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Zinc in PDB 9j9n: Artificial Mononuclear Zn-Bound Metalloprotein 2 (M2:Zn)

Protein crystallography data

The structure of Artificial Mononuclear Zn-Bound Metalloprotein 2 (M2:Zn), PDB code: 9j9n 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) 29.47 / 2.86
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 136.12, 136.12, 48.88, 90, 90, 120
R / Rfree (%) 19.4 / 25

Zinc Binding Sites:

The binding sites of Zinc atom in the Artificial Mononuclear Zn-Bound Metalloprotein 2 (M2:Zn) (pdb code 9j9n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Artificial Mononuclear Zn-Bound Metalloprotein 2 (M2:Zn), PDB code: 9j9n:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 9j9n

Go back to Zinc Binding Sites List in 9j9n
Zinc binding site 1 out of 2 in the Artificial Mononuclear Zn-Bound Metalloprotein 2 (M2:Zn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Artificial Mononuclear Zn-Bound Metalloprotein 2 (M2:Zn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:85.0
occ:1.00
NE2 A:HIS83 2.2 63.7 1.0
O A:HOH501 2.3 39.7 1.0
NE2 A:HIS102 2.3 58.2 1.0
OD1 A:ASP132 2.6 99.0 1.0
CD2 A:HIS83 3.0 65.5 1.0
CD2 A:HIS102 3.1 62.8 1.0
CE1 A:HIS83 3.3 71.4 1.0
CE1 A:HIS102 3.4 60.0 1.0
CG A:ASP132 3.6 99.0 1.0
NH2 A:ARG82 3.7 79.9 1.0
OD2 A:ASP132 3.9 124.7 1.0
CG A:HIS83 4.2 66.6 1.0
CZ A:ARG82 4.2 78.0 1.0
ND1 A:HIS83 4.3 69.1 1.0
CG A:HIS102 4.3 59.4 1.0
ND1 A:HIS102 4.4 56.2 1.0
O A:ARG82 4.7 55.3 1.0
NH1 A:ARG82 4.7 78.2 1.0
O A:HOH503 4.8 49.6 1.0
NE A:ARG82 4.8 74.1 1.0
CB A:ARG82 4.8 59.3 1.0
CB A:ASP132 4.9 83.2 1.0

Zinc binding site 2 out of 2 in 9j9n

Go back to Zinc Binding Sites List in 9j9n
Zinc binding site 2 out of 2 in the Artificial Mononuclear Zn-Bound Metalloprotein 2 (M2:Zn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Artificial Mononuclear Zn-Bound Metalloprotein 2 (M2:Zn) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:88.0
occ:1.00
NE2 B:HIS102 2.2 65.2 1.0
O B:HOH501 2.3 41.7 1.0
CE1 B:HIS83 2.5 69.2 1.0
ND1 B:HIS83 2.7 69.9 1.0
OD1 B:ASP132 2.7 98.1 1.0
CD2 B:HIS102 3.1 70.8 1.0
CE1 B:HIS102 3.2 67.2 1.0
NE2 B:HIS83 3.8 76.7 1.0
O B:HOH505 4.0 46.3 1.0
CG B:ASP132 4.0 102.0 1.0
NH2 B:ARG82 4.0 81.6 1.0
CG B:HIS83 4.1 71.0 1.0
CZ B:ARG82 4.1 77.8 1.0
CG B:HIS102 4.2 66.5 1.0
ND1 B:HIS102 4.3 62.3 1.0
NH1 B:ARG82 4.3 76.8 1.0
CD2 B:HIS83 4.6 72.9 1.0
NE B:ARG82 4.7 79.0 1.0
OD2 B:ASP132 4.8 111.1 1.0
CB B:ARG82 4.8 63.8 1.0
CB B:ASP132 4.9 93.3 1.0
O B:ARG82 4.9 63.0 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 18:20:42 2025

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