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

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

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

Other elements in 9ofc:

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

Magnesium (Mg) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers (pdb code 9ofc). 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 Three Intact Dimers, PDB code: 9ofc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 9ofc

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Zinc binding site 1 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three 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 Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:181.0
occ:1.00
 OD1 A:ASP548 2.2 127.5 1.0
NE2 A:HIS260 2.3 115.9 1.0
NE2 A:HIS461 2.3 135.0 1.0
NE2 A:HIS262 2.3 101.2 1.0
CD2 A:HIS262 2.8 102.7 1.0
CE1 A:HIS461 2.9 137.1 1.0
CE1 A:HIS260 3.2 114.4 1.0
CD2 A:HIS260 3.3 117.5 1.0
CG A:ASP548 3.3 120.1 1.0
CE1 A:HIS262 3.5 110.4 1.0
CD2 A:HIS461 3.5 133.6 1.0
N1 A:ATP701 3.5 171.1 1.0
C6 A:ATP701 3.8 170.5 1.0
OD2 A:ASP548 3.8 121.4 1.0
C2 A:ATP701 4.0 171.9 1.0
N6 A:ATP701 4.0 168.0 1.0
CG A:HIS262 4.1 101.0 1.0
ND1 A:HIS461 4.1 137.9 1.0
HN62 A:ATP701 4.2 169.2 1.0
H2 A:ATP701 4.2 171.0 1.0
ND1 A:HIS260 4.3 111.7 1.0
ND1 A:HIS262 4.4 110.7 1.0
CG A:HIS260 4.4 115.0 1.0
HN61 A:ATP701 4.4 169.8 1.0
C5 A:ATP701 4.4 172.9 1.0
CG A:HIS461 4.5 133.4 1.0
CB A:ASP548 4.6 115.1 1.0
CE1 A:HIS485 4.6 136.3 1.0
N3 A:ATP701 4.6 171.3 1.0
OD1 A:ASN549 4.7 120.7 1.0
CA A:ASP548 4.7 114.4 1.0
C4 A:ATP701 4.7 173.1 1.0
NE2 A:HIS485 4.9 138.5 1.0
NH1 A:ARG350 4.9 101.4 1.0

Zinc binding site 2 out of 6 in 9ofc

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Zinc binding site 2 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three 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 Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:167.7
occ:1.00
 CE1 B:HIS461 2.0 126.5 1.0
NE2 B:HIS260 2.3 102.7 1.0
ND1 B:HIS461 2.3 122.4 1.0
NE2 B:HIS262 2.3 110.8 1.0
CE1 B:HIS262 2.7 115.3 1.0
CE1 B:HIS260 3.0 105.0 1.0
NE2 B:HIS461 3.3 126.2 1.0
CD2 B:HIS260 3.5 106.0 1.0
CD2 B:HIS262 3.6 108.1 1.0
OD1 B:ASP548 3.7 121.8 1.0
CG B:HIS461 3.7 117.7 1.0
C6 B:ATP701 4.0 153.1 1.0
ND1 B:HIS262 4.0 113.8 1.0
C5 B:ATP701 4.1 153.8 1.0
CD2 B:HIS461 4.1 122.6 1.0
HN62 B:ATP701 4.2 149.8 1.0
ND1 B:HIS260 4.2 103.6 1.0
N1 B:ATP701 4.2 155.5 1.0
N6 B:ATP701 4.3 147.2 1.0
CG B:HIS262 4.4 108.1 1.0
C4 B:ATP701 4.5 151.6 1.0
CG B:HIS260 4.5 100.7 1.0
C2 B:ATP701 4.5 154.1 1.0
N7 B:ATP701 4.6 151.9 1.0
N3 B:ATP701 4.7 149.4 1.0
CB B:HIS461 4.7 113.3 1.0
HN61 B:ATP701 4.8 150.4 1.0
CG B:ASP548 4.8 125.3 1.0
NH1 B:ARG350 4.9 98.1 1.0
CE1 B:HIS485 5.0 124.8 1.0
CD B:ARG350 5.0 93.3 1.0

Zinc binding site 3 out of 6 in 9ofc

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Zinc binding site 3 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three 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 Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn704

b:159.2
occ:1.00
 HN62 G:ATP701 1.8 130.0 1.0
OD1 G:ASP548 2.1 103.9 1.0
NE2 G:HIS262 2.3 86.0 1.0
NE2 G:HIS260 2.3 85.2 1.0
NE2 G:HIS461 2.3 107.9 1.0
N6 G:ATP701 2.6 127.7 1.0
CE1 G:HIS461 2.8 112.1 1.0
CE1 G:HIS262 3.0 83.5 1.0
CE1 G:HIS260 3.2 85.7 1.0
C6 G:ATP701 3.2 131.5 1.0
HN61 G:ATP701 3.2 130.6 1.0
CG G:ASP548 3.3 99.0 1.0
CD2 G:HIS260 3.3 86.7 1.0
CD2 G:HIS262 3.4 82.4 1.0
CD2 G:HIS461 3.6 105.1 1.0
C5 G:ATP701 3.7 132.5 1.0
CE1 G:HIS485 3.8 104.1 1.0
OD2 G:ASP548 3.9 102.3 1.0
N7 G:ATP701 3.9 131.9 1.0
N1 G:ATP701 4.0 132.5 1.0
ND1 G:HIS461 4.0 112.7 1.0
ND1 G:HIS262 4.2 83.7 1.0
OD1 G:ASN549 4.3 98.9 1.0
ND1 G:HIS260 4.3 84.4 1.0
CG G:HIS260 4.4 85.3 1.0
CG G:HIS262 4.4 78.9 1.0
NE2 G:HIS485 4.4 108.6 1.0
CB G:ASP548 4.4 91.8 1.0
CG G:HIS461 4.5 107.5 1.0
CA G:ASP548 4.6 88.3 1.0
ND1 G:HIS485 4.8 102.3 1.0
C4 G:ATP701 4.8 131.8 1.0
C G:ASP548 4.9 102.1 1.0
C8 G:ATP701 5.0 130.5 1.0
C2 G:ATP701 5.0 131.9 1.0

Zinc binding site 4 out of 6 in 9ofc

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Zinc binding site 4 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three 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 Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn704

b:161.3
occ:1.00
 OD1 H:ASP548 1.9 120.2 1.0
NE2 H:HIS262 2.3 103.8 1.0
NE2 H:HIS260 2.3 89.6 1.0
HN61 H:ATP703 2.5 146.8 1.0
CE1 H:HIS461 2.8 116.8 1.0
N6 H:ATP703 2.9 147.1 1.0
CG H:ASP548 2.9 117.2 1.0
CD2 H:HIS262 3.1 100.8 1.0
C6 H:ATP703 3.2 150.4 1.0
CE1 H:HIS260 3.2 88.2 1.0
OD2 H:ASP548 3.3 120.8 1.0
CD2 H:HIS260 3.3 89.4 1.0
C5 H:ATP703 3.3 150.2 1.0
N7 H:ATP703 3.3 146.2 1.0
CE1 H:HIS262 3.4 101.0 1.0
HN62 H:ATP703 3.5 147.3 1.0
NE2 H:HIS461 3.7 118.8 1.0
ND1 H:HIS461 3.8 115.6 1.0
N1 H:ATP703 4.1 152.1 1.0
CB H:ASP548 4.2 108.9 1.0
CG H:HIS262 4.3 97.5 1.0
C8 H:ATP703 4.3 149.3 1.0
ND1 H:HIS260 4.3 89.2 1.0
C4 H:ATP703 4.3 150.9 1.0
ND1 H:HIS262 4.4 99.6 1.0
CG H:HIS260 4.4 87.0 1.0
NE2 H:HIS485 4.5 114.1 1.0
CA H:ASP548 4.6 108.3 1.0
CD2 H:HIS485 4.7 113.4 1.0
H8 H:ATP703 4.8 147.5 1.0
OD1 H:ASN549 4.8 114.1 1.0
N9 H:ATP703 4.8 152.7 1.0
C2 H:ATP703 4.9 150.0 1.0
CD2 H:HIS461 5.0 115.4 1.0
O H:ASP548 5.0 117.9 1.0
C H:ASP548 5.0 115.7 1.0
CG H:HIS461 5.0 112.9 1.0

Zinc binding site 5 out of 6 in 9ofc

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Zinc binding site 5 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three 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 Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn704

b:186.8
occ:1.00
 NE2 K:HIS461 2.3 149.2 1.0
NE2 K:HIS260 2.3 124.5 1.0
CE1 K:HIS260 2.3 124.6 1.0
NE2 K:HIS262 2.3 118.0 1.0
CD2 K:HIS461 2.7 147.6 1.0
CE1 K:HIS262 2.9 119.1 1.0
HN62 K:ATP701 3.0 188.5 1.0
CE1 K:HIS461 3.3 147.8 1.0
N6 K:ATP701 3.5 187.8 1.0
ND1 K:HIS260 3.6 123.4 1.0
CD2 K:HIS262 3.6 118.1 1.0
CD2 K:HIS260 3.6 121.7 1.0
N7 K:ATP701 3.7 189.4 1.0
C6 K:ATP701 3.7 190.2 1.0
C5 K:ATP701 3.7 189.4 1.0
CG K:HIS461 3.8 143.5 1.0
ND1 K:HIS461 4.1 145.5 1.0
ND1 K:HIS262 4.1 116.9 1.0
CG K:HIS260 4.2 122.9 1.0
HN61 K:ATP701 4.2 189.3 1.0
OD1 K:ASP548 4.2 145.6 1.0
NE2 K:HIS485 4.4 153.8 1.0
C8 K:ATP701 4.5 190.7 1.0
CG K:HIS262 4.5 114.2 1.0
N1 K:ATP701 4.5 191.8 1.0
C4 K:ATP701 4.6 189.2 1.0
O K:HOH805 4.8 133.4 1.0
CE1 K:HIS485 4.9 152.6 1.0
H8 K:ATP701 4.9 189.6 1.0
NH1 K:ARG350 5.0 115.8 1.0
CD K:ARG350 5.0 110.3 1.0

Zinc binding site 6 out of 6 in 9ofc

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Zinc binding site 6 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three 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 Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn704

b:168.5
occ:1.00
 NE2 L:HIS260 2.3 123.4 1.0
NE2 L:HIS262 2.3 113.5 1.0
HN61 L:ATP703 2.6 172.4 1.0
CE1 L:HIS260 2.7 122.4 1.0
N6 L:ATP703 3.0 172.5 1.0
OD1 L:ASP548 3.1 128.5 1.0
ND1 L:HIS461 3.1 121.0 1.0
CE1 L:HIS262 3.1 114.2 1.0
C6 L:ATP703 3.3 174.7 1.0
CE1 L:HIS461 3.3 123.6 1.0
CD2 L:HIS262 3.4 114.0 1.0
C5 L:ATP703 3.5 174.1 1.0
N7 L:ATP703 3.5 171.8 1.0
HN62 L:ATP703 3.6 172.8 1.0
CD2 L:HIS260 3.6 119.1 1.0
ND1 L:HIS260 4.0 118.7 1.0
CG L:ASP548 4.0 128.0 1.0
N1 L:ATP703 4.1 175.0 1.0
NE2 L:HIS485 4.2 120.8 1.0
ND1 L:HIS262 4.3 115.2 1.0
OD2 L:ASP548 4.3 129.7 1.0
CG L:HIS461 4.4 119.6 1.0
C4 L:ATP703 4.4 173.9 1.0
CG L:HIS262 4.4 114.2 1.0
CG L:HIS260 4.4 118.5 1.0
C8 L:ATP703 4.5 172.5 1.0
NE2 L:HIS461 4.5 125.1 1.0
ND2 L:ASN549 4.6 112.3 1.0
CD2 L:HIS485 4.8 117.1 1.0
C2 L:ATP703 4.9 174.8 1.0
N9 L:ATP703 5.0 172.7 1.0
H8 L:ATP703 5.0 172.7 1.0

Reference:

M.Roth, Y.Shu, D.Trasandidou, Y.Zhao, J.Van Der Oost, H.Li. Sequential Conformational Activation of A Carf-Fused Adenosine Deaminase By Cyclic Oligoadenylates To Be Published.
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