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Zinc in PDB 9ofe: Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers

Enzymatic activity of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers

All present enzymatic activity of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers:
3.5.4.4;

Other elements in 9ofe:

The structure of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers (pdb code 9ofe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers, PDB code: 9ofe:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 9ofe

Go back to Zinc Binding Sites List in 9ofe
Zinc binding site 1 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:92.9
occ:1.00
 OD1 A:ASP548 2.1 36.9 1.0
NE2 A:HIS260 2.3 28.9 1.0
NE2 A:HIS461 2.3 51.3 1.0
NE2 A:HIS262 2.3 25.6 1.0
CE1 A:HIS260 3.0 23.3 1.0
CG A:ASP548 3.1 32.1 1.0
CD2 A:HIS461 3.2 47.9 1.0
CD2 A:HIS262 3.2 23.7 1.0
CE1 A:HIS262 3.3 32.8 1.0
N6 A:ATP701 3.3 103.4 1.0
CE1 A:HIS461 3.3 54.7 1.0
HN62 A:ATP701 3.4 104.1 1.0
CD2 A:HIS260 3.4 17.0 1.0
C6 A:ATP701 3.4 105.9 1.0
OD2 A:ASP548 3.5 38.2 1.0
HN61 A:ATP701 3.6 105.2 1.0
CE1 A:HIS485 3.6 43.6 1.0
C5 A:ATP701 3.7 106.0 1.0
N1 A:ATP701 4.0 108.2 1.0
N7 A:ATP701 4.0 105.6 1.0
ND1 A:HIS260 4.2 24.0 1.0
CG A:HIS260 4.4 22.8 1.0
ND1 A:HIS262 4.4 33.0 1.0
CG A:HIS262 4.4 27.1 1.0
CG A:HIS461 4.4 47.8 1.0
ND1 A:HIS461 4.4 49.8 1.0
CB A:ASP548 4.4 24.8 1.0
NE2 A:HIS485 4.5 42.4 1.0
C4 A:ATP701 4.5 106.8 1.0
ND1 A:HIS485 4.6 43.3 1.0
C2 A:ATP701 4.7 107.8 1.0
CA A:ASP548 4.7 13.8 1.0
ND2 A:ASN549 4.8 25.6 1.0
C8 A:ATP701 4.9 106.2 1.0
N3 A:ATP701 5.0 106.5 1.0

Zinc binding site 2 out of 6 in 9ofe

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Zinc binding site 2 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:75.8
occ:1.00
 NE2 B:HIS260 2.3 33.8 1.0
NE2 B:HIS461 2.3 47.2 1.0
NE2 B:HIS262 2.3 26.1 1.0
CE1 B:HIS461 2.5 45.0 1.0
CE1 B:HIS262 2.9 28.8 1.0
OD1 B:ASP548 3.0 33.4 1.0
CE1 B:HIS260 3.0 28.7 1.0
CD2 B:HIS461 3.1 39.8 1.0
ND1 B:HIS461 3.3 36.9 1.0
CD2 B:HIS260 3.5 19.5 1.0
CD2 B:HIS262 3.6 25.0 1.0
C6 B:ATP701 3.7 120.4 1.0
CE1 B:HIS485 3.7 58.0 1.0
CG B:HIS461 3.7 31.4 1.0
N1 B:ATP701 3.8 121.9 1.0
N6 B:ATP701 3.9 118.6 1.0
CG B:ASP548 4.0 36.3 1.0
C5 B:ATP701 4.0 120.7 1.0
ND1 B:HIS262 4.1 26.5 1.0
HN61 B:ATP701 4.1 119.0 1.0
HN62 B:ATP701 4.2 118.1 1.0
ND1 B:HIS260 4.2 29.5 1.0
C2 B:ATP701 4.3 121.4 1.0
OD2 B:ASP548 4.3 40.3 1.0
ND1 B:HIS485 4.4 56.8 1.0
C4 B:ATP701 4.4 121.8 1.0
CG B:HIS260 4.5 22.7 1.0
CG B:HIS262 4.5 19.1 1.0
N3 B:ATP701 4.6 120.8 1.0
N7 B:ATP701 4.6 120.0 1.0
NE2 B:HIS485 4.7 59.2 1.0
NH1 B:ARG350 4.7 38.3 1.0
H2 B:ATP701 4.7 121.5 1.0
CB B:HIS461 5.0 31.2 1.0

Zinc binding site 3 out of 6 in 9ofe

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Zinc binding site 3 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn702

b:105.7
occ:1.00
 CE1 G:HIS461 2.0 44.1 1.0
NE2 G:HIS260 2.3 29.6 1.0
NE2 G:HIS262 2.3 41.9 1.0
NE2 G:HIS461 2.3 38.5 1.0
OD1 G:ASP548 2.4 29.5 1.0
CE1 G:HIS260 3.0 27.8 1.0
CE1 G:HIS262 3.1 47.1 1.0
ND1 G:HIS461 3.3 41.5 1.0
CD2 G:HIS262 3.4 37.5 1.0
CD2 G:HIS260 3.4 26.3 1.0
CG G:ASP548 3.5 26.5 1.0
CE1 G:HIS485 3.6 28.5 1.0
CD2 G:HIS461 3.6 37.2 1.0
OD2 G:ASP548 3.8 26.2 1.0
CG G:HIS461 4.1 37.7 1.0
ND1 G:HIS260 4.2 24.5 1.0
ND1 G:HIS262 4.3 47.7 1.0
CG G:HIS260 4.4 23.4 1.0
NE2 G:HIS485 4.4 26.4 1.0
CG G:HIS262 4.4 41.2 1.0
NH2 G:ARG397 4.5 110.0 1.0
ND1 G:HIS485 4.5 30.8 1.0
HN62 G:ATP701 4.5 75.3 1.0
N1 G:ATP701 4.7 78.0 1.0
CB G:ASP548 4.8 24.6 1.0
C6 G:ATP701 4.8 75.6 1.0
N6 G:ATP701 4.9 78.7 1.0

Zinc binding site 4 out of 6 in 9ofe

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Zinc binding site 4 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn703

b:139.0
occ:1.00
 CE1 H:HIS461 2.0 42.7 1.0
NE2 H:HIS262 2.3 40.9 1.0
NE2 H:HIS461 2.3 39.8 1.0
NE2 H:HIS260 2.3 38.3 1.0
CE1 H:HIS262 2.9 40.4 1.0
CE1 H:HIS260 3.0 37.0 1.0
ND1 H:HIS461 3.0 40.6 1.0
CD2 H:HIS461 3.4 37.9 1.0
OD1 H:ASP548 3.4 37.5 1.0
CD2 H:HIS260 3.5 35.2 1.0
CD2 H:HIS262 3.6 37.5 1.0
CG H:HIS461 3.7 38.2 1.0
ND1 H:HIS262 4.1 38.5 1.0
C5 H:ATP702 4.1 41.9 1.0
C6 H:ATP702 4.2 41.8 1.0
ND1 H:HIS260 4.2 34.3 1.0
CE1 H:HIS485 4.3 38.8 1.0
NH1 H:ARG350 4.4 33.5 1.0
C4 H:ATP702 4.4 42.6 1.0
N1 H:ATP702 4.5 42.4 1.0
CG H:ASP548 4.5 36.1 1.0
CG H:HIS260 4.5 33.4 1.0
CG H:HIS262 4.5 36.6 1.0
N7 H:ATP702 4.5 41.1 1.0
N6 H:ATP702 4.6 40.5 1.0
C2 H:ATP702 4.7 42.4 1.0
OD2 H:ASP430 4.7 33.9 1.0
N3 H:ATP702 4.7 42.8 1.0
HN62 H:ATP702 4.7 39.7 1.0
CD H:ARG350 4.9 32.3 1.0
N9 H:ATP702 4.9 42.1 1.0
ND1 H:HIS485 4.9 38.4 1.0
OD2 H:ASP548 4.9 36.3 1.0
C8 H:ATP702 4.9 41.3 1.0
HN61 H:ATP702 5.0 40.5 1.0

Zinc binding site 5 out of 6 in 9ofe

Go back to Zinc Binding Sites List in 9ofe
Zinc binding site 5 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn702

b:94.8
occ:1.00
 CE1 K:HIS461 1.8 33.6 1.0
NE2 K:HIS260 2.3 21.1 1.0
NE2 K:HIS461 2.3 33.3 1.0
NE2 K:HIS262 2.3 19.9 1.0
OD1 K:ASP548 2.9 18.9 1.0
CE1 K:HIS260 3.1 19.4 1.0
ND1 K:HIS461 3.1 28.5 1.0
CE1 K:HIS262 3.1 22.5 1.0
CD2 K:HIS262 3.1 17.4 1.0
CD2 K:HIS260 3.4 15.4 1.0
CD2 K:HIS461 3.6 30.4 1.0
N7 K:ATP701 3.7 40.2 1.0
HN62 K:ATP701 3.8 38.8 1.0
CG K:ASP548 3.8 21.3 1.0
CG K:HIS461 4.0 30.5 1.0
OD2 K:ASP548 4.1 26.7 1.0
C5 K:ATP701 4.1 39.6 1.0
ND1 K:HIS262 4.1 19.7 1.0
CG K:HIS262 4.2 15.7 1.0
N6 K:ATP701 4.2 39.8 1.0
CE1 K:HIS485 4.2 23.7 1.0
ND1 K:HIS260 4.3 17.1 1.0
C6 K:ATP701 4.4 39.0 1.0
C8 K:ATP701 4.4 39.0 1.0
CG K:HIS260 4.5 15.5 1.0
H8 K:ATP701 4.6 37.6 1.0
HN61 K:ATP701 4.8 39.0 1.0
NH1 K:ARG350 4.8 17.0 1.0
C4 K:ATP701 5.0 41.1 1.0

Zinc binding site 6 out of 6 in 9ofe

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Zinc binding site 6 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Two Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn702

b:81.7
occ:1.00
 NE2 L:HIS260 2.3 21.7 1.0
NE2 L:HIS262 2.3 29.3 1.0
OD1 L:ASP548 2.5 25.3 1.0
CE1 L:HIS461 3.0 30.9 1.0
CD2 L:HIS262 3.0 27.5 1.0
CE1 L:HIS260 3.1 19.9 1.0
CE1 L:HIS262 3.3 32.9 1.0
CD2 L:HIS260 3.4 16.3 1.0
CG L:ASP548 3.5 25.1 1.0
N7 L:ATP701 3.8 57.3 1.0
ND1 L:HIS461 3.9 34.2 1.0
OD2 L:ASP548 3.9 31.8 1.0
NE2 L:HIS461 4.0 32.0 1.0
CE1 L:HIS485 4.0 30.1 1.0
C5 L:ATP701 4.1 56.4 1.0
CG L:HIS262 4.2 29.1 1.0
C8 L:ATP701 4.2 55.5 1.0
ND1 L:HIS260 4.3 19.7 1.0
ND1 L:HIS262 4.3 31.9 1.0
HN61 L:ATP701 4.4 53.2 1.0
CG L:HIS260 4.4 18.2 1.0
C6 L:ATP701 4.5 55.1 1.0
H8 L:ATP701 4.5 53.0 1.0
N6 L:ATP701 4.6 53.8 1.0
C4 L:ATP701 4.6 55.7 1.0
CB L:ASP548 4.7 17.4 1.0
N9 L:ATP701 4.7 55.2 1.0
CA L:ASP548 4.8 19.1 1.0
ND1 L:HIS485 4.8 32.1 1.0
NH1 L:ARG350 4.9 16.0 1.0
ND2 L:ASN549 4.9 27.3 1.0
NE2 L:HIS485 5.0 30.2 1.0
CD L:ARG350 5.0 16.5 1.0

Reference:

Y.Zhao, H.Li. Sequential Conformational Activation of A Carf-Fused Adenosine Deaminase By Cyclic Oligoadenylates To Be Published.
Page generated: Tue Aug 26 22:04:50 2025

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