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Zinc in PDB 5ze3: Crystal Structure of Human Lysyl Oxidase-Like 2 (HLOXL2) in A Precursor State

Enzymatic activity of Crystal Structure of Human Lysyl Oxidase-Like 2 (HLOXL2) in A Precursor State

All present enzymatic activity of Crystal Structure of Human Lysyl Oxidase-Like 2 (HLOXL2) in A Precursor State:
1.4.3.13;

Protein crystallography data

The structure of Crystal Structure of Human Lysyl Oxidase-Like 2 (HLOXL2) in A Precursor State, PDB code: 5ze3 was solved by X.Zhang, M.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.50 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.095, 61.487, 137.883, 90.00, 102.33, 90.00
R / Rfree (%) 21.7 / 23.9

Other elements in 5ze3:

The structure of Crystal Structure of Human Lysyl Oxidase-Like 2 (HLOXL2) in A Precursor State also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Lysyl Oxidase-Like 2 (HLOXL2) in A Precursor State (pdb code 5ze3). 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 Lysyl Oxidase-Like 2 (HLOXL2) in A Precursor State, PDB code: 5ze3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5ze3

Go back to Zinc Binding Sites List in 5ze3
Zinc binding site 1 out of 2 in the Crystal Structure of Human Lysyl Oxidase-Like 2 (HLOXL2) in A Precursor State


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 Lysyl Oxidase-Like 2 (HLOXL2) in A Precursor State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn803

b:18.5
occ:1.00
OH A:TYR689 1.9 45.2 1.0
NE2 A:HIS630 2.0 17.6 1.0
NE2 A:HIS628 2.0 12.4 1.0
ND1 A:HIS626 2.1 31.3 1.0
CE1 A:HIS630 2.7 19.9 1.0
CZ A:TYR689 2.8 35.8 1.0
CE1 A:HIS628 3.0 12.7 1.0
CE1 A:HIS626 3.0 29.6 1.0
CD2 A:HIS628 3.0 13.2 1.0
CD2 A:HIS630 3.1 24.8 1.0
CG A:HIS626 3.1 34.0 1.0
CE2 A:TYR689 3.4 35.4 1.0
CB A:HIS626 3.5 18.0 1.0
CE1 A:TYR689 3.8 34.9 1.0
N A:CYS657 3.8 24.9 1.0
CB A:CYS657 3.9 24.9 1.0
ND1 A:HIS630 3.9 20.6 1.0
CG A:HIS630 4.1 13.6 1.0
ND1 A:HIS628 4.1 13.7 1.0
NE2 A:HIS626 4.1 39.3 1.0
CG A:HIS628 4.1 22.6 1.0
CD2 A:HIS626 4.2 34.4 1.0
CA A:CYS657 4.5 14.8 1.0
CD2 A:TYR689 4.6 27.2 1.0
C A:PHE656 4.7 32.3 1.0
O A:SER655 4.7 16.2 1.0
ND1 A:HIS623 4.8 34.7 1.0
CA A:PHE656 4.8 22.8 1.0
CB A:HIS623 4.9 23.3 1.0
CG A:HIS623 4.9 27.8 1.0
CD1 A:TYR689 4.9 25.0 1.0

Zinc binding site 2 out of 2 in 5ze3

Go back to Zinc Binding Sites List in 5ze3
Zinc binding site 2 out of 2 in the Crystal Structure of Human Lysyl Oxidase-Like 2 (HLOXL2) in A Precursor State


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 Lysyl Oxidase-Like 2 (HLOXL2) in A Precursor State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn804

b:57.6
occ:1.00
NE2 B:HIS628 1.9 87.3 1.0
NE2 B:HIS630 2.0 83.9 1.0
ND1 B:HIS626 2.1 90.0 1.0
OH B:TYR689 2.2 58.8 1.0
CE1 B:HIS628 2.3 71.2 1.0
CD2 B:HIS630 2.9 75.1 1.0
CE1 B:HIS630 3.0 79.2 1.0
CE1 B:HIS626 3.1 82.8 1.0
CG B:HIS626 3.1 84.5 1.0
CD2 B:HIS628 3.1 78.8 1.0
CZ B:TYR689 3.2 55.5 1.0
CB B:HIS626 3.5 75.1 1.0
ND1 B:HIS628 3.5 73.5 1.0
CE2 B:TYR689 3.7 56.0 1.0
CG B:HIS628 3.9 71.2 1.0
CG B:HIS630 4.0 74.0 1.0
ND1 B:HIS630 4.1 79.7 1.0
N B:CYS657 4.1 54.1 1.0
NE2 B:HIS626 4.2 85.0 1.0
CE1 B:TYR689 4.2 55.0 1.0
CD2 B:HIS626 4.2 87.2 1.0
CB B:CYS657 4.4 56.2 1.0
C B:PHE656 4.7 58.8 1.0
CA B:PHE656 4.8 54.2 1.0
CB B:HIS623 4.9 62.3 1.0
CA B:CYS657 4.9 53.8 1.0
CD2 B:TYR689 5.0 56.1 1.0
O B:SER655 5.0 56.4 1.0
CA B:HIS626 5.0 73.4 1.0

Reference:

X.Zhang, Q.Wang, J.Wu, J.Wang, Y.Shi, M.Liu. Crystal Structure of Human Lysyl Oxidase-Like 2 (HLOXL2) in A Precursor State. Proc. Natl. Acad. Sci. V. 115 3828 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29581294
DOI: 10.1073/PNAS.1720859115
Page generated: Wed Dec 16 11:26:14 2020

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