Atomistry » Platinum » PDB 5yky-7bpr » 6g5y
Atomistry »
  Platinum »
    PDB 5yky-7bpr »
      6g5y »

Platinum in PDB 6g5y: The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH)

Enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH)

All present enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH):
3.2.1.17;

Protein crystallography data

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH), PDB code: 6g5y was solved by A.Merlino, G.Ferraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.50 / 1.49
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.490, 78.490, 36.730, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24

Platinum Binding Sites:

The binding sites of Platinum atom in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH) (pdb code 6g5y). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 8 binding sites of Platinum where determined in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH), PDB code: 6g5y:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Platinum binding site 1 out of 8 in 6g5y

Go back to Platinum Binding Sites List in 6g5y
Platinum binding site 1 out of 8 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt204

b:33.8
occ:0.75
 OE2 A:GLU7 2.2 26.4 1.0
O A:HOH373 2.2 30.1 0.8
NZ A:LYS1 2.2 37.1 0.8
S A:DMS212 2.2 53.2 0.8
CE A:LYS1 2.6 16.2 0.2
CD A:GLU7 3.0 23.8 1.0
O A:DMS212 3.0 56.1 0.8
O A:HOH316 3.1 14.9 0.2
NZ A:LYS1 3.1 14.7 0.2
OE1 A:GLU7 3.2 23.7 1.0
C1 A:DMS212 3.2 56.0 0.8
C2 A:DMS212 3.4 52.9 0.8
CE A:LYS1 3.5 38.0 0.8
CD A:LYS1 4.0 15.5 0.2
CG A:GLU7 4.3 24.1 1.0
CG A:LYS1 4.7 16.7 0.2
CD A:LYS1 4.7 32.8 0.8

Platinum binding site 2 out of 8 in 6g5y

Go back to Platinum Binding Sites List in 6g5y
Platinum binding site 2 out of 8 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt205

b:28.5
occ:0.60
 S A:DMS217 2.2 30.9 0.6
O A:HOH382 2.2 17.7 0.6
NH2 A:ARG14 2.2 29.5 1.0
NE2 A:HIS15 2.3 29.3 1.0
O A:DMS217 2.9 36.1 0.6
CZ A:ARG14 3.1 27.8 1.0
CE1 A:HIS15 3.2 31.6 1.0
NE A:ARG14 3.2 30.4 1.0
C1 A:DMS217 3.3 29.0 0.6
CD2 A:HIS15 3.3 31.0 1.0
C2 A:DMS217 3.5 29.6 0.6
O A:DMS213 4.1 25.9 0.5
NH1 A:ARG14 4.2 29.7 1.0
ND1 A:HIS15 4.3 32.4 1.0
OD1 A:ASP87 4.4 36.5 1.0
CG A:HIS15 4.4 26.7 1.0
CD A:ARG14 4.6 31.0 1.0
OG1 A:THR89 4.7 34.1 1.0
N A:ILE88 4.9 26.3 1.0

Platinum binding site 3 out of 8 in 6g5y

Go back to Platinum Binding Sites List in 6g5y
Platinum binding site 3 out of 8 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt206

b:31.5
occ:0.75
 S A:DMS216 2.2 33.9 0.8
S A:DMS218 2.2 40.0 0.8
O A:HOH310 2.2 18.0 0.8
ND1 A:HIS15 2.3 32.4 1.0
O A:DMS218 2.7 50.5 0.8
O A:DMS216 3.0 50.0 0.8
CG A:HIS15 3.2 26.7 1.0
C1 A:DMS216 3.2 34.1 0.8
CE1 A:HIS15 3.3 31.6 1.0
CB A:HIS15 3.4 29.8 1.0
C2 A:DMS216 3.4 42.5 0.8
C1 A:DMS218 3.4 45.6 0.8
CA A:HIS15 3.4 27.1 1.0
C2 A:DMS218 3.5 38.7 0.8
O A:HIS15 3.9 31.6 1.0
C A:HIS15 4.1 27.0 1.0
O A:HOH358 4.3 33.5 1.0
CD2 A:HIS15 4.3 31.0 1.0
NE2 A:HIS15 4.4 29.3 1.0
CG2 A:THR89 4.6 32.5 1.0
N A:HIS15 4.6 26.9 1.0
OG1 A:THR89 4.7 34.1 1.0
O A:ARG14 4.8 26.6 1.0

Platinum binding site 4 out of 8 in 6g5y

Go back to Platinum Binding Sites List in 6g5y
Platinum binding site 4 out of 8 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt207

b:41.3
occ:0.40
 S A:DMS214 1.7 36.3 0.4
NZ A:LYS13 1.9 27.8 1.0
C1 A:DMS214 2.6 38.1 0.4
OXT A:LEU129 2.7 61.0 1.0
O A:DMS214 2.7 39.2 0.4
CE A:LYS13 2.8 36.1 1.0
C2 A:DMS214 3.0 38.8 0.4
C A:LEU129 3.8 50.9 1.0
CD A:LYS13 4.0 32.3 1.0
O A:LEU129 4.1 52.8 1.0
O A:HOH333 4.6 27.4 0.5
CA A:LEU129 4.9 44.7 1.0
CB A:LEU129 4.9 46.4 1.0

Platinum binding site 5 out of 8 in 6g5y

Go back to Platinum Binding Sites List in 6g5y
Platinum binding site 5 out of 8 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt208

b:47.2
occ:0.45
 O A:HOH381 2.2 33.4 0.5
O A:HOH386 2.2 25.1 0.5
NZ A:LYS96 2.3 32.7 1.0
CE A:LYS96 3.1 28.9 1.0
C2 A:DMS218 3.2 38.7 0.8
CD A:LYS96 3.5 29.3 1.0
O A:HIS15 4.4 31.6 1.0
S A:DMS218 4.7 40.0 0.8
CE1 A:TYR20 4.8 24.7 1.0
CG A:LYS96 4.9 24.3 1.0

Platinum binding site 6 out of 8 in 6g5y

Go back to Platinum Binding Sites List in 6g5y
Platinum binding site 6 out of 8 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt209

b:45.1
occ:0.30
 ND2 A:ASN93 1.9 37.0 0.5
O A:HOH390 2.2 35.3 0.3
NZ A:LYS97 2.6 50.6 1.0
O A:HOH380 2.6 41.8 0.3
CG A:ASN93 2.8 31.0 0.5
OD1 A:ASN93 3.0 36.4 0.5
CG A:ASN93 4.1 32.7 0.5
CE A:LYS97 4.1 49.5 1.0
CB A:ASN93 4.1 30.5 0.5
CB A:ASN93 4.1 31.1 0.5
ND2 A:ASN93 4.2 29.0 0.5
OD1 A:ASN93 4.5 34.6 0.5
O A:ASN93 4.6 27.2 0.5
O A:ASN93 4.7 27.4 0.5
CA A:ASN93 4.8 28.4 0.5
CA A:ASN93 4.9 28.6 0.5
C A:ASN93 4.9 27.2 0.5
C A:ASN93 4.9 27.2 0.5

Platinum binding site 7 out of 8 in 6g5y

Go back to Platinum Binding Sites List in 6g5y
Platinum binding site 7 out of 8 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt210

b:43.2
occ:0.30
 O A:HOH304 2.0 37.0 1.0
O A:HOH402 2.2 23.3 0.3
O A:HOH411 2.5 52.3 1.0
OD2 A:ASP101 3.7 42.8 1.0
ND2 A:ASN103 4.3 37.5 0.5
CG A:ASP101 4.3 40.0 1.0
O A:HOH306 4.5 26.1 1.0
CB A:ASP101 4.9 34.5 1.0
OD1 A:ASP101 4.9 38.7 1.0
O A:ASP101 5.0 36.5 1.0

Platinum binding site 8 out of 8 in 6g5y

Go back to Platinum Binding Sites List in 6g5y
Platinum binding site 8 out of 8 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 8 of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (Acid pH) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt211

b:49.1
occ:0.20
 O A:HOH322 1.5 11.4 0.2
O A:HOH391 2.2 15.5 0.2
N A:LYS1 2.5 16.8 0.2
N A:LYS1 2.6 22.6 0.8
CA A:LYS1 3.3 17.0 0.2
CA A:LYS1 3.3 23.8 0.8
O A:HOH305 3.7 38.9 1.0
CB A:LYS1 3.7 16.6 0.2
CB A:LYS1 3.7 28.8 0.8
NE2 A:GLN41 4.1 21.7 1.0
CB A:SER86 4.3 31.8 1.0
O A:HOH332 4.3 22.1 1.0
OG1 A:THR40 4.7 18.7 1.0
C A:LYS1 4.7 18.3 0.2
CD A:GLN41 4.7 23.3 1.0
C A:LYS1 4.7 23.0 0.8
CG A:GLN41 4.9 20.2 1.0
CA A:SER86 4.9 28.3 1.0
CG A:LYS1 5.0 32.6 0.8

Reference:

G.Ferraro, T.Marzo, T.Infrasca, A.Cilibrizzi, R.Vilar, L.Messori, A.Merlino. A Case of Extensive Protein Platination: the Reaction of Lysozyme with A Pt(II)-Terpyridine Complex. Dalton Trans V. 47 8716 2018.
ISSN: ESSN 1477-9234
PubMed: 29904761
DOI: 10.1039/C8DT01254G
Page generated: Wed Dec 16 02:05:35 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy