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Zinc in PDB 7u5h: Cryo-Em Structure of Dnpep

Enzymatic activity of Cryo-Em Structure of Dnpep

All present enzymatic activity of Cryo-Em Structure of Dnpep:
3.4.11.21;

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Dnpep (pdb code 7u5h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Cryo-Em Structure of Dnpep, PDB code: 7u5h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 7u5h

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Zinc binding site 1 out of 24 in the Cryo-Em Structure of Dnpep


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Dnpep within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:104.8
occ:1.00
OD2 A:ASP260 1.7 84.9 1.0
OE2 A:GLU298 1.9 88.1 1.0
NE2 A:HIS436 2.1 84.8 1.0
CD A:GLU298 2.7 88.1 1.0
OE1 A:GLU298 2.8 88.1 1.0
CG A:ASP260 2.9 84.9 1.0
CE1 A:HIS436 3.0 84.8 1.0
CD2 A:HIS436 3.1 84.8 1.0
ZN A:ZN502 3.2 103.4 1.0
OD1 A:ASP260 3.6 84.9 1.0
CB A:ASP260 4.0 84.9 1.0
NE2 A:HIS90 4.0 80.2 1.0
CE1 A:HIS90 4.0 80.2 1.0
OD2 A:ASP342 4.1 82.6 1.0
CG A:GLU298 4.1 88.1 1.0
ND1 A:HIS436 4.1 84.8 1.0
CG A:HIS436 4.2 84.8 1.0
OD1 A:ASP342 4.3 82.6 1.0
CG A:ASP342 4.7 82.6 1.0
CD A:PRO94 4.8 79.4 1.0
OE2 A:GLU297 4.8 87.0 1.0

Zinc binding site 2 out of 24 in 7u5h

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Zinc binding site 2 out of 24 in the Cryo-Em Structure of Dnpep


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Dnpep within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:103.4
occ:1.00
OD1 A:ASP342 1.4 82.6 1.0
CG A:ASP342 1.8 82.6 1.0
OD2 A:ASP342 1.9 82.6 1.0
NE2 A:HIS90 2.0 80.2 1.0
OD2 A:ASP260 2.8 84.9 1.0
CE1 A:HIS90 3.0 80.2 1.0
CD2 A:HIS90 3.1 80.2 1.0
CB A:ASP342 3.2 82.6 1.0
ZN A:ZN501 3.2 104.8 1.0
CG A:ASP260 3.5 84.9 1.0
OD1 A:ASP260 3.8 84.9 1.0
OE2 A:GLU298 3.8 88.1 1.0
CG A:ASN261 3.9 82.1 1.0
CA A:ASP342 4.0 82.6 1.0
ND2 A:ASN261 4.1 82.1 1.0
ND1 A:HIS90 4.1 80.2 1.0
O A:ASP260 4.1 84.9 1.0
CB A:ASN261 4.2 82.1 1.0
CG A:HIS90 4.2 80.2 1.0
OD1 A:ASN261 4.2 82.1 1.0
OE2 A:GLU297 4.3 87.0 1.0
N A:MET343 4.5 82.7 1.0
C A:ASP260 4.6 84.9 1.0
C A:ASP342 4.6 82.6 1.0
CB A:ASP260 4.6 84.9 1.0
CD A:GLU298 4.9 88.1 1.0
N A:ASN261 5.0 82.1 1.0

Zinc binding site 3 out of 24 in 7u5h

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Zinc binding site 3 out of 24 in the Cryo-Em Structure of Dnpep


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Dnpep within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:104.8
occ:1.00
OD2 B:ASP260 1.7 84.9 1.0
OE2 B:GLU298 1.9 88.1 1.0
NE2 B:HIS436 2.1 84.8 1.0
CD B:GLU298 2.7 88.1 1.0
OE1 B:GLU298 2.8 88.1 1.0
CG B:ASP260 2.9 84.9 1.0
CE1 B:HIS436 3.0 84.8 1.0
CD2 B:HIS436 3.1 84.8 1.0
ZN B:ZN502 3.2 103.4 1.0
OD1 B:ASP260 3.6 84.9 1.0
CB B:ASP260 4.0 84.9 1.0
NE2 B:HIS90 4.0 80.2 1.0
CE1 B:HIS90 4.0 80.2 1.0
OD2 B:ASP342 4.1 82.6 1.0
CG B:GLU298 4.1 88.1 1.0
ND1 B:HIS436 4.1 84.8 1.0
CG B:HIS436 4.2 84.8 1.0
OD1 B:ASP342 4.3 82.6 1.0
CG B:ASP342 4.7 82.6 1.0
CD B:PRO94 4.8 79.4 1.0
OE2 B:GLU297 4.8 87.0 1.0

Zinc binding site 4 out of 24 in 7u5h

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Zinc binding site 4 out of 24 in the Cryo-Em Structure of Dnpep


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Dnpep within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:103.4
occ:1.00
OD1 B:ASP342 1.4 82.6 1.0
CG B:ASP342 1.8 82.6 1.0
OD2 B:ASP342 1.9 82.6 1.0
NE2 B:HIS90 2.0 80.2 1.0
OD2 B:ASP260 2.8 84.9 1.0
CE1 B:HIS90 3.0 80.2 1.0
CD2 B:HIS90 3.1 80.2 1.0
CB B:ASP342 3.2 82.6 1.0
ZN B:ZN501 3.2 104.8 1.0
CG B:ASP260 3.5 84.9 1.0
OD1 B:ASP260 3.8 84.9 1.0
OE2 B:GLU298 3.8 88.1 1.0
CG B:ASN261 3.9 82.1 1.0
CA B:ASP342 4.0 82.6 1.0
ND2 B:ASN261 4.1 82.1 1.0
ND1 B:HIS90 4.1 80.2 1.0
O B:ASP260 4.1 84.9 1.0
CB B:ASN261 4.2 82.1 1.0
CG B:HIS90 4.2 80.2 1.0
OD1 B:ASN261 4.2 82.1 1.0
OE2 B:GLU297 4.3 87.0 1.0
N B:MET343 4.5 82.7 1.0
C B:ASP260 4.6 84.9 1.0
C B:ASP342 4.6 82.6 1.0
CB B:ASP260 4.6 84.9 1.0
CD B:GLU298 4.9 88.1 1.0
N B:ASN261 5.0 82.1 1.0

Zinc binding site 5 out of 24 in 7u5h

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Zinc binding site 5 out of 24 in the Cryo-Em Structure of Dnpep


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Dnpep within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:104.8
occ:1.00
OD2 C:ASP260 1.7 84.9 1.0
OE2 C:GLU298 1.9 88.1 1.0
NE2 C:HIS436 2.1 84.8 1.0
CD C:GLU298 2.7 88.1 1.0
OE1 C:GLU298 2.8 88.1 1.0
CG C:ASP260 2.9 84.9 1.0
CE1 C:HIS436 3.0 84.8 1.0
CD2 C:HIS436 3.1 84.8 1.0
ZN C:ZN502 3.2 103.4 1.0
OD1 C:ASP260 3.6 84.9 1.0
CB C:ASP260 4.0 84.9 1.0
NE2 C:HIS90 4.0 80.2 1.0
CE1 C:HIS90 4.0 80.2 1.0
OD2 C:ASP342 4.1 82.6 1.0
CG C:GLU298 4.1 88.1 1.0
ND1 C:HIS436 4.1 84.8 1.0
CG C:HIS436 4.2 84.8 1.0
OD1 C:ASP342 4.3 82.6 1.0
CG C:ASP342 4.7 82.6 1.0
CD C:PRO94 4.8 79.4 1.0
OE2 C:GLU297 4.8 87.0 1.0

Zinc binding site 6 out of 24 in 7u5h

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Zinc binding site 6 out of 24 in the Cryo-Em Structure of Dnpep


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Dnpep within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:103.4
occ:1.00
OD1 C:ASP342 1.4 82.6 1.0
CG C:ASP342 1.8 82.6 1.0
OD2 C:ASP342 1.9 82.6 1.0
NE2 C:HIS90 2.0 80.2 1.0
OD2 C:ASP260 2.8 84.9 1.0
CE1 C:HIS90 3.0 80.2 1.0
CD2 C:HIS90 3.1 80.2 1.0
CB C:ASP342 3.2 82.6 1.0
ZN C:ZN501 3.2 104.8 1.0
CG C:ASP260 3.5 84.9 1.0
OD1 C:ASP260 3.8 84.9 1.0
OE2 C:GLU298 3.8 88.1 1.0
CG C:ASN261 3.9 82.1 1.0
CA C:ASP342 4.0 82.6 1.0
ND2 C:ASN261 4.1 82.1 1.0
ND1 C:HIS90 4.1 80.2 1.0
O C:ASP260 4.1 84.9 1.0
CB C:ASN261 4.2 82.1 1.0
CG C:HIS90 4.2 80.2 1.0
OD1 C:ASN261 4.2 82.1 1.0
OE2 C:GLU297 4.3 87.0 1.0
N C:MET343 4.5 82.7 1.0
C C:ASP260 4.6 84.9 1.0
C C:ASP342 4.6 82.6 1.0
CB C:ASP260 4.6 84.9 1.0
CD C:GLU298 4.9 88.1 1.0
N C:ASN261 5.0 82.1 1.0

Zinc binding site 7 out of 24 in 7u5h

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Zinc binding site 7 out of 24 in the Cryo-Em Structure of Dnpep


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Dnpep within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:104.8
occ:1.00
OD2 D:ASP260 1.7 84.9 1.0
OE2 D:GLU298 1.9 88.1 1.0
NE2 D:HIS436 2.1 84.8 1.0
CD D:GLU298 2.7 88.1 1.0
OE1 D:GLU298 2.8 88.1 1.0
CG D:ASP260 2.9 84.9 1.0
CE1 D:HIS436 3.0 84.8 1.0
CD2 D:HIS436 3.1 84.8 1.0
ZN D:ZN502 3.2 103.4 1.0
OD1 D:ASP260 3.6 84.9 1.0
CB D:ASP260 4.0 84.9 1.0
NE2 D:HIS90 4.0 80.2 1.0
CE1 D:HIS90 4.0 80.2 1.0
OD2 D:ASP342 4.1 82.6 1.0
CG D:GLU298 4.1 88.1 1.0
ND1 D:HIS436 4.1 84.8 1.0
CG D:HIS436 4.2 84.8 1.0
OD1 D:ASP342 4.3 82.6 1.0
CG D:ASP342 4.7 82.6 1.0
CD D:PRO94 4.8 79.4 1.0
OE2 D:GLU297 4.8 87.0 1.0

Zinc binding site 8 out of 24 in 7u5h

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Zinc binding site 8 out of 24 in the Cryo-Em Structure of Dnpep


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Dnpep within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:103.4
occ:1.00
OD1 D:ASP342 1.4 82.6 1.0
CG D:ASP342 1.8 82.6 1.0
OD2 D:ASP342 1.9 82.6 1.0
NE2 D:HIS90 2.0 80.2 1.0
OD2 D:ASP260 2.8 84.9 1.0
CE1 D:HIS90 3.0 80.2 1.0
CD2 D:HIS90 3.1 80.2 1.0
CB D:ASP342 3.2 82.6 1.0
ZN D:ZN501 3.2 104.8 1.0
CG D:ASP260 3.5 84.9 1.0
OD1 D:ASP260 3.8 84.9 1.0
OE2 D:GLU298 3.8 88.1 1.0
CG D:ASN261 3.9 82.1 1.0
CA D:ASP342 4.0 82.6 1.0
ND2 D:ASN261 4.1 82.1 1.0
ND1 D:HIS90 4.1 80.2 1.0
O D:ASP260 4.1 84.9 1.0
CB D:ASN261 4.2 82.1 1.0
CG D:HIS90 4.2 80.2 1.0
OD1 D:ASN261 4.2 82.1 1.0
OE2 D:GLU297 4.3 87.0 1.0
N D:MET343 4.5 82.7 1.0
C D:ASP260 4.6 84.9 1.0
C D:ASP342 4.6 82.6 1.0
CB D:ASP260 4.6 84.9 1.0
CD D:GLU298 4.9 88.1 1.0
N D:ASN261 5.0 82.1 1.0

Zinc binding site 9 out of 24 in 7u5h

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Zinc binding site 9 out of 24 in the Cryo-Em Structure of Dnpep


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cryo-Em Structure of Dnpep within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:104.8
occ:1.00
OD2 E:ASP260 1.7 84.9 1.0
OE2 E:GLU298 1.9 88.1 1.0
NE2 E:HIS436 2.1 84.8 1.0
CD E:GLU298 2.7 88.1 1.0
OE1 E:GLU298 2.8 88.1 1.0
CG E:ASP260 2.9 84.9 1.0
CE1 E:HIS436 3.0 84.8 1.0
CD2 E:HIS436 3.1 84.8 1.0
ZN E:ZN502 3.2 103.4 1.0
OD1 E:ASP260 3.6 84.9 1.0
CB E:ASP260 4.0 84.9 1.0
NE2 E:HIS90 4.0 80.2 1.0
CE1 E:HIS90 4.0 80.2 1.0
OD2 E:ASP342 4.1 82.6 1.0
CG E:GLU298 4.1 88.1 1.0
ND1 E:HIS436 4.1 84.8 1.0
CG E:HIS436 4.2 84.8 1.0
OD1 E:ASP342 4.3 82.6 1.0
CG E:ASP342 4.7 82.6 1.0
CD E:PRO94 4.8 79.4 1.0
OE2 E:GLU297 4.8 87.0 1.0

Zinc binding site 10 out of 24 in 7u5h

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Zinc binding site 10 out of 24 in the Cryo-Em Structure of Dnpep


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cryo-Em Structure of Dnpep within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn502

b:103.4
occ:1.00
OD1 E:ASP342 1.4 82.6 1.0
CG E:ASP342 1.8 82.6 1.0
OD2 E:ASP342 1.9 82.6 1.0
NE2 E:HIS90 2.0 80.2 1.0
OD2 E:ASP260 2.8 84.9 1.0
CE1 E:HIS90 3.0 80.2 1.0
CD2 E:HIS90 3.1 80.2 1.0
CB E:ASP342 3.2 82.6 1.0
ZN E:ZN501 3.2 104.8 1.0
CG E:ASP260 3.5 84.9 1.0
OD1 E:ASP260 3.8 84.9 1.0
OE2 E:GLU298 3.8 88.1 1.0
CG E:ASN261 3.9 82.1 1.0
CA E:ASP342 4.0 82.6 1.0
ND2 E:ASN261 4.1 82.1 1.0
ND1 E:HIS90 4.1 80.2 1.0
O E:ASP260 4.1 84.9 1.0
CB E:ASN261 4.2 82.1 1.0
CG E:HIS90 4.2 80.2 1.0
OD1 E:ASN261 4.2 82.1 1.0
OE2 E:GLU297 4.3 87.0 1.0
N E:MET343 4.5 82.7 1.0
C E:ASP260 4.6 84.9 1.0
C E:ASP342 4.6 82.6 1.0
CB E:ASP260 4.6 84.9 1.0
CD E:GLU298 4.9 88.1 1.0
N E:ASN261 5.0 82.1 1.0

Reference:

C.E.Morgan, M.Miyagi, M.Golczak, E.W.Yu. Towards Structural-Omics of the Bovine Retinal Pigment Epithelium Cell Rep 2022.
ISSN: ESSN 2211-1247
DOI: 10.1016/J.CELREP.2022.111876
Page generated: Sat Apr 8 03:53:20 2023

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