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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

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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

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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

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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

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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

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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

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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

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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

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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: Thu Oct 10 11:44:11 2024

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