Atomistry » Zinc » PDB 3d7h-3dgd » 3d7v
Atomistry »
  Zinc »
    PDB 3d7h-3dgd »
      3d7v »

Zinc in PDB 3d7v: Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand

Protein crystallography data

The structure of Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand, PDB code: 3d7v was solved by E.F.Lee, P.E.Czabotar, P.M.Colman, W.D.Fairlie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.03
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 51.171, 69.635, 120.654, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand (pdb code 3d7v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand, PDB code: 3d7v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3d7v

Go back to Zinc Binding Sites List in 3d7v
Zinc binding site 1 out of 4 in the Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand


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 Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:33.1
occ:1.00
NE2 A:HIS252 2.1 22.1 1.0
O B:HOH77 2.3 13.4 1.0
CD2 A:HIS252 2.9 20.0 1.0
CE1 A:HIS252 3.2 23.2 1.0
NH2 B:ARG63 4.0 14.2 1.0
NH1 B:ARG63 4.0 16.0 1.0
CG A:HIS252 4.2 21.2 1.0
ND1 A:HIS252 4.3 24.2 1.0
CZ B:ARG63 4.3 17.9 1.0
CG2 B:ILE56 4.4 28.4 1.0
O A:HOH399 4.4 42.6 1.0
O A:HIS252 4.8 15.9 1.0
OG A:SER255 5.0 18.0 1.0

Zinc binding site 2 out of 4 in 3d7v

Go back to Zinc Binding Sites List in 3d7v
Zinc binding site 2 out of 4 in the Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand


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 Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:29.8
occ:1.00
OE1 B:GLU68 1.9 22.8 1.0
NE2 A:HIS224 2.0 17.1 1.0
O B:HOH102 2.1 35.1 1.0
O A:HOH347 2.3 14.7 1.0
CD B:GLU68 2.8 22.1 1.0
CE1 A:HIS224 2.9 16.6 1.0
CD2 A:HIS224 3.0 17.9 1.0
OE2 B:GLU68 3.0 25.0 1.0
O B:HOH103 3.5 31.7 1.0
O B:HOH82 3.5 26.9 1.0
ND1 A:HIS224 4.1 18.2 1.0
CG A:HIS224 4.1 19.6 1.0
CG B:GLU68 4.2 20.2 1.0
CB A:ASN223 4.5 24.1 1.0
N B:ALA69 4.8 17.4 1.0
CB B:GLU68 4.8 17.7 1.0
CG2 B:ILE65 4.8 16.8 1.0
CB B:ALA69 4.9 17.2 1.0
CA B:ALA69 4.9 18.1 1.0
O B:ILE65 4.9 17.1 1.0

Zinc binding site 3 out of 4 in 3d7v

Go back to Zinc Binding Sites List in 3d7v
Zinc binding site 3 out of 4 in the Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand


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 Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:49.3
occ:0.50
SG A:CYS286 2.3 40.6 1.0
CB A:CYS286 3.1 37.0 1.0
O A:HOH384 3.3 30.6 0.5
OE1 A:GLU288 3.3 44.6 1.0
CD A:GLU288 3.6 39.5 1.0
OE2 A:GLU288 3.6 41.4 1.0
CB A:GLU288 4.5 29.9 1.0
CA A:CYS286 4.5 37.2 1.0
CG A:GLU288 4.6 33.5 1.0

Zinc binding site 4 out of 4 in 3d7v

Go back to Zinc Binding Sites List in 3d7v
Zinc binding site 4 out of 4 in the Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand


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 Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:34.1
occ:1.00
NE2 A:HIS320 2.1 21.7 1.0
OE1 A:GLU322 2.2 40.4 1.0
O A:HOH362 2.3 41.6 1.0
CG A:GLU322 2.7 36.9 1.0
CD A:GLU322 2.9 39.3 1.0
CD2 A:HIS320 3.0 20.6 1.0
CE1 A:HIS320 3.1 22.1 1.0
OE2 A:GLU322 4.1 43.9 1.0
O A:HOH389 4.2 39.3 1.0
CG A:HIS320 4.2 20.6 1.0
ND1 A:HIS320 4.2 22.4 1.0
CB A:GLU322 4.2 36.8 1.0
O A:VAL321 4.6 32.3 1.0
CA A:GLU322 4.8 36.4 1.0
N A:GLU322 5.0 34.2 1.0

Reference:

E.F.Lee, P.E.Czabotar, M.F.Van Delft, E.M.Michalak, M.J.Boyle, S.N.Willis, H.Puthalakath, P.Bouillet, P.M.Colman, D.C.S.Huang, W.D.Fairlie. A Novel BH3 Ligand That Selectively Targets Mcl-1 Reveals That Apoptosis Can Proceed Without Mcl-1 Degradation. J.Cell Biol. V. 180 341 2008.
ISSN: ISSN 0021-9525
PubMed: 18209102
DOI: 10.1083/JCB.200708096
Page generated: Wed Dec 16 04:12:22 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy