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Zinc in PDB 3v1e: Crystal Structure of De Novo Designed MID1-Zinc H12E Mutant

Protein crystallography data

The structure of Crystal Structure of De Novo Designed MID1-Zinc H12E Mutant, PDB code: 3v1e was solved by B.S.Der, M.Machius, M.J.Miley, B.Kuhlman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.92 / 1.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 27.052, 47.212, 55.352, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 15.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of De Novo Designed MID1-Zinc H12E Mutant (pdb code 3v1e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of De Novo Designed MID1-Zinc H12E Mutant, PDB code: 3v1e:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3v1e

Go back to Zinc Binding Sites List in 3v1e
Zinc binding site 1 out of 2 in the Crystal Structure of De Novo Designed MID1-Zinc H12E Mutant


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 De Novo Designed MID1-Zinc H12E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:8.1
occ:1.00
HE1 A:HIS16 1.6 16.3 0.3
OE2 A:GLU12 1.9 11.9 1.0
NE2 A:HIS16 2.0 6.1 0.7
NE2 B:HIS35 2.0 8.9 1.0
NE2 B:HIS39 2.0 10.9 1.0
CE1 A:HIS16 2.2 13.6 0.3
O A:HOH251 2.5 20.4 1.0
NE2 A:HIS16 2.6 13.0 0.3
CD2 B:HIS35 2.9 8.7 1.0
CD2 A:HIS16 2.9 5.6 0.7
CD A:GLU12 3.0 11.8 1.0
CE1 A:HIS16 3.0 7.5 0.7
CD2 B:HIS39 3.0 9.9 1.0
CE1 B:HIS39 3.0 12.2 1.0
HD2 B:HIS35 3.0 10.4 1.0
CE1 B:HIS35 3.0 9.7 1.0
HG3 A:GLU12 3.1 12.7 1.0
HD2 A:HIS16 3.1 6.7 0.7
HD2 B:HIS39 3.2 11.9 1.0
HE1 B:HIS39 3.2 14.6 1.0
HE1 A:HIS16 3.2 9.1 0.7
HG2 A:GLU12 3.2 12.7 1.0
HE1 B:HIS35 3.3 11.6 1.0
CG A:GLU12 3.3 10.6 1.0
ND1 A:HIS16 3.3 13.0 0.3
O A:HOH233 3.6 22.0 1.0
HD1 A:HIS16 3.7 15.6 0.3
CD2 A:HIS16 3.8 12.1 0.3
CG B:HIS35 4.1 7.9 1.0
ND1 A:HIS16 4.1 8.1 0.7
ND1 B:HIS35 4.1 9.7 1.0
CG A:HIS16 4.1 5.9 0.7
OE1 A:GLU12 4.1 13.2 1.0
ND1 B:HIS39 4.1 12.1 1.0
CG B:HIS39 4.1 10.6 1.0
CG A:HIS16 4.2 11.1 0.3
HD2 A:HIS16 4.6 14.5 0.3
O A:HOH224 4.7 19.9 1.0
CB A:GLU12 4.8 8.4 1.0
HD1 A:HIS16 4.9 9.7 0.7
HD1 B:HIS35 4.9 11.7 1.0
HD1 B:HIS39 4.9 14.6 1.0
O A:GLU12 4.9 6.0 1.0
O A:HOH222 4.9 12.4 0.6
O B:HIS35 5.0 6.7 1.0

Zinc binding site 2 out of 2 in 3v1e

Go back to Zinc Binding Sites List in 3v1e
Zinc binding site 2 out of 2 in the Crystal Structure of De Novo Designed MID1-Zinc H12E Mutant


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 De Novo Designed MID1-Zinc H12E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:9.4
occ:1.00
OE1 B:GLU12 2.0 16.1 1.0
NE2 A:HIS39 2.0 10.8 1.0
NE2 A:HIS35 2.0 13.1 1.0
NE2 B:HIS16 2.0 8.7 1.0
CD2 A:HIS35 3.0 10.9 1.0
CD2 A:HIS39 3.0 10.1 1.0
CE1 A:HIS39 3.0 11.6 1.0
CD2 B:HIS16 3.0 6.3 1.0
CE1 A:HIS35 3.0 14.2 1.0
CE1 B:HIS16 3.0 11.1 1.0
CD B:GLU12 3.0 14.2 1.0
HD2 A:HIS35 3.1 13.1 1.0
HD2 B:HIS16 3.2 7.5 1.0
HD2 A:HIS39 3.2 12.1 1.0
HE1 A:HIS39 3.2 13.9 1.0
HE1 A:HIS35 3.2 17.0 1.0
HE1 B:HIS16 3.2 13.4 1.0
OE2 B:GLU12 3.5 17.2 1.0
ND1 A:HIS35 4.1 13.2 1.0
ND1 A:HIS39 4.1 11.8 1.0
CG A:HIS35 4.1 10.1 1.0
ND1 B:HIS16 4.1 10.2 1.0
CG A:HIS39 4.1 10.0 1.0
CG B:HIS16 4.1 6.2 1.0
HB3 B:GLU12 4.3 9.5 1.0
CG B:GLU12 4.3 11.6 1.0
HG3 B:GLU12 4.5 13.9 1.0
O B:HOH125 4.7 16.4 1.0
CB B:GLU12 4.8 7.9 1.0
O A:HOH246 4.8 33.0 1.0
HD1 A:HIS35 4.9 15.9 1.0
HD1 A:HIS39 4.9 14.1 1.0
HD1 B:HIS16 4.9 12.2 1.0
HA B:GLU12 4.9 6.9 1.0

Reference:

B.S.Der, M.Machius, M.J.Miley, J.L.Mills, T.Szyperski, B.Kuhlman. Metal-Mediated Affinity and Orientation Specificity in A Computationally Designed Protein Homodimer. J.Am.Chem.Soc. V. 134 375 2012.
ISSN: ISSN 0002-7863
PubMed: 22092237
DOI: 10.1021/JA208015J
Page generated: Wed Dec 16 04:55:26 2020

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