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Zinc in PDB 9hfs: Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site

Enzymatic activity of Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site

All present enzymatic activity of Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site:
3.5.4.5;

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site (pdb code 9hfs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site, PDB code: 9hfs:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 9hfs

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Zinc binding site 1 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site


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 Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:42.8
occ:1.00
 OE1 A:GLU157 2.0 15.2 1.0
ND1 A:HIS109 2.0 15.8 1.0
SG A:CYS134 2.3 19.6 1.0
SG A:CYS137 2.3 20.0 1.0
CG A:HIS109 3.0 12.8 1.0
CD A:GLU157 3.0 18.7 1.0
CE1 A:HIS109 3.1 13.7 1.0
CB A:CYS137 3.1 10.6 1.0
CB A:HIS109 3.3 4.8 1.0
CB A:CYS134 3.4 10.1 1.0
OE2 A:GLU157 3.6 26.1 1.0
N A:CYS134 3.8 12.0 1.0
N A:CYS137 4.0 10.1 1.0
CG A:GLU157 4.1 16.9 1.0
CD2 A:HIS109 4.1 12.3 1.0
NE2 A:HIS109 4.1 15.8 1.0
CA A:CYS137 4.1 9.8 1.0
CA A:CYS134 4.2 7.1 1.0
C A:CYS134 4.8 7.2 1.0
CA A:HIS109 4.8 10.4 1.0
O A:CYS134 4.8 13.5 1.0
CB A:GLU157 4.9 17.4 1.0
C A:PRO133 4.9 10.4 1.0
OE1 A:GLN112 5.0 14.6 1.0

Zinc binding site 2 out of 12 in 9hfs

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Zinc binding site 2 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site


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 Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:54.7
occ:1.00
 ND1 A:HIS398 2.0 21.4 1.0
SG A:CYS429 2.3 27.5 1.0
SG A:CYS426 2.3 25.1 1.0
N4 A:DCP603 2.4 28.2 1.0
C4 A:DCP603 2.5 28.4 1.0
CE1 A:HIS398 2.9 18.1 1.0
N3 A:DCP603 3.0 25.5 1.0
CG A:HIS398 3.1 15.3 1.0
CB A:CYS426 3.2 22.4 1.0
C5 A:DCP603 3.3 26.7 1.0
CB A:CYS429 3.4 19.1 1.0
N A:CYS426 3.4 20.9 1.0
CB A:HIS398 3.5 10.2 1.0
O A:HOH701 3.8 10.0 1.0
CA A:CYS426 3.8 19.8 1.0
C2 A:DCP603 3.9 27.4 1.0
C6 A:DCP603 4.1 28.3 1.0
NE2 A:HIS398 4.1 15.3 1.0
CD2 A:HIS398 4.2 16.0 1.0
N1 A:DCP603 4.4 28.8 1.0
C A:PRO425 4.5 22.8 1.0
N A:CYS429 4.5 25.2 1.0
CA A:CYS429 4.6 19.4 1.0
C A:CYS426 4.6 22.4 1.0
O2 A:DCP603 4.7 27.4 1.0
CA A:PRO425 4.7 24.4 1.0
O A:CYS426 4.8 21.1 1.0
CA A:HIS398 4.9 9.2 1.0
CG A:GLU428 5.0 22.8 1.0

Zinc binding site 3 out of 12 in 9hfs

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Zinc binding site 3 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site


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 Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:40.8
occ:1.00
 OE1 B:GLU157 2.0 11.4 1.0
ND1 B:HIS109 2.0 17.3 1.0
SG B:CYS137 2.3 22.9 1.0
SG B:CYS134 2.3 15.5 1.0
CD B:GLU157 3.0 16.8 1.0
CG B:HIS109 3.0 11.1 1.0
CE1 B:HIS109 3.1 11.2 1.0
CB B:CYS137 3.1 11.5 1.0
CB B:HIS109 3.3 3.5 1.0
CB B:CYS134 3.5 9.0 1.0
OE2 B:GLU157 3.5 25.1 1.0
N B:CYS134 3.8 13.2 1.0
N B:CYS137 4.0 9.4 1.0
CG B:GLU157 4.1 14.2 1.0
CD2 B:HIS109 4.1 10.8 1.0
NE2 B:HIS109 4.1 14.1 1.0
CA B:CYS137 4.2 9.8 1.0
CA B:CYS134 4.2 8.6 1.0
C B:CYS134 4.8 6.1 1.0
O B:CYS134 4.8 12.7 1.0
CA B:HIS109 4.8 9.3 1.0
CB B:GLU157 4.9 15.2 1.0
C B:PRO133 4.9 13.0 1.0
OE1 B:GLN112 5.0 12.2 1.0

Zinc binding site 4 out of 12 in 9hfs

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Zinc binding site 4 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site


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 Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:57.0
occ:1.00
 ND1 B:HIS398 2.0 21.8 1.0
N4 B:DCP603 2.3 26.6 1.0
SG B:CYS429 2.3 28.8 1.0
SG B:CYS426 2.3 24.6 1.0
C4 B:DCP603 2.5 27.2 1.0
N3 B:DCP603 2.9 23.0 1.0
CE1 B:HIS398 3.0 18.5 1.0
CG B:HIS398 3.1 15.2 1.0
CB B:CYS426 3.2 19.9 1.0
C5 B:DCP603 3.2 24.2 1.0
CB B:CYS429 3.4 19.8 1.0
N B:CYS426 3.4 18.9 1.0
CB B:HIS398 3.5 9.1 1.0
O B:HOH701 3.7 5.5 1.0
C2 B:DCP603 3.8 23.7 1.0
CA B:CYS426 3.8 18.7 1.0
C6 B:DCP603 4.1 24.6 1.0
NE2 B:HIS398 4.1 14.3 1.0
CD2 B:HIS398 4.2 15.0 1.0
N1 B:DCP603 4.3 25.1 1.0
C B:PRO425 4.5 19.6 1.0
CA B:CYS429 4.6 19.8 1.0
N B:CYS429 4.6 23.7 1.0
C B:CYS426 4.6 24.0 1.0
O2 B:DCP603 4.7 23.4 1.0
CA B:PRO425 4.7 23.6 1.0
O B:CYS426 4.8 20.3 1.0
CA B:HIS398 4.9 9.2 1.0

Zinc binding site 5 out of 12 in 9hfs

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Zinc binding site 5 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site


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 Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:40.0
occ:1.00
 OE1 C:GLU157 2.0 12.4 1.0
ND1 C:HIS109 2.0 14.7 1.0
SG C:CYS137 2.3 21.2 1.0
SG C:CYS134 2.3 16.3 1.0
CD C:GLU157 3.0 17.7 1.0
CG C:HIS109 3.0 13.7 1.0
CE1 C:HIS109 3.0 9.1 1.0
CB C:CYS137 3.1 11.0 1.0
CB C:HIS109 3.3 1.9 1.0
CB C:CYS134 3.4 10.5 1.0
OE2 C:GLU157 3.5 24.6 1.0
N C:CYS134 3.8 14.1 1.0
N C:CYS137 4.0 12.0 1.0
NE2 C:HIS109 4.1 12.4 1.0
CG C:GLU157 4.1 15.1 1.0
CD2 C:HIS109 4.1 9.4 1.0
CA C:CYS134 4.1 7.6 1.0
CA C:CYS137 4.1 10.4 1.0
C C:CYS134 4.7 6.8 1.0
O C:CYS134 4.7 12.5 1.0
CA C:HIS109 4.8 7.3 1.0
C C:PRO133 4.9 12.3 1.0
CB C:GLU157 5.0 16.4 1.0
OE1 C:GLN112 5.0 13.1 1.0

Zinc binding site 6 out of 12 in 9hfs

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Zinc binding site 6 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site


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 Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:56.0
occ:1.00
 ND1 C:HIS398 2.0 22.9 1.0
SG C:CYS429 2.3 28.9 1.0
N4 C:DCP603 2.3 26.8 1.0
SG C:CYS426 2.3 23.4 1.0
C4 C:DCP603 2.6 29.6 1.0
CE1 C:HIS398 2.9 17.9 1.0
N3 C:DCP603 3.0 24.9 1.0
CB C:CYS426 3.1 19.9 1.0
CG C:HIS398 3.1 15.2 1.0
C5 C:DCP603 3.3 27.2 1.0
CB C:CYS429 3.3 20.7 1.0
N C:CYS426 3.4 18.3 1.0
CB C:HIS398 3.5 7.4 1.0
CA C:CYS426 3.8 16.9 1.0
O C:HOH701 3.9 6.4 1.0
C2 C:DCP603 4.0 25.1 1.0
NE2 C:HIS398 4.1 12.6 1.0
C6 C:DCP603 4.1 27.4 1.0
CD2 C:HIS398 4.2 15.7 1.0
N C:CYS429 4.3 23.2 1.0
CA C:CYS429 4.4 19.5 1.0
N1 C:DCP603 4.5 26.7 1.0
C C:PRO425 4.5 21.0 1.0
C C:CYS426 4.6 21.9 1.0
O C:CYS426 4.7 21.7 1.0
CA C:PRO425 4.7 22.5 1.0
O2 C:DCP603 4.8 26.0 1.0

Zinc binding site 7 out of 12 in 9hfs

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Zinc binding site 7 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site


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 Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:41.8
occ:1.00
 OE1 D:GLU157 2.0 11.8 1.0
ND1 D:HIS109 2.0 16.2 1.0
SG D:CYS137 2.3 23.1 1.0
SG D:CYS134 2.3 17.0 1.0
CD D:GLU157 3.0 16.8 1.0
CG D:HIS109 3.0 11.9 1.0
CE1 D:HIS109 3.1 11.4 1.0
CB D:CYS137 3.2 9.9 1.0
CB D:HIS109 3.3 0.5 1.0
CB D:CYS134 3.5 8.4 1.0
OE2 D:GLU157 3.5 25.7 1.0
N D:CYS134 3.8 11.3 1.0
N D:CYS137 4.0 9.1 1.0
CG D:GLU157 4.1 13.4 1.0
CD2 D:HIS109 4.1 10.8 1.0
NE2 D:HIS109 4.1 12.9 1.0
CA D:CYS137 4.2 9.4 1.0
CA D:CYS134 4.2 7.0 1.0
C D:CYS134 4.8 5.8 1.0
O D:CYS134 4.8 13.9 1.0
CA D:HIS109 4.8 9.5 1.0
CB D:GLU157 4.9 14.5 1.0
C D:PRO133 4.9 10.0 1.0
OE1 D:GLN112 5.0 13.3 1.0

Zinc binding site 8 out of 12 in 9hfs

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Zinc binding site 8 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site


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 Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:57.8
occ:1.00
 ND1 D:HIS398 2.0 20.6 1.0
SG D:CYS429 2.3 30.6 1.0
SG D:CYS426 2.3 24.2 1.0
N4 D:DCP603 2.3 25.9 1.0
C4 D:DCP603 2.5 26.6 1.0
N3 D:DCP603 2.9 23.0 1.0
CE1 D:HIS398 2.9 19.9 1.0
CG D:HIS398 3.1 14.9 1.0
CB D:CYS426 3.2 18.7 1.0
C5 D:DCP603 3.2 23.6 1.0
CB D:CYS429 3.4 19.8 1.0
N D:CYS426 3.4 17.6 1.0
CB D:HIS398 3.5 7.9 1.0
O D:HOH701 3.7 6.2 1.0
C2 D:DCP603 3.8 24.8 1.0
CA D:CYS426 3.9 17.5 1.0
C6 D:DCP603 4.0 25.1 1.0
NE2 D:HIS398 4.1 15.4 1.0
CD2 D:HIS398 4.2 15.3 1.0
N1 D:DCP603 4.3 26.7 1.0
C D:PRO425 4.5 19.4 1.0
CA D:CYS429 4.6 19.7 1.0
N D:CYS429 4.6 24.2 1.0
C D:CYS426 4.6 22.4 1.0
O2 D:DCP603 4.7 24.2 1.0
CA D:PRO425 4.7 23.9 1.0
O D:CYS426 4.8 20.5 1.0
CA D:HIS398 4.9 8.3 1.0

Zinc binding site 9 out of 12 in 9hfs

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Zinc binding site 9 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site


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 Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn601

b:41.3
occ:1.00
 OE1 E:GLU157 2.0 9.7 1.0
ND1 E:HIS109 2.0 14.0 1.0
SG E:CYS137 2.3 19.2 1.0
SG E:CYS134 2.3 17.9 1.0
CD E:GLU157 3.0 15.9 1.0
CG E:HIS109 3.0 11.2 1.0
CE1 E:HIS109 3.0 7.5 1.0
CB E:CYS137 3.1 8.1 1.0
CB E:HIS109 3.3 0.0 1.0
CB E:CYS134 3.4 9.1 1.0
OE2 E:GLU157 3.5 23.7 1.0
N E:CYS134 3.8 13.2 1.0
N E:CYS137 4.0 9.5 1.0
NE2 E:HIS109 4.1 11.7 1.0
CG E:GLU157 4.1 11.8 1.0
CD2 E:HIS109 4.1 7.1 1.0
CA E:CYS134 4.1 5.6 1.0
CA E:CYS137 4.1 8.7 1.0
C E:CYS134 4.7 3.6 1.0
O E:CYS134 4.7 12.1 1.0
CA E:HIS109 4.8 5.1 1.0
C E:PRO133 4.9 12.1 1.0
CB E:GLU157 4.9 14.1 1.0
OE1 E:GLN112 5.0 10.2 1.0

Zinc binding site 10 out of 12 in 9hfs

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Zinc binding site 10 out of 12 in the Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site


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 Human CDADC1 Inactive Mutant (E400A): Hexamer with Dctp Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn602

b:57.7
occ:1.00
 ND1 E:HIS398 2.0 22.1 1.0
N4 E:DCP603 2.3 25.8 1.0
SG E:CYS429 2.3 29.2 1.0
SG E:CYS426 2.3 20.1 1.0
C4 E:DCP603 2.5 28.5 1.0
CE1 E:HIS398 3.0 17.4 1.0
N3 E:DCP603 3.0 23.2 1.0
CG E:HIS398 3.1 13.4 1.0
CB E:CYS426 3.2 18.7 1.0
C5 E:DCP603 3.3 25.8 1.0
CB E:CYS429 3.3 16.6 1.0
N E:CYS426 3.4 14.4 1.0
CB E:HIS398 3.5 5.2 1.0
O E:HOH701 3.8 5.3 1.0
CA E:CYS426 3.9 14.7 1.0
C2 E:DCP603 3.9 22.6 1.0
NE2 E:HIS398 4.1 12.2 1.0
C6 E:DCP603 4.1 24.3 1.0
CD2 E:HIS398 4.2 13.1 1.0
N1 E:DCP603 4.4 25.9 1.0
CA E:CYS429 4.5 16.9 1.0
N E:CYS429 4.5 23.0 1.0
C E:PRO425 4.5 17.7 1.0
C E:CYS426 4.6 20.8 1.0
CA E:PRO425 4.7 21.7 1.0
O2 E:DCP603 4.7 22.6 1.0
O E:CYS426 4.8 19.8 1.0
CA E:HIS398 4.9 6.2 1.0
CG E:GLU428 4.9 19.6 1.0

Reference:

A.Slyvka, I.Rathore, R.Yang, T.Kanai, G.Lountos, Z.Wang, K.Skowronek, M.Czarnocki-Cieciura, A.Wlodawer, M.Bochtler. Cryo-Em Structure of Human CDADC1 Inactive Mutant (E400A): Trimer Without A Ligand To Be Published 2025.
Page generated: Fri Aug 22 18:03:44 2025

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