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Zinc in PDB 2ypt: Crystal Structure of the Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A

Enzymatic activity of Crystal Structure of the Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A

All present enzymatic activity of Crystal Structure of the Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A:
3.4.24.84;

Protein crystallography data

The structure of Crystal Structure of the Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A, PDB code: 2ypt was solved by A.C.W.Pike, Y.Y.Dong, A.Quigley, L.Dong, P.Savitsky, C.D.O.Cooper, A.Chaikuad, S.Goubin, L.Shrestha, Q.Li, S.Mukhopadhyay, J.Yang, X.Xia, C.A.Shintre, A.J.Barr, G.Berridge, R.Chalk, J.E.Bray, F.Von Delft, A.Bullock, C.Bountra, C.H.Arrowsmith, A.Edwards, N.Burgess-Brown, E.P.Carpenter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.50 / 3.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.320, 95.540, 132.030, 76.26, 79.67, 72.30
R / Rfree (%) 26.3 / 28.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A (pdb code 2ypt). 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 the Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A, PDB code: 2ypt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2ypt

Go back to Zinc Binding Sites List in 2ypt
Zinc binding site 1 out of 4 in the Crystal Structure of the Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A


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 Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn600

b:0.6
occ:1.00
 O F:SER662 2.0 0.3 1.0
OE2 A:GLU415 2.1 0.3 1.0
NE2 A:HIS339 2.2 0.2 1.0
NE2 A:HIS335 2.2 0.1 1.0
CD A:GLU415 2.9 0.3 1.0
CD2 A:HIS335 3.0 0.1 1.0
CD2 A:HIS339 3.0 0.6 1.0
OE1 A:GLU415 3.1 0.8 1.0
C F:SER662 3.3 0.3 1.0
CE1 A:HIS335 3.3 0.8 1.0
CE1 A:HIS339 3.3 0.4 1.0
CG A:HIS335 4.1 0.3 1.0
N F:ILE663 4.2 0.3 1.0
N F:SER662 4.2 0.3 1.0
CG A:HIS339 4.2 0.9 1.0
ND1 A:HIS335 4.2 0.2 1.0
CA F:ILE663 4.3 0.7 1.0
CA F:SER662 4.3 0.5 1.0
ND1 A:HIS339 4.4 0.1 1.0
CG A:GLU415 4.4 0.8 1.0
CB F:CYS661 4.5 0.6 1.0
CB A:ALA418 4.7 0.4 1.0
C F:CYS661 4.8 0.8 1.0
NE2 A:HIS459 4.8 0.9 1.0
O A:HIS335 5.0 0.3 1.0

Zinc binding site 2 out of 4 in 2ypt

Go back to Zinc Binding Sites List in 2ypt
Zinc binding site 2 out of 4 in the Crystal Structure of the Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A


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 Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn600

b:1.0
occ:1.00
 O G:SER662 2.1 0.1 1.0
OE2 B:GLU415 2.1 0.3 1.0
NE2 B:HIS339 2.2 0.7 1.0
NE2 B:HIS335 2.2 0.5 1.0
CD B:GLU415 2.9 0.4 1.0
CD2 B:HIS335 3.0 0.8 1.0
CD2 B:HIS339 3.0 0.2 1.0
OE1 B:GLU415 3.1 0.9 1.0
CE1 B:HIS335 3.3 0.5 1.0
C G:SER662 3.3 0.5 1.0
CE1 B:HIS339 3.3 0.6 1.0
CG B:HIS335 4.1 0.6 1.0
N G:SER662 4.1 0.4 1.0
N G:ILE663 4.1 0.8 1.0
CA G:ILE663 4.2 0.7 1.0
CG B:HIS339 4.2 0.5 1.0
CB G:CYS661 4.2 0.3 1.0
ND1 B:HIS335 4.2 0.2 1.0
CA G:SER662 4.3 0.5 1.0
ND1 B:HIS339 4.4 0.2 1.0
CG B:GLU415 4.4 0.5 1.0
C G:CYS661 4.6 0.8 1.0
CB B:ALA418 4.6 0.1 1.0
NE2 B:HIS459 4.8 0.4 1.0
O B:HIS335 5.0 0.4 1.0

Zinc binding site 3 out of 4 in 2ypt

Go back to Zinc Binding Sites List in 2ypt
Zinc binding site 3 out of 4 in the Crystal Structure of the Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A


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 Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn600

b:0.5
occ:1.00
 O H:SER662 2.0 0.6 1.0
OE2 D:GLU415 2.1 0.3 1.0
NE2 D:HIS339 2.2 0.4 1.0
NE2 D:HIS335 2.2 0.3 1.0
CD D:GLU415 2.9 0.0 1.0
CD2 D:HIS335 3.0 0.3 1.0
CD2 D:HIS339 3.0 1.0 1.0
OE1 D:GLU415 3.1 0.3 1.0
CE1 D:HIS335 3.3 0.6 1.0
C H:SER662 3.3 0.2 1.0
CE1 D:HIS339 3.3 0.3 1.0
N H:SER662 4.0 0.6 1.0
CG D:HIS335 4.1 0.2 1.0
CB H:CYS661 4.1 0.6 1.0
N H:ILE663 4.2 0.1 1.0
CG D:HIS339 4.2 0.7 1.0
ND1 D:HIS335 4.2 0.4 1.0
CA H:SER662 4.2 0.4 1.0
CA H:ILE663 4.3 0.1 1.0
CG D:GLU415 4.4 0.8 1.0
ND1 D:HIS339 4.4 0.3 1.0
C H:CYS661 4.5 0.6 1.0
CB D:ALA418 4.7 1.0 1.0
NE2 D:HIS459 4.8 0.1 1.0
CA H:CYS661 5.0 0.5 1.0
O D:HIS335 5.0 0.7 1.0
O H:CYS661 5.0 0.1 1.0

Zinc binding site 4 out of 4 in 2ypt

Go back to Zinc Binding Sites List in 2ypt
Zinc binding site 4 out of 4 in the Crystal Structure of the Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A


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 Human Nuclear Membrane Zinc Metalloprotease ZMPSTE24 Mutant (E336A) in Complex with A Synthetic Csim Tetrapeptide From the C-Terminus of Prelamin A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn600

b:0.1
occ:1.00
 O I:SER662 2.1 0.1 1.0
OE2 E:GLU415 2.1 0.4 1.0
NE2 E:HIS339 2.2 0.1 1.0
NE2 E:HIS335 2.2 0.5 1.0
CD E:GLU415 3.0 0.5 1.0
CD2 E:HIS335 3.0 0.2 1.0
CD2 E:HIS339 3.0 0.9 1.0
OE1 E:GLU415 3.1 0.7 1.0
CE1 E:HIS335 3.3 0.6 1.0
C I:SER662 3.3 0.1 1.0
CE1 E:HIS339 3.3 0.1 1.0
CG E:HIS335 4.1 0.6 1.0
N I:ILE663 4.2 0.8 1.0
N I:SER662 4.2 0.0 1.0
CG E:HIS339 4.2 0.3 1.0
CA I:ILE663 4.2 0.3 1.0
ND1 E:HIS335 4.3 0.2 1.0
CA I:SER662 4.3 0.0 1.0
ND1 E:HIS339 4.4 0.9 1.0
CG E:GLU415 4.4 1.0 1.0
CB I:CYS661 4.5 0.0 1.0
CB E:ALA418 4.7 0.1 1.0
C I:CYS661 4.8 0.7 1.0
NE2 E:HIS459 4.8 0.5 1.0
C I:ILE663 4.8 0.2 1.0
O E:HIS335 5.0 0.3 1.0
O I:ILE663 5.0 0.5 1.0

Reference:

A.Quigley, Y.Y.Dong, A.C.W.Pike, L.Dong, L.Shrestha, G.Berridge, P.J.Stansfeld, M.S.P.Sansom, A.M.Edwards, C.Bountra, F.Von Delft, A.N.Bullock, N.A.Burgess-Brown, E.P.Carpenter. The Structural Basis of ZMPSTE24-Dependent Laminopathies. Science V. 339 1604 2013.
ISSN: ISSN 0036-8075
PubMed: 23539603
DOI: 10.1126/SCIENCE.1231513
Page generated: Thu Oct 17 05:54:53 2024

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