Zinc in PDB 6ux8: Structure of Monobody 33 Mlkl N-Terminal Domain Complex

Protein crystallography data

The structure of Structure of Monobody 33 Mlkl N-Terminal Domain Complex, PDB code: 6ux8 was solved by R.W.Birkinshaw, E.J.Petrie, J.M.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.76 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.294, 59.418, 68.043, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 29.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Monobody 33 Mlkl N-Terminal Domain Complex (pdb code 6ux8). 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 Monobody 33 Mlkl N-Terminal Domain Complex, PDB code: 6ux8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6ux8

Go back to Zinc Binding Sites List in 6ux8
Zinc binding site 1 out of 4 in the Structure of Monobody 33 Mlkl N-Terminal Domain Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Monobody 33 Mlkl N-Terminal Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:61.4
occ:1.00
OE1 A:GLU19 2.0 97.4 1.0
NE2 A:HIS15 2.0 83.0 1.0
NE2 A:HIS33 2.0 87.8 1.0
O A:HOH307 2.1 60.2 1.0
CD2 A:HIS33 2.8 83.3 1.0
CE1 A:HIS15 2.8 82.0 1.0
CD A:GLU19 3.1 95.8 1.0
CD2 A:HIS15 3.2 77.9 1.0
CE1 A:HIS33 3.2 86.1 1.0
OE2 A:GLU19 3.9 99.7 1.0
CG A:GLU19 4.0 90.6 1.0
ND1 A:HIS15 4.0 80.4 1.0
CG A:HIS33 4.0 78.7 1.0
NH2 A:ARG29 4.1 82.8 1.0
ND1 A:HIS33 4.2 83.2 1.0
CG A:HIS15 4.2 75.6 1.0
CZ A:ARG29 4.8 80.2 1.0
CD1 A:LEU36 4.8 45.7 1.0

Zinc binding site 2 out of 4 in 6ux8

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Zinc binding site 2 out of 4 in the Structure of Monobody 33 Mlkl N-Terminal Domain Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Monobody 33 Mlkl N-Terminal Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:60.0
occ:1.00
O A:HOH301 2.1 51.5 1.0
SG A:CYS86 2.2 75.8 1.0
CB A:CYS86 3.0 76.0 1.0
NH1 A:ARG82 3.8 80.6 1.0
CA A:CYS86 4.4 75.5 1.0
CE2 A:PHE148 5.0 93.1 1.0
CZ A:ARG82 5.0 78.8 1.0
CZ A:PHE148 5.0 90.6 1.0

Zinc binding site 3 out of 4 in 6ux8

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Zinc binding site 3 out of 4 in the Structure of Monobody 33 Mlkl N-Terminal Domain Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Monobody 33 Mlkl N-Terminal Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:67.5
occ:1.00
OE2 A:GLU71 2.0 0.6 1.0
NZ A:LYS104 2.2 0.7 1.0
CD A:GLU71 2.9 95.7 1.0
CE A:LYS104 3.1 89.2 1.0
OE1 A:GLU71 3.3 96.9 1.0
CD A:LYS104 3.4 77.9 1.0
CG A:GLU71 4.3 86.2 1.0
CG A:LYS104 4.7 68.3 1.0

Zinc binding site 4 out of 4 in 6ux8

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Zinc binding site 4 out of 4 in the Structure of Monobody 33 Mlkl N-Terminal Domain Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Monobody 33 Mlkl N-Terminal Domain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:58.9
occ:1.00
OD2 B:ASP72 2.0 0.5 1.0
OD1 B:ASP72 2.0 99.2 1.0
OD1 B:ASN94 2.0 92.6 1.0
CG B:ASP72 2.2 94.7 1.0
CG B:ASN94 3.0 80.5 1.0
CB B:ASN94 3.5 72.7 1.0
CB B:ASP72 3.6 83.1 1.0
ND2 B:ASN94 4.2 78.2 1.0
OG1 B:THR44 4.3 87.7 1.0
CG2 B:THR44 4.6 99.3 1.0
CB B:THR44 4.7 94.8 1.0
CA B:ASP72 4.7 69.3 1.0
CA B:ASN94 4.8 64.9 1.0
O B:TYR73 4.9 54.9 1.0
C B:ASP72 5.0 60.9 1.0

Reference:

E.J.Petrie, R.W.Birkinshaw, A.Koide, E.Denbaum, J.M.Hildebrand, S.E.Garnish, K.A.Davies, A.L.Samson, X.Gavin, C.Fitzgibbon, S.N.Young, P.J.Hennessy, P.Smith, E.D.Hawkins, P.E.Czabotar, S.Koide, J.M.Murphy. Identification of Mlkl Membrane Translocation As A Checkpoint in Necroptotic Cell Death Using Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1919960117
Page generated: Wed Dec 16 13:00:26 2020

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