Atomistry » Platinum » PDB 5djm-5v6i » 5hmv
Atomistry »
  Platinum »
    PDB 5djm-5v6i »
      5hmv »

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

Go back to Platinum Binding Sites List in 5hmv
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

Go back to Platinum Binding Sites List in 5hmv
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

Go back to Platinum Binding Sites List in 5hmv
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

Go back to Platinum Binding Sites List in 5hmv
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy