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Zinc in PDB 9ofd: Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with One Intact Dimer

Enzymatic activity of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with One Intact Dimer

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

Other elements in 9ofd:

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

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 9ofd

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


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 One Intact Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:105.3
occ:1.00
 NE2 A:HIS260 2.3 62.8 1.0
NE2 A:HIS262 2.3 49.0 1.0
NE2 A:HIS461 2.3 85.6 1.0
CE1 A:HIS461 2.4 80.7 1.0
OD1 A:ASP548 2.6 61.3 1.0
CE1 A:HIS260 3.1 57.0 1.0
CE1 A:HIS262 3.2 57.6 1.0
CD2 A:HIS461 3.3 77.8 1.0
CD2 A:HIS262 3.3 53.3 1.0
ND1 A:HIS461 3.4 81.9 1.0
CD2 A:HIS260 3.4 52.9 1.0
C6 A:ATP701 3.7 108.5 1.0
C5 A:ATP701 3.7 108.9 1.0
CG A:ASP548 3.7 65.4 1.0
N6 A:ATP701 3.8 103.1 1.0
CG A:HIS461 3.9 76.2 1.0
CE1 A:HIS485 3.9 91.1 1.0
HN62 A:ATP701 3.9 105.3 1.0
N7 A:ATP701 3.9 104.8 1.0
OD2 A:ASP548 4.1 68.9 1.0
HN61 A:ATP701 4.2 105.7 1.0
N1 A:ATP701 4.2 112.8 1.0
C4 A:ATP701 4.2 108.4 1.0
ND1 A:HIS260 4.3 57.3 1.0
ND1 A:HIS262 4.3 62.2 1.0
CG A:HIS262 4.4 52.9 1.0
CG A:HIS260 4.5 50.3 1.0
C8 A:ATP701 4.5 105.0 1.0
ND1 A:HIS485 4.6 90.1 1.0
C2 A:ATP701 4.6 110.3 1.0
N9 A:ATP701 4.7 107.4 1.0
N3 A:ATP701 4.8 106.0 1.0
NE2 A:HIS485 4.8 92.0 1.0
CB A:ASP548 5.0 58.3 1.0

Zinc binding site 2 out of 6 in 9ofd

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


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 One Intact Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:151.4
occ:1.00
 CE1 B:HIS461 1.1 80.0 1.0
ND1 B:HIS461 1.9 80.7 1.0
NE2 B:HIS262 2.3 52.5 1.0
NE2 B:HIS461 2.3 80.2 1.0
NE2 B:HIS260 2.3 55.1 1.0
CE1 B:HIS260 2.8 55.4 1.0
CE1 B:HIS262 2.9 56.2 1.0
CG B:HIS461 3.1 74.5 1.0
CD2 B:HIS461 3.3 75.8 1.0
OD1 B:ASP548 3.5 65.4 1.0
CD2 B:HIS262 3.6 48.2 1.0
CD2 B:HIS260 3.6 51.0 1.0
C6 B:ATP701 3.8 87.8 1.0
C5 B:ATP701 3.9 87.1 1.0
N6 B:ATP701 3.9 85.2 1.0
HN62 B:ATP701 4.0 84.3 1.0
CE1 B:HIS485 4.0 59.4 1.0
ND1 B:HIS260 4.1 50.0 1.0
ND1 B:HIS262 4.1 50.4 1.0
N1 B:ATP701 4.2 89.8 1.0
N7 B:ATP701 4.2 85.9 1.0
HN61 B:ATP701 4.3 84.7 1.0
ND1 B:HIS485 4.4 59.9 1.0
C4 B:ATP701 4.4 86.1 1.0
CB B:HIS461 4.4 69.3 1.0
CG B:HIS262 4.5 47.1 1.0
CG B:HIS260 4.5 47.1 1.0
NH1 B:ARG350 4.6 34.8 1.0
CG B:ASP548 4.6 63.9 1.0
C2 B:ATP701 4.6 85.7 1.0
N3 B:ATP701 4.8 83.5 1.0
C8 B:ATP701 4.9 85.7 1.0
OD2 B:ASP548 4.9 70.2 1.0

Zinc binding site 3 out of 6 in 9ofd

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


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 One Intact Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn702

b:123.1
occ:1.00
 CE1 G:HIS461 1.7 85.4 1.0
NE2 G:HIS262 2.3 68.5 1.0
NE2 G:HIS260 2.3 63.1 1.0
NE2 G:HIS461 2.3 90.2 1.0
ND1 G:HIS461 2.8 77.4 1.0
CE1 G:HIS260 2.9 62.2 1.0
CE1 G:HIS262 3.0 63.6 1.0
OD1 G:ASP548 3.4 67.7 1.0
CD2 G:HIS461 3.4 82.7 1.0
CD2 G:HIS262 3.5 64.6 1.0
CD2 G:HIS260 3.5 59.4 1.0
CG G:HIS461 3.6 79.9 1.0
CE1 G:HIS485 4.1 79.3 1.0
ND1 G:HIS260 4.2 58.6 1.0
ND1 G:HIS262 4.2 60.7 1.0
CG G:HIS262 4.5 60.8 1.0
CG G:ASP548 4.5 72.0 1.0
CG G:HIS260 4.5 55.8 1.0
HN62 G:ATP701 4.5 113.6 1.0
ND1 G:HIS485 4.7 78.6 1.0
N7 G:ATP701 4.8 113.7 1.0
NE2 G:HIS485 4.9 79.2 1.0
OD2 G:ASP548 4.9 75.1 1.0
N6 G:ATP701 4.9 114.1 1.0

Zinc binding site 4 out of 6 in 9ofd

Go back to Zinc Binding Sites List in 9ofd
Zinc binding site 4 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with One Intact Dimer


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 One Intact Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn703

b:130.1
occ:1.00
 CE1 H:HIS461 1.9 78.8 1.0
NE2 H:HIS461 2.3 75.9 1.0
NE2 H:HIS260 2.3 62.2 1.0
NE2 H:HIS262 2.3 69.6 1.0
CE1 H:HIS262 2.8 66.7 1.0
CE1 H:HIS260 3.0 58.8 1.0
ND1 H:HIS461 3.1 77.5 1.0
CD2 H:HIS260 3.5 59.6 1.0
OD1 H:ASP548 3.5 71.6 1.0
CD2 H:HIS262 3.6 61.9 1.0
CD2 H:HIS461 3.6 73.4 1.0
CG H:HIS461 4.0 76.6 1.0
ND1 H:HIS262 4.1 58.1 1.0
C5 H:ATP702 4.1 99.2 1.0
C6 H:ATP702 4.1 100.2 1.0
ND1 H:HIS260 4.3 54.1 1.0
NH1 H:ARG350 4.3 48.5 1.0
N6 H:ATP702 4.3 96.3 1.0
N7 H:ATP702 4.3 96.5 1.0
HN62 H:ATP702 4.4 96.3 1.0
NE2 H:HIS485 4.5 81.4 1.0
CG H:HIS262 4.5 58.3 1.0
CG H:HIS260 4.5 57.6 1.0
HN61 H:ATP702 4.5 96.1 1.0
CD H:ARG350 4.6 51.0 1.0
CG H:ASP548 4.6 73.9 1.0
C4 H:ATP702 4.7 97.1 1.0
N1 H:ATP702 4.7 97.7 1.0
OD2 H:ASP430 4.9 70.2 1.0
C8 H:ATP702 4.9 99.1 1.0

Zinc binding site 5 out of 6 in 9ofd

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


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 One Intact Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn703

b:157.5
occ:1.00
 CE1 K:HIS461 1.5 51.5 1.0
NE2 K:HIS262 2.3 38.4 1.0
NE2 K:HIS260 2.3 40.4 1.0
NE2 K:HIS461 2.3 48.1 1.0
ND1 K:HIS461 2.6 49.2 1.0
CE1 K:HIS262 2.8 35.3 1.0
CE1 K:HIS260 3.1 38.0 1.0
CD2 K:HIS260 3.3 35.2 1.0
CD2 K:HIS461 3.5 47.3 1.0
CD2 K:HIS262 3.5 31.2 1.0
CG K:HIS461 3.6 48.7 1.0
OD2 K:ASP430 3.8 54.5 1.0
CD K:ARG350 3.9 26.6 1.0
ND1 K:HIS262 4.1 39.7 1.0
NE K:ARG350 4.1 32.1 1.0
ND1 K:HIS260 4.2 33.3 1.0
CG K:HIS260 4.3 33.4 1.0
CG K:HIS262 4.4 32.1 1.0
CZ K:ARG350 4.5 33.7 1.0
N6 K:ATP701 4.5 109.9 1.0
HN62 K:ATP701 4.5 109.1 1.0
C6 K:ATP701 4.6 112.6 1.0
OD1 K:ASP548 4.7 26.1 1.0
NH1 K:ARG350 4.7 36.5 1.0
C5 K:ATP701 4.7 114.7 1.0
CG K:ASP430 4.7 51.1 1.0
HN61 K:ATP701 4.8 111.7 1.0
N7 K:ATP701 4.9 113.7 1.0
CB K:HIS461 5.0 45.0 1.0

Zinc binding site 6 out of 6 in 9ofd

Go back to Zinc Binding Sites List in 9ofd
Zinc binding site 6 out of 6 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with One Intact Dimer


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 One Intact Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn702

b:176.5
occ:1.00
 NE2 L:HIS262 2.3 50.2 1.0
NE2 L:HIS260 2.3 39.2 1.0
NE2 L:HIS461 2.3 62.1 1.0
CE1 L:HIS262 2.4 47.2 1.0
NH1 L:ARG350 2.8 44.0 1.0
CD2 L:HIS260 2.9 36.5 1.0
CE1 L:HIS260 3.2 41.1 1.0
CE1 L:HIS461 3.2 62.0 1.0
CD2 L:HIS461 3.3 55.5 1.0
CD L:ARG350 3.4 34.0 1.0
CD2 L:HIS262 3.5 46.6 1.0
ND1 L:HIS262 3.6 40.6 1.0
OD2 L:ASP430 3.8 49.7 1.0
CZ L:ARG350 3.9 39.2 1.0
CG L:HIS260 4.0 34.2 1.0
NE L:ARG350 4.1 32.5 1.0
ND1 L:HIS260 4.1 40.8 1.0
CG L:HIS262 4.1 44.0 1.0
ND1 L:HIS461 4.4 65.3 1.0
CG L:HIS461 4.4 57.2 1.0
OD1 L:ASP548 4.6 41.6 1.0
CG L:ARG350 4.7 36.5 1.0
CG L:ASP430 4.8 43.7 1.0
CB L:ARG350 4.9 29.0 1.0
OD1 L:ASP430 4.9 44.7 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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