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Platinum in PDB 5hmv: Re Refinement of 4MWK.

Enzymatic activity of Re Refinement of 4MWK.

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

Protein crystallography data

The structure of Re Refinement of 4MWK., PDB code: 5hmv 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) 29.28 / 0.98
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 26.998, 31.807, 34.072, 89.08, 72.00, 67.81
R / Rfree (%) 12.4 / 14.7

Other elements in 5hmv:

The structure of Re Refinement of 4MWK. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Re Refinement of 4MWK. (pdb code 5hmv). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 7 binding sites of Platinum where determined in the Re Refinement of 4MWK., PDB code: 5hmv:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7;

Platinum binding site 1 out of 7 in 5hmv

Go back to Platinum Binding Sites List in 5hmv
Platinum binding site 1 out of 7 in the Re Refinement of 4MWK.


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 4MWK. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt207

b:12.8
occ:0.22
 PT A:PT218 1.5 0.4 0.6
NE2 A:HIS15 2.1 30.0 1.0
CL A:CL219 2.3 6.8 0.2
CL A:CL217 2.3 6.2 0.2
PT A:PT208 2.4 13.9 0.2
PT A:PT209 2.6 12.7 0.1
CD2 A:HIS15 2.9 26.0 1.0
CE1 A:HIS15 3.2 31.0 1.0
NE A:ARG14 4.0 11.3 1.0
CG A:HIS15 4.1 22.1 1.0
CB A:ARG14 4.2 9.2 1.0
ND1 A:HIS15 4.2 36.0 1.0
CD A:ARG14 4.3 11.1 1.0
PT A:PT211 4.3 19.4 0.1
OG1 A:THR89 4.9 11.6 1.0
CG A:ARG14 4.9 10.6 1.0

Platinum binding site 2 out of 7 in 5hmv

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Platinum binding site 2 out of 7 in the Re Refinement of 4MWK.


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 4MWK. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt208

b:13.9
occ:0.25
 PT A:PT207 2.4 12.8 0.2
NE2 A:HIS15 3.1 30.0 1.0
CE1 A:HIS15 3.2 31.0 1.0
PT A:PT218 3.3 0.4 0.6
CL A:CL217 3.3 6.2 0.2
PT A:PT209 3.6 12.7 0.1
CD2 A:HIS15 4.1 26.0 1.0
NE A:ARG14 4.2 11.3 1.0
ND1 A:HIS15 4.3 36.0 1.0
OG1 A:THR89 4.4 11.6 1.0
NH2 A:ARG14 4.5 12.4 1.0
CL A:CL219 4.7 6.8 0.2
CG A:HIS15 4.8 22.1 1.0
CB A:ALA11 4.8 5.6 1.0
CZ A:ARG14 4.9 10.6 1.0
O A:ALA11 4.9 6.3 1.0
O A:HOH303 4.9 13.4 1.0

Platinum binding site 3 out of 7 in 5hmv

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Platinum binding site 3 out of 7 in the Re Refinement of 4MWK.


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 4MWK. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt209

b:12.7
occ:0.07
 PT A:PT218 1.4 0.4 0.6
NE2 A:HIS15 2.5 30.0 1.0
PT A:PT207 2.6 12.8 0.2
CE1 A:HIS15 3.0 31.0 1.0
OG1 A:THR89 3.3 11.6 1.0
CL A:CL219 3.4 6.8 0.2
PT A:PT208 3.6 13.9 0.2
O3 A:NO3204 3.6 24.8 0.5
PT A:PT211 3.7 19.4 0.1
O A:HOH303 3.7 13.4 1.0
CD2 A:HIS15 3.7 26.0 1.0
CL A:CL217 4.0 6.2 0.2
ND1 A:HIS15 4.2 36.0 1.0
O A:HOH301 4.4 20.7 1.0
CB A:THR89 4.5 7.7 1.0
CG A:HIS15 4.5 22.1 1.0
CG2 A:THR89 4.6 9.9 1.0
N A:NO3204 5.0 10.8 0.5

Platinum binding site 4 out of 7 in 5hmv

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Platinum binding site 4 out of 7 in the Re Refinement of 4MWK.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Re Refinement of 4MWK. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt210

b:4.3
occ:0.22
 PT A:PT211 1.8 19.4 0.1
CB A:HIS15 3.4 14.2 1.0
O A:HOH415 3.5 11.4 1.0
CG A:HIS15 3.5 22.1 1.0
CA A:HIS15 3.8 10.7 1.0
CD2 A:HIS15 3.8 26.0 1.0
ND1 A:HIS15 3.9 36.0 1.0
OD1 A:ASN93 3.9 18.1 1.0
O A:HIS15 4.0 15.4 1.0
O A:HOH383 4.1 23.3 1.0
NZ A:LYS96 4.3 10.7 1.0
C A:HIS15 4.4 10.3 1.0
NE2 A:HIS15 4.4 30.0 1.0
CE1 A:HIS15 4.4 31.0 1.0
CG2 A:THR89 4.6 9.9 1.0
CG A:ASN93 4.9 12.4 1.0

Platinum binding site 5 out of 7 in 5hmv

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Platinum binding site 5 out of 7 in the Re Refinement of 4MWK.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Re Refinement of 4MWK. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt211

b:19.4
occ:0.13
 PT A:PT210 1.8 4.3 0.2
CD2 A:HIS15 2.3 26.0 1.0
CG A:HIS15 2.4 22.1 1.0
NE2 A:HIS15 2.6 30.0 1.0
ND1 A:HIS15 2.8 36.0 1.0
CE1 A:HIS15 2.9 31.0 1.0
CB A:HIS15 3.1 14.2 1.0
CA A:HIS15 3.6 10.7 1.0
PT A:PT209 3.7 12.7 0.1
PT A:PT218 4.0 0.4 0.6
CL A:CL219 4.2 6.8 0.2
PT A:PT207 4.3 12.8 0.2
CG2 A:THR89 4.3 9.9 1.0
OG1 A:THR89 4.4 11.6 1.0
N A:HIS15 4.4 8.9 1.0
O A:ARG14 4.5 9.9 1.0
O A:HOH415 4.5 11.4 1.0
C A:HIS15 4.7 10.3 1.0
O A:HIS15 4.7 15.4 1.0
O A:HOH383 4.8 23.3 1.0
C A:ARG14 4.8 7.5 1.0
CB A:THR89 4.9 7.7 1.0

Platinum binding site 6 out of 7 in 5hmv

Go back to Platinum Binding Sites List in 5hmv
Platinum binding site 6 out of 7 in the Re Refinement of 4MWK.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Re Refinement of 4MWK. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt212

b:11.4
occ:0.15
 N A:LYS1 2.2 6.4 0.6
N A:LYS1 2.3 6.2 0.4
O A:HOH371 2.9 24.2 1.0
O A:HOH398 3.2 20.3 1.0
OG A:SER86 3.2 12.9 0.5
CA A:LYS1 3.2 5.8 0.4
CA A:LYS1 3.2 6.2 0.6
O A:HOH312 3.5 7.8 1.0
CB A:LYS1 3.5 5.9 0.4
CB A:LYS1 3.8 5.9 0.6
O A:HOH305 4.0 8.5 1.0
O A:HOH337 4.0 24.6 1.0
NE2 A:GLN41 4.1 6.2 1.0
OG1 A:THR40 4.1 5.5 1.0
CD A:GLN41 4.1 7.1 1.0
CG A:GLN41 4.3 5.9 1.0
CB A:SER86 4.3 9.1 0.5
O A:HOH416 4.5 22.7 1.0
CB A:SER86 4.5 10.0 0.5
C A:LYS1 4.5 5.8 0.6
C A:LYS1 4.5 5.9 0.4
OE1 A:GLN41 4.7 11.1 1.0
CG A:LYS1 4.9 6.0 0.4
O A:LYS1 4.9 6.2 0.6
O A:LYS1 5.0 5.7 0.4

Platinum binding site 7 out of 7 in 5hmv

Go back to Platinum Binding Sites List in 5hmv
Platinum binding site 7 out of 7 in the Re Refinement of 4MWK.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of Re Refinement of 4MWK. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt218

b:0.4
occ:0.60
 PT A:PT209 1.4 12.7 0.1
PT A:PT207 1.5 12.8 0.2
CL A:CL219 2.2 6.8 0.2
NE2 A:HIS15 2.4 30.0 1.0
CL A:CL217 2.8 6.2 0.2
PT A:PT208 3.3 13.9 0.2
CE1 A:HIS15 3.4 31.0 1.0
CD2 A:HIS15 3.4 26.0 1.0
PT A:PT211 4.0 19.4 0.1
OG1 A:THR89 4.4 11.6 1.0
ND1 A:HIS15 4.5 36.0 1.0
CG A:HIS15 4.5 22.1 1.0
O A:HOH303 4.8 13.4 1.0
O3 A:NO3204 5.0 24.8 0.5

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: Thu Oct 10 11:35:40 2024

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