Atomistry » Platinum » PDB 5v6i-7kem » 6g5y
Atomistry »
  Platinum »
    PDB 5v6i-7kem »
      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

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy