Zinc in PDB 5vxa: Structure of the Human MESH1-Nadph Complex

All present enzymatic activity of Structure of the Human MESH1-Nadph Complex:
3.1.7.2;

The structure of Structure of the Human MESH1-Nadph Complex, PDB code: 5vxa was solved by J.Rose, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.07 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.780, 80.370, 114.460, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20.6

The structure of Structure of the Human MESH1-Nadph Complex also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Structure of the Human MESH1-Nadph Complex (pdb code 5vxa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Human MESH1-Nadph Complex, PDB code: 5vxa:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Human MESH1-Nadph Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Human MESH1-Nadph Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:19.2 occ:1.00 NE2 A:HIS35 1.9 18.0 1.0 NE2 A:HIS61 2.0 22.8 1.0 O A:HOH313 2.1 33.2 1.0 OD1 A:ASP122 2.2 18.1 1.0 OD2 A:ASP62 2.4 27.1 1.0 CE1 A:HIS61 2.8 21.4 1.0 CD2 A:HIS35 2.9 12.2 1.0 CG A:ASP122 2.9 18.6 1.0 CE1 A:HIS35 3.0 17.4 1.0 O1X A:NDP202 3.0 46.9 1.0 CD2 A:HIS61 3.0 19.8 1.0 OD2 A:ASP122 3.1 20.0 1.0 CG A:ASP62 3.3 27.8 1.0 OD1 A:ASP62 3.6 28.6 1.0 P2B A:NDP202 3.9 44.6 1.0 ND1 A:HIS61 4.0 17.9 1.0 O2X A:NDP202 4.0 45.3 1.0 ND1 A:HIS35 4.0 15.7 1.0 CG A:HIS35 4.0 10.9 1.0 O A:HOH307 4.1 32.1 1.0 CG A:HIS61 4.1 18.9 1.0 CB A:ASP122 4.2 12.5 1.0 OH A:TYR32 4.3 20.0 1.0 O3X A:NDP202 4.3 43.5 1.0 CB A:ASP62 4.7 19.8 1.0 CG2 A:VAL39 4.8 10.3 1.0 ND2 A:ASN126 4.8 12.2 1.0 CA A:ASP122 5.0 12.6 1.0

Zinc binding site 2 out of 2 in the Structure of the Human MESH1-Nadph Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Human MESH1-Nadph Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:15.9 occ:1.00 O B:HOH312 1.9 18.0 1.0 NE2 B:HIS61 2.0 11.9 1.0 NE2 B:HIS35 2.0 9.5 1.0 OD2 B:ASP62 2.2 15.3 1.0 OD1 B:ASP122 2.2 16.8 1.0 CE1 B:HIS61 2.9 7.3 1.0 CD2 B:HIS35 3.0 6.8 1.0 CD2 B:HIS61 3.0 8.0 1.0 CE1 B:HIS35 3.1 7.4 1.0 CG B:ASP122 3.1 16.3 1.0 O2X B:NDP202 3.1 36.3 1.0 CG B:ASP62 3.1 12.4 1.0 OD1 B:ASP62 3.3 14.6 1.0 OD2 B:ASP122 3.4 18.4 1.0 O B:HOH308 3.9 29.3 1.0 ND1 B:HIS61 4.0 12.0 1.0 CG B:HIS61 4.1 7.9 1.0 CG B:HIS35 4.1 7.2 1.0 OH B:TYR32 4.1 20.8 1.0 ND1 B:HIS35 4.1 9.3 1.0 P2B B:NDP202 4.2 39.8 1.0 O1X B:NDP202 4.3 48.8 1.0 CB B:ASP122 4.4 10.6 1.0 O3X B:NDP202 4.4 40.2 1.0 CB B:ASP62 4.6 9.1 1.0 ND2 B:ASN126 4.6 10.5 1.0 CG2 B:VAL39 4.9 7.7 1.0 O B:HOH331 4.9 25.5 1.0

C.-K.C.Ding, J.Rose, P.Zhou, J.-T.A.Chi. Mammalian Stringent-Like Response Mediated By the Cytosolic Nadph Phosphatase MESH1 Biorxiv 2018.
DOI: 10.1101/325266