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Zinc in PDB 3mjh: Crystal Structure of Human RAB5A in Complex with the C2H2 Zinc Finger of EEA1

Enzymatic activity of Crystal Structure of Human RAB5A in Complex with the C2H2 Zinc Finger of EEA1

All present enzymatic activity of Crystal Structure of Human RAB5A in Complex with the C2H2 Zinc Finger of EEA1:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Human RAB5A in Complex with the C2H2 Zinc Finger of EEA1, PDB code: 3mjh was solved by A.K.Mishra, S.Eathiraj, D.G.Lambright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.412, 80.398, 103.495, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 26

Other elements in 3mjh:

The structure of Crystal Structure of Human RAB5A in Complex with the C2H2 Zinc Finger of EEA1 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human RAB5A in Complex with the C2H2 Zinc Finger of EEA1 (pdb code 3mjh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human RAB5A in Complex with the C2H2 Zinc Finger of EEA1, PDB code: 3mjh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3mjh

Go back to Zinc Binding Sites List in 3mjh
Zinc binding site 1 out of 2 in the Crystal Structure of Human RAB5A in Complex with the C2H2 Zinc Finger of EEA1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human RAB5A in Complex with the C2H2 Zinc Finger of EEA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn70

b:39.2
occ:1.00
NE2 B:HIS59 2.1 38.3 1.0
NE2 B:HIS64 2.3 35.4 1.0
SG B:CYS43 2.3 33.9 1.0
SG B:CYS46 2.3 37.5 1.0
CE1 B:HIS59 3.0 37.6 1.0
CD2 B:HIS59 3.1 37.6 1.0
CB B:CYS43 3.1 35.0 1.0
CD2 B:HIS64 3.1 36.2 1.0
CE1 B:HIS64 3.3 36.8 1.0
CB B:CYS46 3.5 38.9 1.0
N B:CYS46 3.7 38.7 1.0
ND1 B:HIS59 4.1 38.1 1.0
CA B:CYS46 4.1 38.8 1.0
CG B:HIS59 4.2 37.2 1.0
CG B:HIS64 4.3 39.3 1.0
ND1 B:HIS64 4.3 38.0 1.0
CB B:GLN45 4.4 38.6 1.0
CB B:LYS48 4.4 42.5 1.0
CA B:CYS43 4.6 35.2 1.0
C B:GLN45 4.6 38.5 1.0
C B:CYS46 4.8 38.9 1.0
CA B:GLN45 4.8 38.2 1.0
N B:GLN45 4.9 37.0 1.0
N B:LYS48 4.9 40.9 1.0
C B:CYS43 4.9 35.1 1.0
O B:CYS43 5.0 35.3 1.0
N B:MET47 5.0 39.4 1.0

Zinc binding site 2 out of 2 in 3mjh

Go back to Zinc Binding Sites List in 3mjh
Zinc binding site 2 out of 2 in the Crystal Structure of Human RAB5A in Complex with the C2H2 Zinc Finger of EEA1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human RAB5A in Complex with the C2H2 Zinc Finger of EEA1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn70

b:40.2
occ:1.00
NE2 D:HIS59 2.0 29.0 1.0
NE2 D:HIS64 2.1 36.9 1.0
SG D:CYS43 2.3 37.1 1.0
SG D:CYS46 2.4 41.5 1.0
CD2 D:HIS64 2.8 36.5 1.0
CE1 D:HIS59 2.8 31.9 1.0
CD2 D:HIS59 3.1 32.4 1.0
CE1 D:HIS64 3.2 37.4 1.0
CB D:CYS43 3.2 39.5 1.0
CB D:CYS46 3.5 43.9 1.0
N D:CYS46 3.7 43.2 1.0
ND1 D:HIS59 4.0 31.8 1.0
CG D:HIS64 4.0 36.2 1.0
CG D:HIS59 4.1 32.8 1.0
CA D:CYS46 4.1 44.2 1.0
ND1 D:HIS64 4.2 36.3 1.0
CB D:GLN45 4.6 42.5 1.0
CD D:LYS48 4.6 20.0 1.0
CA D:CYS43 4.6 39.6 1.0
C D:GLN45 4.7 42.8 1.0
CB D:LYS48 4.7 20.0 1.0
CG D:LYS48 4.7 20.0 1.0
C D:CYS46 4.8 45.2 1.0
N D:GLN45 4.9 41.5 1.0
N D:MET47 4.9 46.1 1.0
CA D:GLN45 4.9 42.5 1.0
C D:CYS43 5.0 39.7 1.0

Reference:

A.Mishra, S.Eathiraj, S.Corvera, D.G.Lambright. Structural Basis For Rab Gtpase Recognition and Endosome Tethering By the C2H2 Zinc Finger of Early Endosomal Autoantigen 1 (EEA1). Proc.Natl.Acad.Sci.Usa V. 107 10866 2010.
ISSN: ISSN 0027-8424
PubMed: 20534488
DOI: 10.1073/PNAS.1000843107
Page generated: Wed Dec 16 04:35:21 2020

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