Zinc in PDB 9j3q: Human Pigment Epithelium-Derived Factor with Zinc Ion Crystallized in P22(1)2(1) Space Group

The structure of Human Pigment Epithelium-Derived Factor with Zinc Ion Crystallized in P22(1)2(1) Space Group, PDB code: 9j3q was solved by A.S.Belousov, D.V.Chistyakov, V.E.Baksheeva, T.K.Bulgakov, A.A.Zamyatnin, D.V.Zinchenko, L.Wu, P.O.Tsvetkov, S.E.Permyakov, E.Y.Zernii, V.I.Borshchevskiy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.23 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	174.974, 61.603, 44.796, 90, 90, 90
R / Rfree (%)	18.9 / 23.3

The binding sites of Zinc atom in the Human Pigment Epithelium-Derived Factor with Zinc Ion Crystallized in P22(1)2(1) Space Group (pdb code 9j3q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Human Pigment Epithelium-Derived Factor with Zinc Ion Crystallized in P22(1)2(1) Space Group, PDB code: 9j3q:

Zinc binding site 1 out of 1 in the Human Pigment Epithelium-Derived Factor with Zinc Ion Crystallized in P22(1)2(1) Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Pigment Epithelium-Derived Factor with Zinc Ion Crystallized in P22(1)2(1) Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:44.9 occ:1.00 O A:HOH722 2.0 47.4 1.0 OD1 A:ASP44 2.2 46.7 1.0 NE2 A:HIS299 2.2 42.4 1.0 OD2 A:ASP44 2.6 58.7 1.0 CG A:ASP44 2.7 49.6 1.0 CD2 A:HIS299 3.0 35.3 1.0 HD2 A:HIS299 3.0 42.5 1.0 CE1 A:HIS299 3.4 42.6 1.0 H42 A:PG0537 3.4 123.2 1.0 HD2 A:PRO45 3.5 62.0 1.0 HB3 A:PHE46 3.6 43.6 1.0 HE1 A:HIS299 3.7 51.1 1.0 H A:PHE46 3.7 44.4 1.0 HD3 A:ARG303 3.8 67.7 1.0 HB2 A:PHE46 3.9 43.6 1.0 HG3 A:ARG303 4.0 57.3 1.0 HE A:ARG303 4.0 62.3 1.0 CB A:ASP44 4.1 52.9 1.0 O2 A:PG0537 4.2 102.1 1.0 CG A:HIS299 4.2 36.6 1.0 CB A:PHE46 4.2 36.3 1.0 H52 A:PG0538 4.2 89.5 1.0 C4 A:PG0537 4.2 102.7 1.0 NE A:ARG303 4.3 51.9 1.0 ND1 A:HIS299 4.3 41.0 1.0 CD A:PRO45 4.4 51.6 1.0 HA A:ASP44 4.4 61.8 1.0 CD A:ARG303 4.4 56.4 1.0 N A:PHE46 4.5 37.0 1.0 HB2 A:ASP44 4.6 63.5 1.0 HB3 A:ASP44 4.6 63.5 1.0 CG A:ARG303 4.7 47.7 1.0 CA A:ASP44 4.7 51.5 1.0 N A:PRO45 4.7 44.9 1.0 HD3 A:PRO45 4.8 62.0 1.0 H41 A:PG0537 4.8 123.2 1.0 C A:ASP44 4.9 45.6 1.0 H41 A:PG0538 5.0 106.3 1.0 H32 A:PG0537 5.0 127.1 1.0 HD2 A:PHE47 5.0 47.5 1.0

D.V.Chistyakov, M.P.Shevelyova, E.N.Iomdina, V.E.Baksheeva, L.Wu, N.G.Shebardina, A.M.Moysenovich, T.K.Bulgakov, S.Y.Petrov, V.V.Tiulina, E.I.Pogodina, O.S.Gancharova, A.S.Belousov, O.M.Filippova, A.V.Baldin, S.V.Goriainov, A.I.Nikolskaya, A.O.Zalevsky, A.A.Deviatkin, A.A.Vologzhannikova, N.V.Gorokhovets, E.A.Litus, A.A.Zamyatnin, S.V.Komarov, F.Devred, M.G.Sergeeva, A.A.Zamyatnin Jr, I.I.Senin, D.V.Zinchenko, P.O.Tsvetkov, V.I.Borshchevskiy, S.E.Permyakov, E.Y.Zernii. Zinc-Mediated Mechanism of Neurodegeneration in Glaucoma: A Role of Pigment Epithelium-Derived Factor To Be Published.