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Platinum in PDB 5i5q: Re Refinement of 4MWN.

Enzymatic activity of Re Refinement of 4MWN.

All present enzymatic activity of Re Refinement of 4MWN.:
3.2.1.17;

Protein crystallography data

The structure of Re Refinement of 4MWN., PDB code: 5i5q 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) 32.31 / 1.42
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 27.346, 32.134, 34.296, 88.04, 71.17, 68.35
R / Rfree (%) 18.5 / 23.7

Platinum Binding Sites:

The binding sites of Platinum atom in the Re Refinement of 4MWN. (pdb code 5i5q). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 3 binding sites of Platinum where determined in the Re Refinement of 4MWN., PDB code: 5i5q:
Jump to Platinum binding site number: 1; 2; 3;

Platinum binding site 1 out of 3 in 5i5q

Go back to Platinum Binding Sites List in 5i5q
Platinum binding site 1 out of 3 in the Re Refinement of 4MWN.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Re Refinement of 4MWN. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt203

b:26.0
occ:0.29
PT A:PT205 2.1 27.5 0.3
NE2 A:HIS15 2.9 39.6 1.0
CE1 A:HIS15 3.4 32.6 1.0
CD2 A:HIS15 3.6 31.9 1.0
NE A:ARG14 4.3 25.5 1.0
ND1 A:HIS15 4.3 22.2 1.0
CG A:HIS15 4.4 25.9 1.0
CD A:ARG14 4.7 26.5 1.0
CB A:ARG14 4.7 19.4 1.0
OG1 A:THR89 4.9 21.6 1.0

Platinum binding site 2 out of 3 in 5i5q

Go back to Platinum Binding Sites List in 5i5q
Platinum binding site 2 out of 3 in the Re Refinement of 4MWN.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Re Refinement of 4MWN. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt204

b:24.6
occ:0.36
ND1 A:HIS15 2.0 22.2 1.0
CE1 A:HIS15 2.9 32.6 1.0
CG A:HIS15 2.9 25.9 1.0
CB A:HIS15 3.4 18.9 1.0
OD1 A:ASN93 3.6 26.9 1.0
NE2 A:HIS15 3.9 39.6 1.0
CA A:HIS15 3.9 15.1 1.0
CD2 A:HIS15 3.9 31.9 1.0
O A:HIS15 4.1 21.2 1.0
CG2 A:THR89 4.2 20.6 1.0
NZ A:LYS96 4.3 18.5 1.0
C A:HIS15 4.5 15.6 1.0
CG A:ASN93 4.5 24.0 1.0
ND2 A:ASN93 4.7 25.2 1.0

Platinum binding site 3 out of 3 in 5i5q

Go back to Platinum Binding Sites List in 5i5q
Platinum binding site 3 out of 3 in the Re Refinement of 4MWN.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Re Refinement of 4MWN. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt205

b:27.5
occ:0.33
PT A:PT203 2.1 26.0 0.3
NE2 A:HIS15 3.2 39.6 1.0
CD2 A:HIS15 3.6 31.9 1.0
OD1 A:ASP87 4.1 24.9 1.0
CE1 A:HIS15 4.3 32.6 1.0
OG1 A:THR89 4.4 21.6 1.0
NE A:ARG14 4.6 25.5 1.0
NH2 A:ARG14 4.8 27.0 1.0
CG A:HIS15 4.8 25.9 1.0

Reference:

S.W.Tanley, J.R.Helliwell. Comment on "Structural Dynamics of Cisplatin Binding to Histidine in A Protein" [Struct. Dyn. 1, 034701 (2014)]. Struct Dyn V. 3 37101 2016.
ISSN: ESSN 2329-7778
PubMed: 27226979
DOI: 10.1063/1.4948613
Page generated: Wed Dec 16 02:05:18 2020

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