Atomistry » Iodine » PDB 4k1c-4mw7 » 4mr1
Atomistry »
  Iodine »
    PDB 4k1c-4mw7 »
      4mr1 »

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
 N3 A:YPT201 0.0 40.5 0.5
I1 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
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
N3 A:YPT201 3.4 40.5 0.5
I1 A:YPT201 3.4 28.3 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
N3 A:YPT201 3.4 40.5 0.5
I1 A:YPT201 3.4 28.3 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
N3 A:YPT201 5.0 40.5 0.5
I1 A:YPT201 5.0 28.3 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: Fri Aug 8 17:54:21 2025

Last articles

Zn in 9QM9
Zn in 9S44
Zn in 9OFE
Zn in 9OFC
Zn in 9OFD
Zn in 9OF1
Zn in 9OFB
Zn in 9N0J
Zn in 9M5X
Zn in 9LGI
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy