Zinc in PDB 6qfi: Structure of Human Mcl-1 in Complex with Bim BH3 Peptide

Protein crystallography data

The structure of Structure of Human Mcl-1 in Complex with Bim BH3 Peptide, PDB code: 6qfi was solved by P.Dokurno, J.Murray, J.Davidson, I.Chen, B.Davis, C.J.Graham, R.Harris, A.M.Jordan, N.Matassova, C.Pedder, S.Ray, S.Roughley, J.Smith, C.Walmsley, Y.Wang, N.Whitehead, D.S.Williamson, P.Casara, T.Le Diguarher, J.Hickman, J.Stark, A.Kotschy, O.Geneste, R.E.Hubbard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 52.753, 71.700, 117.678, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23.6

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 6qfi

Go back to Zinc Binding Sites List in 6qfi
Zinc binding site 1 out of 4 in the Structure of Human Mcl-1 in Complex with Bim BH3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Mcl-1 in Complex with Bim BH3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:35.5
occ:1.00
NE2 A:HIS224 1.9 25.6 1.0
OE1 B:GLU158 2.3 42.7 1.0
OE2 B:GLU158 2.4 42.8 1.0
CD B:GLU158 2.6 41.2 1.0
CD2 A:HIS224 2.8 26.0 1.0
CE1 A:HIS224 3.0 29.6 1.0
CG A:HIS224 4.0 29.5 1.0
ND1 A:HIS224 4.1 26.1 1.0
CG B:GLU158 4.1 37.4 1.0
NH1 B:ARG154 4.2 27.6 1.0
CG1 B:ILE155 4.7 31.5 1.0

Zinc binding site 2 out of 4 in 6qfi

Go back to Zinc Binding Sites List in 6qfi
Zinc binding site 2 out of 4 in the Structure of Human Mcl-1 in Complex with Bim BH3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Mcl-1 in Complex with Bim BH3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:42.6
occ:1.00
NE2 A:HIS252 2.1 35.0 1.0
CD2 A:HIS252 3.0 31.8 1.0
CE1 A:HIS252 3.0 36.5 1.0
CG2 B:ILE146 3.9 52.9 1.0
ND1 A:HIS252 4.1 35.9 1.0
CG A:HIS252 4.2 31.5 1.0
O B:HOH208 4.5 48.7 1.0

Zinc binding site 3 out of 4 in 6qfi

Go back to Zinc Binding Sites List in 6qfi
Zinc binding site 3 out of 4 in the Structure of Human Mcl-1 in Complex with Bim BH3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Mcl-1 in Complex with Bim BH3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:88.3
occ:0.50
O A:HOH539 2.0 74.0 1.0
O A:HOH538 2.8 45.4 1.0
SG A:CYS286 2.9 78.8 1.0
CB A:CYS286 4.4 78.7 1.0
CA A:CYS286 4.6 73.8 1.0

Zinc binding site 4 out of 4 in 6qfi

Go back to Zinc Binding Sites List in 6qfi
Zinc binding site 4 out of 4 in the Structure of Human Mcl-1 in Complex with Bim BH3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Mcl-1 in Complex with Bim BH3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:63.7
occ:1.00
OE1 A:GLU322 2.0 74.7 1.0
NE2 A:HIS320 2.1 46.0 1.0
CD A:GLU322 2.9 88.5 1.0
CE1 A:HIS320 2.9 40.4 1.0
CD2 A:HIS320 3.3 40.2 1.0
OE2 A:GLU322 3.3 96.7 1.0
ND1 A:HIS320 4.1 39.2 1.0
CG A:GLU322 4.1 93.2 1.0
CG A:HIS320 4.3 41.4 1.0
CA A:GLU322 4.6 85.9 1.0
CB A:GLU322 4.6 90.5 1.0
O A:VAL321 4.7 69.7 1.0

Reference:

J.B.Murray, J.Davidson, I.Chen, B.Davis, P.Dokurno, C.J.Graham, R.Harris, A.Jordan, N.Matassova, C.Pedder, S.Ray, S.D.Roughley, J.Smith, C.Walmsley, Y.Wang, N.Whitehead, D.S.Williamson, P.Casara, T.Le Diguarher, J.Hickman, J.Stark, A.Kotschy, O.Geneste, R.E.Hubbard. Establishing Drug Discovery and Identification of Hit Series For the Anti-Apoptotic Proteins, Bcl-2 and Mcl-1. Acs Omega V. 4 8892 2019.
ISSN: ESSN 2470-1343
PubMed: 31459977
DOI: 10.1021/ACSOMEGA.9B00611
Page generated: Wed Dec 16 12:34:07 2020

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