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Zinc in PDB 9ja4: Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn)

Enzymatic activity of Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn)

All present enzymatic activity of Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn):
5.1.3.13;

Protein crystallography data

The structure of Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn), PDB code: 9ja4 was solved by W.J.Jeong, W.J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.24 / 2.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 52.494, 63.822, 73.524, 89.95, 89.81, 66.28
R / Rfree (%) 27.5 / 29.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn) (pdb code 9ja4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn), PDB code: 9ja4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9ja4

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Zinc binding site 1 out of 8 in the Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:68.0
occ:1.00
 OD2 C:ASP78 2.2 31.6 1.0
OD1 A:ASP78 2.4 28.4 1.0
NE2 A:HIS132 2.4 34.8 1.0
CB A:HIS130 3.1 30.2 1.0
CE1 A:HIS132 3.2 37.0 1.0
CG A:ASP78 3.3 29.8 1.0
CG C:ASP78 3.4 28.8 1.0
OD2 A:ASP78 3.5 31.1 1.0
CD2 A:HIS132 3.5 35.5 1.0
ND1 A:HIS130 3.5 31.2 1.0
CG A:HIS130 3.6 32.7 1.0
O C:HOH304 3.9 10.9 1.0
CB C:ASP78 4.2 29.0 1.0
ND1 A:HIS132 4.4 38.1 1.0
CA A:HIS130 4.4 27.7 1.0
OD1 C:ASP78 4.4 26.7 1.0
C A:HIS130 4.5 25.7 1.0
CG A:HIS132 4.6 32.5 1.0
O A:HIS130 4.7 27.8 1.0
CE1 A:HIS130 4.7 32.7 1.0
CB A:ASP78 4.7 30.1 1.0
O C:ASP78 4.7 31.4 1.0
CD2 A:HIS130 4.8 35.7 1.0
ZN C:ZN201 4.9 65.8 1.0
C A:ASP78 4.9 34.1 1.0

Zinc binding site 2 out of 8 in 9ja4

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Zinc binding site 2 out of 8 in the Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:80.1
occ:1.00
 OE2 A:GLU142 1.9 73.5 1.0
ND1 A:HIS140 2.4 56.9 1.0
CD A:GLU142 3.0 71.6 1.0
CE1 A:HIS140 3.3 57.9 1.0
CG A:HIS140 3.5 55.0 1.0
OE1 A:GLU142 3.6 88.0 1.0
CB A:HIS140 3.8 57.4 1.0
CG A:GLU142 4.1 62.9 1.0
CA A:HIS140 4.2 54.4 1.0
NE2 A:HIS140 4.4 55.1 1.0
CD2 A:HIS140 4.6 53.8 1.0
CD A:PRO141 4.7 55.1 1.0
C A:HIS140 5.0 53.4 1.0

Zinc binding site 3 out of 8 in 9ja4

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Zinc binding site 3 out of 8 in the Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:63.6
occ:1.00
 OD1 B:ASP78 1.9 26.9 1.0
OD2 D:ASP78 2.1 41.4 1.0
NE2 B:HIS132 2.2 32.8 1.0
ND1 B:HIS130 2.3 50.4 1.0
CG B:ASP78 3.0 28.5 1.0
CE1 B:HIS132 3.1 33.2 1.0
CG D:ASP78 3.2 40.5 1.0
CD2 B:HIS132 3.2 31.4 1.0
CG B:HIS130 3.2 42.8 1.0
CE1 B:HIS130 3.3 52.5 1.0
CB B:HIS130 3.3 37.2 1.0
NH2 B:ARG79 3.5 32.9 1.0
OD2 B:ASP78 3.7 29.5 1.0
OD1 D:ASP78 3.7 43.9 1.0
CB B:ASP78 4.2 29.5 1.0
ND1 B:HIS132 4.2 33.3 1.0
CZ B:ARG79 4.3 35.3 1.0
CG B:HIS132 4.3 30.1 1.0
CD2 B:HIS130 4.4 41.9 1.0
NE2 B:HIS130 4.4 46.2 1.0
CB D:ASP78 4.4 38.0 1.0
NH1 B:ARG79 4.5 33.1 1.0
ZN D:ZN201 4.5 79.8 1.0
CA B:HIS130 4.5 30.6 1.0
O B:ASP78 4.5 31.5 1.0
C B:HIS130 4.6 27.5 1.0
C B:ASP78 4.6 32.8 1.0
O B:HIS130 4.6 29.4 1.0
CA B:ASP78 4.7 31.7 1.0
O D:ASP78 4.9 36.8 1.0
N B:ASP78 4.9 29.6 1.0

Zinc binding site 4 out of 8 in 9ja4

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Zinc binding site 4 out of 8 in the Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:85.4
occ:1.00
 OE2 B:GLU142 1.8 66.3 1.0
ND1 B:HIS140 2.2 55.0 1.0
CD B:GLU142 2.7 69.5 1.0
CE1 B:HIS140 3.1 57.1 1.0
OE1 B:GLU142 3.2 80.4 1.0
CG B:HIS140 3.3 56.4 1.0
CB B:HIS140 3.7 61.1 1.0
CG B:GLU142 3.9 65.4 1.0
NE2 B:HIS140 4.2 55.4 1.0
CA B:HIS140 4.3 58.5 1.0
CD2 B:HIS140 4.3 54.9 1.0
CE2 B:TYR143 5.0 71.0 1.0

Zinc binding site 5 out of 8 in 9ja4

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Zinc binding site 5 out of 8 in the Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:65.8
occ:1.00
 OD1 C:ASP78 2.2 26.7 1.0
OD2 A:ASP78 2.2 31.1 1.0
NE2 C:HIS132 2.2 36.0 1.0
ND1 C:HIS130 3.0 40.1 1.0
CE1 C:HIS132 3.0 36.4 1.0
CG C:ASP78 3.1 28.8 1.0
CB C:HIS130 3.1 32.2 1.0
CD2 C:HIS132 3.3 35.4 1.0
OD2 C:ASP78 3.3 31.6 1.0
CG C:HIS130 3.4 37.6 1.0
CG A:ASP78 3.5 29.8 1.0
CE1 C:HIS130 4.2 42.9 1.0
ND1 C:HIS132 4.2 36.4 1.0
O C:HOH304 4.2 10.9 1.0
CB A:ASP78 4.3 30.1 1.0
CG C:HIS132 4.3 32.9 1.0
OD1 A:ASP78 4.3 28.4 1.0
CA C:HIS130 4.4 28.8 1.0
C C:HIS130 4.5 25.3 1.0
CB C:ASP78 4.5 29.0 1.0
O C:HIS130 4.6 25.2 1.0
CD2 C:HIS130 4.7 40.6 1.0
C C:ASP78 4.8 31.8 1.0
O A:ASP78 4.9 30.6 1.0
ZN A:ZN201 4.9 68.0 1.0
NH2 A:ARG76 4.9 41.6 1.0
O C:ASP78 4.9 31.4 1.0

Zinc binding site 6 out of 8 in 9ja4

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Zinc binding site 6 out of 8 in the Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:61.4
occ:1.00
 OE2 C:GLU142 1.9 75.1 1.0
ND1 C:HIS140 2.3 54.0 1.0
CD C:GLU142 2.9 69.8 1.0
CE1 C:HIS140 3.1 56.5 1.0
CG C:HIS140 3.4 54.0 1.0
OE1 C:GLU142 3.4 71.8 1.0
CB C:HIS140 3.8 52.3 1.0
CG C:GLU142 4.0 64.9 1.0
NE2 C:HIS140 4.3 57.3 1.0
CA C:HIS140 4.3 52.5 1.0
CD2 C:HIS140 4.4 56.5 1.0

Zinc binding site 7 out of 8 in 9ja4

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Zinc binding site 7 out of 8 in the Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:79.8
occ:1.00
 OD2 B:ASP78 1.8 29.5 1.0
OD1 D:ASP78 2.0 43.9 1.0
NE2 D:HIS132 2.1 40.3 1.0
ND1 D:HIS130 2.3 42.6 1.0
CE1 D:HIS132 2.9 40.1 1.0
CG B:ASP78 3.0 28.5 1.0
CG D:ASP78 3.0 40.5 1.0
CD2 D:HIS132 3.1 38.6 1.0
CG D:HIS130 3.3 37.7 1.0
CE1 D:HIS130 3.3 45.0 1.0
CB D:HIS130 3.4 33.4 1.0
OD1 B:ASP78 3.6 26.9 1.0
OD2 D:ASP78 3.6 41.4 1.0
NH1 B:ARG79 4.0 33.1 1.0
ND1 D:HIS132 4.1 39.9 1.0
CB D:ASP78 4.1 38.0 1.0
CB B:ASP78 4.2 29.5 1.0
CG D:HIS132 4.2 36.1 1.0
CD2 D:HIS130 4.4 39.5 1.0
NE2 D:HIS130 4.4 43.6 1.0
ZN B:ZN201 4.5 63.6 1.0
NH2 B:ARG79 4.6 32.9 1.0
CA D:HIS130 4.6 28.9 1.0
O B:ASP78 4.6 31.5 1.0
C D:HIS130 4.7 25.7 1.0
O D:HIS130 4.7 27.2 1.0
CZ B:ARG79 4.8 35.3 1.0
C D:ASP78 4.8 37.3 1.0
O D:ASP78 4.8 36.8 1.0
CA D:ASP78 4.9 37.7 1.0

Zinc binding site 8 out of 8 in 9ja4

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Zinc binding site 8 out of 8 in the Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Artificial Dinuclear Zn-Bound Metalloprotein 2 (D2:Zn) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:62.0
occ:1.00
 OE2 D:GLU142 1.8 68.1 1.0
ND1 D:HIS140 2.3 56.0 1.0
CD D:GLU142 2.7 68.1 1.0
CE1 D:HIS140 3.1 58.4 1.0
OE1 D:GLU142 3.3 70.6 1.0
CG D:HIS140 3.3 55.9 1.0
CB D:HIS140 3.7 56.6 1.0
CG D:GLU142 3.9 66.9 1.0
CA D:HIS140 4.2 57.7 1.0
NE2 D:HIS140 4.3 57.7 1.0
CD2 D:HIS140 4.3 55.1 1.0
CD D:PRO141 5.0 66.4 1.0
C D:HIS140 5.0 64.8 1.0

Reference:

W.J.Jeong, W.J.Song. Metal-Installer: A Protein Designer Tool to Create Metal-Binding Sites To Be Published.
Page generated: Fri Aug 22 18:21:50 2025

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