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Platinum in PDB 6g5v: The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (pH 7.0)

Enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (pH 7.0)

All present enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (pH 7.0):
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 (pH 7.0), PDB code: 6g5v 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) 56.18 / 1.96
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.455, 79.455, 36.490, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 25

Other elements in 6g5v:

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (pH 7.0) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

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 (pH 7.0) (pdb code 6g5v). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 6 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 (pH 7.0), PDB code: 6g5v:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6;

Platinum binding site 1 out of 6 in 6g5v

Go back to Platinum Binding Sites List in 6g5v
Platinum binding site 1 out of 6 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (pH 7.0)


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 (pH 7.0) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:47.7
occ:0.50
 O A:HOH332 1.9 45.3 0.5
O A:HOH396 2.2 47.5 0.5
ND1 A:HIS15 2.2 58.6 1.0
O A:HOH322 2.3 35.0 0.5
CE1 A:HIS15 3.1 62.6 1.0
CG A:HIS15 3.1 56.4 1.0
CB A:HIS15 3.5 47.0 1.0
CA A:HIS15 3.6 46.6 1.0
O A:HIS15 4.0 49.1 1.0
NE2 A:HIS15 4.1 55.8 1.0
CD2 A:HIS15 4.2 56.0 1.0
C A:HIS15 4.2 43.7 1.0
O A:ARG14 4.7 42.0 1.0
N A:HIS15 4.7 41.3 1.0
OG1 A:THR89 4.8 47.4 1.0
OD1 A:ASN93 4.8 53.9 1.0

Platinum binding site 2 out of 6 in 6g5v

Go back to Platinum Binding Sites List in 6g5v
Platinum binding site 2 out of 6 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (pH 7.0)


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 (pH 7.0) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:47.9
occ:0.60
 O A:HOH372 2.2 38.5 0.6
O A:HOH371 2.2 34.1 0.6
NZ A:LYS33 2.3 41.4 1.0
CE A:LYS33 3.2 36.4 1.0
OD1 A:ASN37 3.6 47.3 1.0
O A:HOH308 3.7 18.7 0.4
ND2 A:ASN37 4.3 55.1 1.0
CG A:ASN37 4.4 45.7 1.0
CD A:LYS33 4.5 32.2 1.0

Platinum binding site 3 out of 6 in 6g5v

Go back to Platinum Binding Sites List in 6g5v
Platinum binding site 3 out of 6 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (pH 7.0)


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 (pH 7.0) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt203

b:66.3
occ:0.30
 OE2 A:GLU7 2.8 41.6 1.0
OE1 A:GLU7 3.1 33.8 1.0
NZ A:LYS1 3.1 46.9 1.0
CD A:GLU7 3.2 37.3 1.0
CE A:LYS1 3.5 41.3 1.0
CG A:GLU7 4.6 33.8 1.0
CD A:LYS1 4.9 39.5 1.0

Platinum binding site 4 out of 6 in 6g5v

Go back to Platinum Binding Sites List in 6g5v
Platinum binding site 4 out of 6 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (pH 7.0)


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 (pH 7.0) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt204

b:65.4
occ:0.30
 OXT A:LEU129 2.8 57.4 1.0
O A:LEU129 2.8 43.2 1.0
NZ A:LYS13 3.1 47.5 1.0
C A:LEU129 3.2 50.3 1.0
CE A:LYS13 3.6 49.8 1.0
CA A:LEU129 4.7 46.3 1.0
CD A:LYS13 4.8 49.0 1.0

Platinum binding site 5 out of 6 in 6g5v

Go back to Platinum Binding Sites List in 6g5v
Platinum binding site 5 out of 6 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (pH 7.0)


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 (pH 7.0) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt205

b:36.1
occ:0.40
 S A:DMS207 1.9 48.4 0.4
NE2 A:HIS15 2.2 55.8 1.0
NH1 A:ARG14 2.2 60.9 1.0
O A:DMS207 2.8 46.2 0.4
O A:HOH369 2.9 29.4 0.4
C1 A:DMS207 2.9 51.0 0.4
CD2 A:HIS15 3.1 56.0 1.0
CZ A:ARG14 3.2 62.0 1.0
C2 A:DMS207 3.2 49.5 0.4
CE1 A:HIS15 3.2 62.6 1.0
NE A:ARG14 3.4 61.7 1.0
CG A:HIS15 4.2 56.4 1.0
ND1 A:HIS15 4.2 58.6 1.0
OD1 A:ASP87 4.3 53.9 1.0
NH2 A:ARG14 4.3 57.3 1.0
OG1 A:THR89 4.5 47.4 1.0
CD A:ARG14 4.8 57.2 1.0

Platinum binding site 6 out of 6 in 6g5v

Go back to Platinum Binding Sites List in 6g5v
Platinum binding site 6 out of 6 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Lysozyme and A Platinum(II) Terpyridine Compound (pH 7.0)


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 (pH 7.0) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt206

b:41.0
occ:0.30
 NZ A:LYS97 2.8 57.9 1.0
CE A:LYS97 3.2 55.8 1.0
O A:HOH335 3.5 44.3 1.0
O A:HOH355 3.6 33.5 1.0
CB A:ASN93 4.0 40.8 1.0
O A:ASN93 4.6 30.0 1.0
CD A:LYS97 4.6 46.4 1.0
CG A:ASN93 4.7 43.4 1.0
C A:ASN93 4.9 30.2 1.0
CA A:ASN93 4.9 32.8 1.0
CG A:LYS97 5.0 38.2 1.0
ND2 A:ASN93 5.0 54.3 1.0

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

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