 0.7
I A:IOD207 2.6 16.8 0.6
I A:IOD205 2.7 6.8 0.6
HB2 A:CYS6 3.7 16.1 1.0
HB3 A:CYS6 3.9 16.1 1.0
HE A:ARG128 4.0 23.3 1.0
HA A:GLU7 4.1 18.5 1.0
HD2 A:ARG128 4.1 22.1 1.0
CB A:CYS6 4.2 13.4 1.0
N A:GLU7 4.5 13.3 1.0
C A:CYS6 4.5 15.2 1.0
HG2 A:ARG128 4.5 21.9 1.0
NE A:ARG128 4.5 19.4 1.0
H A:GLU7 4.6 16.0 1.0
HB2 A:GLU7 4.7 18.4 1.0
O A:CYS6 4.7 13.2 1.0
CA A:GLU7 4.7 15.4 1.0
CD A:ARG128 4.7 18.4 1.0
H A:ARG128 5.0 22.8 1.0

Platinum binding site 3 out of 3 in 5m1y

Go back to Platinum Binding Sites List in 5m1y
Platinum 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 Platinum with other atoms in the Pt 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:Pt201

b:28.2
occ:0.67
 ND1 B:HIS15 2.3 18.5 1.0
CL B:CL212 2.6 21.9 1.0
I B:IOD202 2.6 34.7 0.7
I B:IOD203 2.7 24.8 0.8
HA B:HIS15 2.8 22.6 1.0
HB3 B:HIS15 3.2 22.2 1.0
CG B:HIS15 3.3 20.1 1.0
CE1 B:HIS15 3.3 18.3 1.0
CB B:HIS15 3.5 18.5 1.0
HE1 B:HIS15 3.5 22.0 1.0
CA B:HIS15 3.5 18.8 1.0
HG23 B:THR89 3.9 17.8 1.0
O B:HIS15 4.1 17.1 1.0
HZ1 B:LYS96 4.2 22.9 1.0
HZ2 B:LYS96 4.2 22.9 1.0
C B:HIS15 4.3 18.6 1.0
NE2 B:HIS15 4.4 17.9 1.0
CD2 B:HIS15 4.4 19.0 1.0
HB2 B:HIS15 4.5 22.2 1.0
NA B:NA213 4.5 16.5 1.0
O B:ARG14 4.6 20.1 1.0
NZ B:LYS96 4.7 19.1 1.0
N B:HIS15 4.7 22.4 1.0
CG2 B:THR89 4.9 14.9 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: Thu Oct 10 11:37:39 2024

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