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Zinc in PDB 5wob: Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin

Enzymatic activity of Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin

All present enzymatic activity of Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin:
3.4.24.56;

Protein crystallography data

The structure of Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin, PDB code: 5wob was solved by L.A.Mccord, W.G.Liang, M.Farcasanu, A.G.Wang, S.Koide, W.J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.54 / 3.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 121.589, 138.190, 376.509, 90.00, 99.36, 90.00
R / Rfree (%) 24.3 / 29.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin (pdb code 5wob). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin, PDB code: 5wob:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5wob

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Zinc binding site 1 out of 8 in the Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:65.9
occ:1.00
 NE2 A:HIS112 2.7 74.3 1.0
CE1 A:HIS108 2.7 71.8 1.0
OE1 A:GLU189 2.9 77.7 1.0
CE1 A:HIS112 3.3 76.4 1.0
CA a:TYR14 3.5 84.8 1.0
NE2 A:HIS108 3.5 70.6 1.0
CD2 A:HIS112 3.5 73.6 1.0
OE2 A:GLU189 3.5 71.4 1.0
O a:SER12 3.5 92.6 1.0
CD A:GLU189 3.6 75.3 1.0
ND1 A:HIS108 3.7 72.9 1.0
NE2 A:GLN111 3.8 74.6 1.0
N a:TYR14 4.0 87.2 1.0
OE1 A:GLN111 4.0 76.4 1.0
O a:LEU13 4.1 89.4 1.0
CD A:GLN111 4.1 73.4 1.0
C a:LEU13 4.2 89.7 1.0
O a:TYR14 4.2 85.1 1.0
CB a:TYR14 4.2 84.1 1.0
ND1 A:HIS112 4.2 74.2 1.0
C a:SER12 4.3 95.9 1.0
C a:TYR14 4.3 84.5 1.0
CG A:HIS112 4.4 73.3 1.0
CD1 a:TYR14 4.4 86.5 1.0
CB a:SER12 4.4 99.7 1.0
OG a:SER12 4.5 87.9 1.0
CD2 A:HIS108 4.6 74.6 1.0
CG A:HIS108 4.7 72.3 1.0
OH A:TYR831 4.8 84.1 1.0
CG a:TYR14 4.8 85.9 1.0
O A:ALA140 5.0 85.2 1.0
CA a:SER12 5.0 0.5 1.0

Zinc binding site 2 out of 8 in 5wob

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Zinc binding site 2 out of 8 in the Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:63.2
occ:1.00
 NE2 B:HIS108 2.3 74.4 1.0
NE2 B:HIS112 2.5 79.5 1.0
OE1 B:GLU189 2.8 81.8 1.0
OE2 B:GLU189 2.9 78.6 1.0
CD2 B:HIS108 3.2 73.8 1.0
CD B:GLU189 3.2 79.4 1.0
CD2 B:HIS112 3.2 81.4 1.0
CE1 B:HIS108 3.4 76.9 1.0
CE1 B:HIS112 3.6 81.9 1.0
NE2 B:GLN111 4.2 75.3 1.0
CG B:HIS108 4.4 73.5 1.0
ND1 B:HIS108 4.5 73.4 1.0
CG B:HIS112 4.5 83.1 1.0
ND1 B:HIS112 4.6 82.0 1.0
CG B:GLU189 4.7 81.0 1.0

Zinc binding site 3 out of 8 in 5wob

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Zinc binding site 3 out of 8 in the Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1101

b:0.2
occ:1.00
 NE2 C:HIS112 2.3 0.3 1.0
CE1 C:HIS112 2.4 0.1 1.0
OE1 C:GLU189 2.9 0.8 1.0
NE2 C:HIS108 3.1 0.6 1.0
OE2 C:GLU189 3.6 0.2 1.0
CA c:TYR14 3.6 0.8 1.0
CD C:GLU189 3.6 0.4 1.0
CD2 C:HIS112 3.6 0.7 1.0
ND1 C:HIS112 3.7 0.2 1.0
O c:LEU13 3.8 0.9 1.0
O c:TYR14 3.8 0.4 1.0
O c:SER12 4.0 0.1 1.0
CD2 C:HIS108 4.0 0.0 1.0
NE2 C:GLN111 4.0 0.2 1.0
CE1 C:HIS108 4.1 0.9 1.0
N c:TYR14 4.1 0.7 1.0
C c:LEU13 4.1 0.2 1.0
C c:TYR14 4.2 0.2 1.0
OH C:TYR831 4.2 0.3 1.0
CG C:HIS112 4.3 0.0 1.0
CB c:SER12 4.4 0.5 1.0
C c:SER12 4.4 0.7 1.0
CD1 c:TYR14 4.6 0.5 1.0
CB c:TYR14 4.6 0.2 1.0
CE1 C:TYR831 4.6 0.8 1.0
OG c:SER12 4.7 0.1 1.0
CZ C:TYR831 4.8 0.6 1.0
CA c:SER12 5.0 0.7 1.0

Zinc binding site 4 out of 8 in 5wob

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Zinc binding site 4 out of 8 in the Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:0.5
occ:1.00
 CE1 D:HIS112 2.4 0.9 1.0
NE2 D:HIS108 2.6 0.2 1.0
OE1 D:GLU189 2.7 0.3 1.0
NE2 D:HIS112 3.0 0.7 1.0
CD2 D:HIS108 3.3 0.0 1.0
OE2 D:GLU189 3.4 0.7 1.0
CD D:GLU189 3.4 0.6 1.0
ND1 D:HIS112 3.5 0.1 1.0
CE1 D:HIS108 3.7 0.8 1.0
NE2 D:GLN111 4.0 0.7 1.0
CD2 D:HIS112 4.3 0.4 1.0
CG D:HIS112 4.5 0.9 1.0
CG D:HIS108 4.6 0.3 1.0
ND1 D:HIS108 4.7 0.1 1.0
CD D:GLN111 4.9 0.9 1.0
CG D:GLU189 4.9 0.4 1.0
O D:ALA140 5.0 0.3 1.0

Zinc binding site 5 out of 8 in 5wob

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Zinc binding site 5 out of 8 in the Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn2001

b:1.0
occ:1.00
 CE1 E:HIS108 2.4 0.2 1.0
OE1 E:GLU189 2.4 0.7 1.0
NE2 E:HIS112 2.6 0.8 1.0
OE2 E:GLU189 2.9 0.4 1.0
NE2 E:HIS108 2.9 0.5 1.0
CD E:GLU189 3.0 0.7 1.0
CE1 E:HIS112 3.2 0.7 1.0
ND1 E:HIS108 3.5 0.6 1.0
CD2 E:HIS112 3.7 0.4 1.0
CA e:TYR14 3.8 0.2 1.0
NE2 E:GLN111 3.9 0.1 1.0
OE1 E:GLN111 4.0 0.4 1.0
CD2 E:HIS108 4.2 0.6 1.0
O e:TYR14 4.2 0.5 1.0
CD E:GLN111 4.3 0.5 1.0
ND1 E:HIS112 4.3 0.4 1.0
O e:LEU13 4.3 0.4 1.0
N e:TYR14 4.4 0.1 1.0
CG E:HIS108 4.5 0.2 1.0
CG E:GLU189 4.5 1.0 1.0
CD1 e:TYR14 4.5 0.8 1.0
C e:TYR14 4.5 0.7 1.0
C e:LEU13 4.5 0.9 1.0
CG E:HIS112 4.6 0.3 1.0
CB e:TYR14 4.6 0.8 1.0
OH E:TYR831 4.8 0.9 1.0
CE1 E:TYR831 4.8 0.0 1.0

Zinc binding site 6 out of 8 in 5wob

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Zinc binding site 6 out of 8 in the Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1101

b:0.6
occ:1.00
 NE2 F:HIS112 2.2 0.6 1.0
NE2 F:HIS108 2.2 0.5 1.0
CE1 F:HIS112 2.3 0.4 1.0
OE1 F:GLU189 2.8 0.3 1.0
OE2 F:GLU189 3.0 0.6 1.0
CD2 F:HIS108 3.1 0.8 1.0
CD F:GLU189 3.2 0.4 1.0
CE1 F:HIS108 3.2 0.4 1.0
CD2 F:HIS112 3.4 0.8 1.0
ND1 F:HIS112 3.5 0.9 1.0
O f:SER12 4.0 0.2 1.0
CG F:HIS112 4.0 0.1 1.0
CG F:HIS108 4.3 0.0 1.0
ND1 F:HIS108 4.3 0.0 1.0
CB f:SER12 4.3 0.3 1.0
OG f:SER12 4.5 0.7 1.0
NE2 F:GLN111 4.5 0.2 1.0
CG F:GLU189 4.6 0.9 1.0
C f:SER12 4.8 0.6 1.0
OE1 F:GLN111 4.9 0.2 1.0

Zinc binding site 7 out of 8 in 5wob

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Zinc binding site 7 out of 8 in the Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn2001

b:64.3
occ:1.00
 NE2 G:HIS108 2.4 84.5 1.0
CD2 G:HIS108 3.0 85.7 1.0
CE1 G:HIS112 3.1 85.3 1.0
NE2 G:HIS112 3.1 85.2 1.0
CE1 G:HIS108 3.6 87.8 1.0
NE2 G:GLN111 3.9 90.5 1.0
CA g:TYR14 4.0 99.3 1.0
O g:SER12 4.2 98.5 1.0
CG G:HIS108 4.3 86.1 1.0
ND1 G:HIS112 4.3 86.7 1.0
CD2 G:HIS112 4.4 87.1 1.0
O g:LEU13 4.5 0.5 1.0
ND1 G:HIS108 4.5 88.0 1.0
O g:TYR14 4.5 0.2 1.0
N g:TYR14 4.5 0.9 1.0
CB g:SER12 4.7 94.6 1.0
CD1 g:TYR14 4.7 96.3 1.0
C g:LEU13 4.7 0.8 1.0
OG g:SER12 4.7 89.1 1.0
CB g:TYR14 4.8 96.5 1.0
C g:TYR14 4.8 0.6 1.0
C g:SER12 4.9 0.4 1.0
CG G:HIS112 4.9 87.7 1.0
CE1 G:TYR831 5.0 99.8 1.0

Zinc binding site 8 out of 8 in 5wob

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Zinc binding site 8 out of 8 in the Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure Analysis of FAB1-Bound Human Insulin Degrading Enzyme (Ide) in Complex with Insulin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1101

b:98.0
occ:1.00
 NE2 H:HIS112 2.2 0.1 1.0
CE1 H:HIS112 2.3 0.6 1.0
OE2 H:GLU189 2.3 0.1 1.0
NE2 H:HIS108 2.4 0.9 1.0
OE1 H:GLU189 2.6 0.8 1.0
CD H:GLU189 2.8 0.8 1.0
CD2 H:HIS108 3.1 99.5 1.0
CE1 H:HIS108 3.4 0.8 1.0
CD2 H:HIS112 3.5 0.4 1.0
ND1 H:HIS112 3.6 0.7 1.0
CG H:HIS112 4.2 0.7 1.0
CG H:GLU189 4.3 0.9 1.0
CG H:HIS108 4.3 99.6 1.0
ND1 H:HIS108 4.4 0.3 1.0
NE2 H:GLN111 4.6 0.1 1.0
CE1 H:TYR831 4.8 1.0 1.0
OE1 H:GLN111 4.9 0.2 1.0
CB H:GLU189 5.0 0.5 1.0
CD H:GLN111 5.0 0.8 1.0

Reference:

Z.Zhang, W.G.Liang, L.J.Bailey, Y.Z.Tan, H.Wei, A.Wang, M.Farcasanu, V.A.Woods, L.A.Mccord, D.Lee, W.Shang, R.Deprez-Poulain, B.Deprez, D.R.Liu, A.Koide, S.Koide, A.A.Kossiakoff, S.Li, B.Carragher, C.S.Potter, W.J.Tang. Ensemble Cryoem Elucidates the Mechanism of Insulin Capture and Degradation By Human Insulin Degrading Enzyme. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29596046
DOI: 10.7554/ELIFE.33572
Page generated: Mon Oct 28 14:29:35 2024

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