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

Enzymatic activity of Structure of the Human MESH1-Nadph Complex

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

Protein crystallography data

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

Other elements in 5vxa:

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

Sodium (Na) 1 atom

Zinc Binding Sites:

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 5vxa

Go back to Zinc Binding Sites List in 5vxa
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 5vxa

Go back to Zinc Binding Sites List in 5vxa
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

Reference:

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
Page generated: Wed Dec 16 11:13:31 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy