Iodine in PDB 4mr1: X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II)

Enzymatic activity of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II)

All present enzymatic activity of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II):
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II), PDB code: 4mr1 was solved by A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.23 / 1.99
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.017, 77.017, 36.834, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.4

Other elements in 4mr1:

The structure of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II) also contains other interesting chemical elements:

Platinum (Pt) 2 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II) (pdb code 4mr1). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II), PDB code: 4mr1:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 4mr1

Go back to Iodine Binding Sites List in 4mr1
Iodine binding site 1 out of 4 in the X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:28.3
occ:0.50
 I1 A:YPT201 0.0 28.3 0.5
N3 A:YPT201 0.0 40.5 0.5
PT2 A:YPT201 2.5 43.0 0.5
PT2 A:YPT201 2.5 43.0 0.5
ND1 A:HIS15 3.3 34.0 1.0
I1 A:YPT201 3.4 56.1 0.5
I2 A:YPT201 3.4 56.1 0.5
N A:ASN93 3.7 28.9 1.0
CG1 A:VAL92 3.8 28.0 1.0
CG A:HIS15 3.8 34.8 1.0
O A:HOH376 3.8 50.1 1.0
CE A:LYS96 3.8 29.1 1.0
CB A:HIS15 3.8 34.6 1.0
O A:THR89 3.9 29.1 1.0
CA A:ASN93 4.0 29.5 1.0
NZ A:LYS96 4.0 32.1 1.0
CB A:VAL92 4.0 29.5 1.0
CB A:ASN93 4.0 31.9 1.0
CE1 A:HIS15 4.1 35.6 1.0
O A:HIS15 4.3 37.9 1.0
C A:VAL92 4.4 28.6 1.0
OD1 A:ASN93 4.5 35.5 1.0
CA A:HIS15 4.6 35.1 1.0
CG2 A:THR89 4.7 23.3 1.0
C A:THR89 4.7 26.8 1.0
CG A:ASN93 4.8 35.5 1.0
CA A:THR89 4.8 26.1 1.0
CD2 A:HIS15 4.8 32.7 1.0
CD A:LYS96 4.8 28.9 1.0
CA A:VAL92 4.9 28.1 1.0
C A:HIS15 4.9 36.2 1.0
NE2 A:HIS15 4.9 32.6 1.0
N3 A:YPT201 5.0 40.5 0.5
I2 A:YPT201 5.0 28.3 0.5

Iodine binding site 2 out of 4 in 4mr1

Go back to Iodine Binding Sites List in 4mr1
Iodine binding site 2 out of 4 in the X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:56.1
occ:0.50
 I1 A:YPT201 0.0 56.1 0.5
I2 A:YPT201 0.0 56.1 0.5
PT2 A:YPT201 2.3 43.0 0.5
PT2 A:YPT201 2.3 43.0 0.5
I1 A:YPT201 3.4 28.3 0.5
N3 A:YPT201 3.4 40.5 0.5
N3 A:YPT201 3.4 40.5 0.5
I2 A:YPT201 3.4 28.3 0.5
O A:HOH376 3.7 50.1 1.0
NZ A:LYS96 3.9 32.1 1.0
O A:HIS15 4.3 37.9 1.0
ND1 A:HIS15 4.4 34.0 1.0
O A:HOH435 4.4 36.2 0.5
CA A:HIS15 4.9 35.1 1.0
CE A:LYS96 4.9 29.1 1.0
C A:HIS15 4.9 36.2 1.0

Iodine binding site 3 out of 4 in 4mr1

Go back to Iodine Binding Sites List in 4mr1
Iodine binding site 3 out of 4 in the X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:56.1
occ:0.50
 I1 A:YPT201 0.0 56.1 0.5
I2 A:YPT201 0.0 56.1 0.5
PT2 A:YPT201 2.3 43.0 0.5
PT2 A:YPT201 2.3 43.0 0.5
I1 A:YPT201 3.4 28.3 0.5
N3 A:YPT201 3.4 40.5 0.5
N3 A:YPT201 3.4 40.5 0.5
I2 A:YPT201 3.4 28.3 0.5
O A:HOH376 3.7 50.1 1.0
NZ A:LYS96 3.9 32.1 1.0
O A:HIS15 4.3 37.9 1.0
ND1 A:HIS15 4.4 34.0 1.0
O A:HOH435 4.4 36.2 0.5
CA A:HIS15 4.9 35.1 1.0
CE A:LYS96 4.9 29.1 1.0
C A:HIS15 4.9 36.2 1.0

Iodine binding site 4 out of 4 in 4mr1

Go back to Iodine Binding Sites List in 4mr1
Iodine binding site 4 out of 4 in the X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of X-Ray Structure of the Adduct Between Hen Egg White Lysozyme and Cis- Diamminediiodoplatinum(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:28.3
occ:0.50
 N3 A:YPT201 0.0 40.5 0.5
I2 A:YPT201 0.0 28.3 0.5
PT2 A:YPT201 2.5 43.0 0.5
PT2 A:YPT201 2.5 43.0 0.5
O A:HOH425 3.1 52.7 1.0
ND1 A:HIS15 3.2 34.0 1.0
NH1 A:ARG14 3.2 42.1 1.0
O A:HOH352 3.3 38.1 1.0
I1 A:YPT201 3.4 56.1 0.5
I2 A:YPT201 3.4 56.1 0.5
CE1 A:HIS15 3.7 35.6 1.0
O A:ARG14 3.7 34.0 1.0
CA A:HIS15 4.1 35.1 1.0
CZ A:ARG14 4.1 40.4 1.0
CG A:HIS15 4.2 34.8 1.0
C A:ARG14 4.5 34.3 1.0
NH2 A:ARG14 4.5 39.1 1.0
CG A:ARG14 4.6 39.1 1.0
CB A:HIS15 4.6 34.6 1.0
N A:HIS15 4.7 34.5 1.0
NE2 A:HIS15 4.7 32.6 1.0
C A:HIS15 4.9 36.2 1.0
I1 A:YPT201 5.0 28.3 0.5
N3 A:YPT201 5.0 40.5 0.5

Reference:

L.Messori, T.Marzo, C.Gabbiani, A.A.Valdes, A.G.Quiroga, A.Merlino. Peculiar Features in the Crystal Structure of the Adduct Formed Between Cis-PTI2(NH3)2 and Hen Egg White Lysozyme. Inorg.Chem. V. 52 13827 2013.
ISSN: ISSN 0020-1669
PubMed: 24256441
DOI: 10.1021/IC402611M
Page generated: Sun Dec 13 19:34:52 2020

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