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Zinc in PDB 3kz0: Mcl-1 Complex with Mcl-1-Specific Selected Peptide

Protein crystallography data

The structure of Mcl-1 Complex with Mcl-1-Specific Selected Peptide, PDB code: 3kz0 was solved by S.Dutta, E.Fire, R.A.Grant, R.T.Sauer, A.E.Keating, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.17 / 2.35
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 64.325, 121.523, 46.379, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 27

Zinc Binding Sites:

The binding sites of Zinc atom in the Mcl-1 Complex with Mcl-1-Specific Selected Peptide (pdb code 3kz0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Mcl-1 Complex with Mcl-1-Specific Selected Peptide, PDB code: 3kz0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3kz0

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Zinc binding site 1 out of 7 in the Mcl-1 Complex with Mcl-1-Specific Selected Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mcl-1 Complex with Mcl-1-Specific Selected Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:41.0
occ:1.00
NE2 A:HIS224 2.1 21.3 1.0
OE2 C:GLU16 2.4 80.6 1.0
O A:HOH330 2.4 10.1 1.0
OE1 C:GLU16 2.6 76.6 1.0
CD C:GLU16 2.7 70.3 1.0
O C:HOH58 2.9 45.7 1.0
CE1 A:HIS224 2.9 33.0 1.0
CD2 A:HIS224 3.2 36.8 1.0
O C:HOH28 3.8 35.5 1.0
ND2 C:ASN17 4.0 25.7 1.0
CB A:ASN223 4.0 59.1 1.0
CG C:GLU16 4.1 53.5 1.0
ND1 A:HIS224 4.1 35.7 1.0
CG A:HIS224 4.3 34.5 1.0
OD1 A:ASN223 4.3 75.3 1.0
CG A:ASN223 4.5 68.5 1.0
CG2 C:ILE13 4.7 28.6 1.0
CG C:ASN17 4.9 25.2 1.0
CB C:GLU16 5.0 36.2 1.0

Zinc binding site 2 out of 7 in 3kz0

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Zinc binding site 2 out of 7 in the Mcl-1 Complex with Mcl-1-Specific Selected Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mcl-1 Complex with Mcl-1-Specific Selected Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:61.5
occ:1.00
OD2 A:ASP304 2.0 42.5 1.0
CG A:ASP304 2.8 36.2 1.0
OD1 A:ASP304 2.8 38.3 1.0
CB A:ASP304 4.2 26.9 1.0

Zinc binding site 3 out of 7 in 3kz0

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Zinc binding site 3 out of 7 in the Mcl-1 Complex with Mcl-1-Specific Selected Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mcl-1 Complex with Mcl-1-Specific Selected Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:76.7
occ:1.00
OE2 B:GLU292 2.1 73.1 1.0
OD1 A:ASP241 2.4 67.8 1.0
OD2 A:ASP241 2.9 65.5 1.0
CG A:ASP241 3.0 68.2 1.0
CD B:GLU292 3.1 69.5 1.0
OE1 B:GLU292 3.5 72.1 1.0
CB B:GLU288 3.8 52.1 1.0
CG A:PRO289 4.2 68.0 1.0
CG B:GLU292 4.3 59.3 1.0
CB A:ASP241 4.5 71.8 1.0
C B:GLU288 4.9 55.0 1.0
N B:PRO289 5.0 52.2 1.0
CA B:GLU288 5.0 52.5 1.0

Zinc binding site 4 out of 7 in 3kz0

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Zinc binding site 4 out of 7 in the Mcl-1 Complex with Mcl-1-Specific Selected Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mcl-1 Complex with Mcl-1-Specific Selected Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:36.7
occ:1.00
NE2 B:HIS224 2.0 33.6 1.0
O B:HOH54 2.3 6.3 1.0
OE2 D:GLU16 2.4 33.1 1.0
O D:HOH80 2.5 39.2 1.0
OE1 D:GLU16 2.7 46.4 1.0
CD D:GLU16 2.8 34.4 1.0
CE1 B:HIS224 2.9 33.3 1.0
CD2 B:HIS224 3.0 31.1 1.0
ND2 D:ASN17 3.9 23.9 1.0
ND1 B:HIS224 4.0 30.1 1.0
CG B:HIS224 4.1 27.3 1.0
CB B:ASN223 4.1 39.0 1.0
CG D:GLU16 4.2 30.6 1.0
ND2 B:ASN223 4.3 42.6 1.0
CG2 D:ILE13 4.5 35.4 1.0
CG B:ASN223 4.7 42.2 1.0

Zinc binding site 5 out of 7 in 3kz0

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Zinc binding site 5 out of 7 in the Mcl-1 Complex with Mcl-1-Specific Selected Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mcl-1 Complex with Mcl-1-Specific Selected Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3

b:46.5
occ:1.00
OD2 B:ASP304 2.1 31.3 1.0
O B:HOH55 2.4 32.5 1.0
O B:HOH9 2.6 35.3 1.0
CG B:ASP304 2.8 28.8 1.0
OD1 B:ASP304 2.9 27.1 1.0
O B:HOH329 3.7 74.4 1.0
CB B:ASP304 4.3 22.4 1.0
O B:HOH65 4.6 46.5 1.0

Zinc binding site 6 out of 7 in 3kz0

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Zinc binding site 6 out of 7 in the Mcl-1 Complex with Mcl-1-Specific Selected Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Mcl-1 Complex with Mcl-1-Specific Selected Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5

b:68.5
occ:1.00
OE1 B:GLU317 2.8 43.9 1.0
ND1 B:HIS320 2.9 60.0 1.0
CG B:HIS320 3.5 54.3 1.0
CE1 B:HIS320 3.7 58.1 1.0
CD B:GLU317 3.7 51.0 1.0
CB B:HIS320 3.8 48.2 1.0
OE2 B:GLU317 3.8 51.8 1.0
CD2 B:HIS320 4.4 54.6 1.0
O B:GLU317 4.5 29.8 1.0
NE2 B:HIS320 4.5 55.9 1.0

Zinc binding site 7 out of 7 in 3kz0

Go back to Zinc Binding Sites List in 3kz0
Zinc binding site 7 out of 7 in the Mcl-1 Complex with Mcl-1-Specific Selected Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Mcl-1 Complex with Mcl-1-Specific Selected Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:76.9
occ:1.00
OE2 A:GLU292 2.4 81.8 1.0
OE2 B:GLU240 2.5 76.1 1.0
OD1 B:ASP241 2.5 77.2 1.0
OD2 B:ASP241 2.6 79.9 1.0
O A:HOH61 2.7 67.3 1.0
OE1 A:GLU292 2.8 78.3 1.0
CD A:GLU292 2.9 77.1 1.0
CG B:ASP241 2.9 78.4 1.0
CD B:GLU240 3.5 73.8 1.0
OE1 A:GLU288 3.8 0.8 1.0
CG B:GLU240 3.8 74.4 1.0
CG A:GLU292 4.3 68.2 1.0
CB B:ASP241 4.4 74.2 1.0
CG B:PRO289 4.6 53.0 1.0
CB A:GLU288 4.6 83.5 1.0
OE1 B:GLU240 4.6 69.9 1.0
CD A:GLU288 4.9 0.3 1.0

Reference:

S.Dutta, S.Gulla, T.S.Chen, E.Fire, R.A.Grant, A.E.Keating. Determinants of BH3 Binding Specificity For Mcl-1 Versus Bcl-Xl. J.Mol.Biol. V. 398 747 2010.
ISSN: ISSN 0022-2836
PubMed: 20363230
DOI: 10.1016/J.JMB.2010.03.058
Page generated: Wed Dec 16 04:31:23 2020

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