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Zinc in PDB 2nl9: Crystal Structure of the Mcl-1:Bim BH3 Complex

Protein crystallography data

The structure of Crystal Structure of the Mcl-1:Bim BH3 Complex, PDB code: 2nl9 was solved by P.E.Czabotar, P.M.Colman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.12 / 1.55
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 52.380, 70.080, 117.180, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.3

Other elements in 2nl9:

The structure of Crystal Structure of the Mcl-1:Bim BH3 Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Mcl-1:Bim BH3 Complex (pdb code 2nl9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of the Mcl-1:Bim BH3 Complex, PDB code: 2nl9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 2nl9

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Zinc binding site 1 out of 7 in the Crystal Structure of the Mcl-1:Bim BH3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Mcl-1:Bim BH3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:37.9
occ:0.80
OE2 A:GLU292 2.1 26.8 1.0
OE1 A:GLU292 2.7 26.6 1.0
CD A:GLU292 2.8 23.5 1.0
O A:HOH2074 3.8 39.6 1.0
CG A:GLU292 4.2 19.8 1.0
CG A:GLU288 4.3 28.6 1.0
O A:HOH2096 4.7 42.2 1.0
CB A:GLU288 4.9 22.1 1.0
O A:HOH2115 4.9 44.9 0.5

Zinc binding site 2 out of 7 in 2nl9

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Zinc binding site 2 out of 7 in the Crystal Structure of the Mcl-1:Bim BH3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Mcl-1:Bim BH3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:14.5
occ:0.90
OE2 A:GLU317 2.0 14.3 1.0
OD1 A:ASP313 2.0 13.8 1.0
CG A:ASP313 2.8 17.0 1.0
CD A:GLU317 2.9 14.5 1.0
OD2 A:ASP313 2.9 15.6 1.0
CG A:GLU317 3.1 13.2 1.0
OE1 A:GLU317 4.0 16.7 1.0
O A:HOH2008 4.2 17.9 1.0
CB A:ASP313 4.2 14.9 1.0
O A:HOH2112 4.3 44.8 1.0
O A:ASP313 4.6 13.8 1.0
CB A:GLU317 4.7 15.2 1.0
CA A:ASP313 4.8 13.5 1.0
NH2 A:ARG310 5.0 16.9 1.0

Zinc binding site 3 out of 7 in 2nl9

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Zinc binding site 3 out of 7 in the Crystal Structure of the Mcl-1:Bim BH3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Mcl-1:Bim BH3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:15.2
occ:0.50
ZN A:ZN1004 2.0 22.1 0.5
NE2 A:HIS252 2.0 25.0 1.0
O A:HOH2106 2.0 24.2 1.0
O B:HOH1035 2.3 15.2 1.0
CD2 A:HIS252 2.8 23.9 1.0
CE1 A:HIS252 3.1 24.7 1.0
NH1 B:ARG63 3.9 22.3 1.0
NH2 B:ARG63 4.0 18.8 1.0
CG A:HIS252 4.0 18.8 1.0
O A:HOH2107 4.0 29.7 1.0
ND1 A:HIS252 4.1 28.2 1.0
CZ B:ARG63 4.2 19.8 1.0
O B:HOH1029 4.4 20.6 0.5
CG2 B:ILE56 4.5 28.7 1.0
O B:HOH1031 4.5 31.0 1.0
CG B:GLN60 4.6 28.9 1.0
O A:HIS252 4.6 16.2 1.0
OG A:SER255 4.7 16.6 1.0

Zinc binding site 4 out of 7 in 2nl9

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Zinc binding site 4 out of 7 in the Crystal Structure of the Mcl-1:Bim BH3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Mcl-1:Bim BH3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1004

b:22.1
occ:0.50
ZN A:ZN1003 2.0 15.2 0.5
NE2 A:HIS252 2.1 25.0 1.0
O A:HOH2107 2.2 29.7 1.0
O A:HOH2106 2.2 24.2 1.0
CE1 A:HIS252 2.2 24.7 1.0
CD2 A:HIS252 3.4 23.9 1.0
ND1 A:HIS252 3.6 28.2 1.0
CG A:HIS252 4.1 18.8 1.0
O B:HOH1035 4.2 15.2 1.0
CG2 B:ILE56 4.4 28.7 1.0
CD1 B:ILE56 4.4 30.5 1.0
OG A:SER255 4.7 16.6 1.0

Zinc binding site 5 out of 7 in 2nl9

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Zinc binding site 5 out of 7 in the Crystal Structure of the Mcl-1:Bim BH3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Mcl-1:Bim BH3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1005

b:45.0
occ:0.50
O A:HOH2104 2.1 45.6 0.5
SG A:CYS286 2.3 23.4 0.5
O A:HOH2103 2.3 37.0 0.5
O A:HOH2102 2.4 27.5 1.0
SG A:CYS286 2.9 23.3 0.5
CB A:CYS286 3.0 24.2 0.5
CB A:CYS286 3.0 24.2 0.5
CA A:CYS286 3.1 24.2 0.5
CA A:CYS286 3.1 24.2 0.5
N A:ILE287 3.8 22.9 1.0
ZN A:ZN1006 3.9 35.7 0.2
C A:CYS286 4.0 23.4 1.0
N A:CYS286 4.3 25.1 1.0
O A:SER285 4.5 28.4 1.0
N A:GLU288 4.7 21.0 1.0
NE A:ARG187 4.8 30.4 1.0
C A:SER285 4.8 27.6 1.0
NH2 A:ARG187 4.9 37.6 1.0
CB A:GLU288 5.0 22.1 1.0
CG1 A:ILE287 5.0 22.1 1.0

Zinc binding site 6 out of 7 in 2nl9

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Zinc binding site 6 out of 7 in the Crystal Structure of the Mcl-1:Bim BH3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Mcl-1:Bim BH3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1006

b:35.7
occ:0.25
SG A:CYS286 2.3 23.3 0.5
O A:HOH2115 2.5 44.9 0.5
SG A:CYS286 2.6 23.4 0.5
CB A:CYS286 3.1 24.2 0.5
CB A:CYS286 3.2 24.2 0.5
ZN A:ZN1005 3.9 45.0 0.5
O A:HOH2085 4.0 23.4 1.0
O A:HOH2099 4.1 41.7 1.0
CA A:CYS286 4.6 24.2 0.5
CA A:CYS286 4.6 24.2 0.5
O A:HOH2103 4.7 37.0 0.5
CB A:GLU288 4.8 22.1 1.0

Zinc binding site 7 out of 7 in 2nl9

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Zinc binding site 7 out of 7 in the Crystal Structure of the Mcl-1:Bim BH3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Mcl-1:Bim BH3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1007

b:24.7
occ:0.60
OE1 B:GLU61 2.1 33.3 1.0
O B:HOH1034 2.3 52.5 1.0
OE2 B:GLU61 2.6 33.7 1.0
CD B:GLU61 2.7 29.8 1.0
O B:HOH1033 3.9 41.9 1.0
NE B:ARG64 4.1 19.7 1.0
CG B:GLU61 4.1 24.5 1.0
NH2 B:ARG64 4.3 21.4 1.0
O B:HOH1019 4.6 42.9 1.0
CZ B:ARG64 4.6 22.2 1.0
CZ2 B:TRP57 4.7 34.8 1.0
CB B:GLU61 4.9 20.3 1.0

Reference:

P.E.Czabotar, E.F.Lee, M.F.Van Delft, C.L.Day, B.J.Smith, D.C.Huang, W.D.Fairlie, M.G.Hinds, P.M.Colman. Structural Insights Into the Degradation of Mcl-1 Induced By BH3 Domains. Proc.Natl.Acad.Sci.Usa V. 104 6217 2007.
ISSN: ISSN 0027-8424
PubMed: 17389404
DOI: 10.1073/PNAS.0701297104
Page generated: Wed Dec 16 03:43:25 2020

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