Zinc in PDB 6mtw: Lysosomal Phospholipase A2 in Complex with Zinc

Protein crystallography data

The structure of Lysosomal Phospholipase A2 in Complex with Zinc, PDB code: 6mtw was solved by R.Bouley, J.J.T.Tesmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.34 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 84.567, 84.567, 321.744, 90.00, 90.00, 120.00
R / Rfree (%) 24.8 / 28.5

Other elements in 6mtw:

The structure of Lysosomal Phospholipase A2 in Complex with Zinc also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Lysosomal Phospholipase A2 in Complex with Zinc (pdb code 6mtw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Lysosomal Phospholipase A2 in Complex with Zinc, PDB code: 6mtw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6mtw

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Zinc binding site 1 out of 8 in the Lysosomal Phospholipase A2 in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Lysosomal Phospholipase A2 in Complex with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:32.8
occ:1.00
 OG A:SER165 2.0 28.9 1.0
O A:HOH594 2.0 31.5 1.0
NE2 A:HIS359 2.1 23.6 1.0
O A:HOH647 2.3 19.5 1.0
CB A:SER165 2.8 22.7 1.0
CD2 A:HIS359 3.0 23.6 1.0
CE1 A:HIS359 3.1 23.3 1.0
OD1 A:ASP13 3.6 35.3 1.0
CA A:SER165 3.6 21.9 1.0
O A:HOH577 3.9 30.5 1.0
N A:MET166 3.9 19.0 1.0
ND1 A:HIS359 4.2 24.9 1.0
CG A:HIS359 4.2 26.6 1.0
C A:SER165 4.2 23.2 1.0
CG2 A:THR329 4.4 27.3 1.0
CG A:ASP13 4.7 34.9 1.0
N A:SER165 4.9 19.1 1.0

Zinc binding site 2 out of 8 in 6mtw

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Zinc binding site 2 out of 8 in the Lysosomal Phospholipase A2 in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Lysosomal Phospholipase A2 in Complex with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:38.9
occ:1.00
 O A:HOH671 1.9 48.3 1.0
O A:HOH664 1.9 35.2 1.0
SG A:CYS322 2.3 37.8 1.0
O A:HOH659 2.6 42.2 1.0
O A:HOH501 2.9 38.7 1.0
O A:HOH673 3.0 46.7 1.0
CB A:CYS322 3.2 37.8 1.0
ZN A:ZN407 3.4 51.1 1.0
ZN A:ZN406 3.4 40.0 1.0
CA A:CYS322 4.5 39.2 1.0
OG A:SER308 4.6 46.9 1.0
O A:HOH608 4.7 28.8 1.0
O A:HOH661 4.9 65.9 1.0

Zinc binding site 3 out of 8 in 6mtw

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Zinc binding site 3 out of 8 in the Lysosomal Phospholipase A2 in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Lysosomal Phospholipase A2 in Complex with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:40.0
occ:1.00
 OD1 A:ASP307 2.1 39.0 1.0
O A:HOH501 2.2 38.7 1.0
SG A:CYS322 2.3 37.8 1.0
CG A:ASP307 2.8 36.6 1.0
OD2 A:ASP307 2.9 37.6 1.0
ZN A:ZN407 3.3 51.1 1.0
O A:HOH671 3.3 48.3 1.0
ZN A:ZN405 3.4 38.9 1.0
CB A:CYS322 3.4 37.8 1.0
OG A:SER308 3.5 46.9 1.0
NZ A:LYS247 4.0 41.3 1.0
O A:HOH652 4.0 54.2 1.0
C A:CYS322 4.3 35.5 1.0
CB A:ASP307 4.3 36.6 1.0
O A:CYS322 4.3 33.9 1.0
CB A:SER308 4.4 43.0 1.0
CA A:CYS322 4.5 39.2 1.0
O A:HOH664 4.6 35.2 1.0
N A:SER308 4.6 30.3 1.0
N A:PHE323 4.6 36.2 1.0
O A:PHE323 4.7 36.6 1.0
C A:ASP307 4.8 35.1 1.0
O A:HOH661 5.0 65.9 1.0
C A:PHE323 5.0 36.1 1.0

Zinc binding site 4 out of 8 in 6mtw

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Zinc binding site 4 out of 8 in the Lysosomal Phospholipase A2 in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Lysosomal Phospholipase A2 in Complex with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:51.1
occ:1.00
 O A:HOH501 1.9 38.7 1.0
O A:HOH671 2.0 48.3 1.0
O A:HOH661 2.0 65.9 1.0
O A:HOH652 2.1 54.2 1.0
ZN A:ZN406 3.3 40.0 1.0
ZN A:ZN405 3.4 38.9 1.0
O A:HOH673 3.4 46.7 1.0
O A:HOH664 3.5 35.2 1.0
OG A:SER308 3.7 46.9 1.0
NZ A:LYS247 4.2 41.3 1.0
SG A:CYS322 4.3 37.8 1.0
CB A:SER308 4.5 43.0 1.0
OD1 A:ASP307 4.6 39.0 1.0

Zinc binding site 5 out of 8 in 6mtw

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Zinc binding site 5 out of 8 in the Lysosomal Phospholipase A2 in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Lysosomal Phospholipase A2 in Complex with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:33.3
occ:1.00
 O B:HOH605 1.9 35.0 1.0
OG B:SER165 2.0 29.7 1.0
NE2 B:HIS359 2.1 22.5 1.0
O B:HOH641 2.3 21.6 1.0
CB B:SER165 2.8 24.8 1.0
CD2 B:HIS359 3.1 22.1 1.0
CE1 B:HIS359 3.1 23.2 1.0
OD1 B:ASP13 3.6 34.0 1.0
CA B:SER165 3.6 21.5 1.0
N B:MET166 4.0 18.8 1.0
ND1 B:HIS359 4.2 24.9 1.0
C B:SER165 4.2 23.1 1.0
CG B:HIS359 4.2 26.0 1.0
CG2 B:THR329 4.4 34.7 1.0
CG B:ASP13 4.8 34.4 1.0
N B:SER165 5.0 20.9 1.0

Zinc binding site 6 out of 8 in 6mtw

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Zinc binding site 6 out of 8 in the Lysosomal Phospholipase A2 in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Lysosomal Phospholipase A2 in Complex with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn405

b:37.2
occ:1.00
 O B:HOH667 1.9 39.2 1.0
O B:HOH658 1.9 36.7 1.0
SG B:CYS322 2.3 37.5 1.0
O B:HOH636 2.8 37.0 1.0
O B:HOH501 3.1 35.8 1.0
ZN B:ZN407 3.2 47.8 1.0
CB B:CYS322 3.3 37.1 1.0
ZN B:ZN406 3.4 38.7 1.0
O B:HOH664 3.5 49.0 1.0
CA B:CYS322 4.6 38.0 1.0
OG B:SER308 4.6 46.2 1.0
O B:HOH653 4.7 52.3 1.0
O B:HOH652 4.8 65.7 1.0

Zinc binding site 7 out of 8 in 6mtw

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Zinc binding site 7 out of 8 in the Lysosomal Phospholipase A2 in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Lysosomal Phospholipase A2 in Complex with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn406

b:38.7
occ:1.00
 O B:HOH501 2.0 35.8 1.0
OD1 B:ASP307 2.1 41.0 1.0
SG B:CYS322 2.2 37.5 1.0
CG B:ASP307 2.8 40.8 1.0
OD2 B:ASP307 2.9 40.8 1.0
O B:HOH667 3.2 39.2 1.0
ZN B:ZN407 3.3 47.8 1.0
ZN B:ZN405 3.4 37.2 1.0
CB B:CYS322 3.4 37.1 1.0
OG B:SER308 3.6 46.2 1.0
O B:HOH653 3.9 52.3 1.0
NZ B:LYS247 4.0 41.4 1.0
C B:CYS322 4.3 35.8 1.0
CB B:ASP307 4.3 38.2 1.0
O B:CYS322 4.4 31.1 1.0
CA B:CYS322 4.4 38.0 1.0
CB B:SER308 4.5 41.9 1.0
O B:HOH658 4.6 36.7 1.0
N B:SER308 4.6 36.9 1.0
N B:PHE323 4.6 36.1 1.0
O B:PHE323 4.7 35.1 1.0
C B:ASP307 4.8 36.6 1.0
O B:HOH652 5.0 65.7 1.0
C B:PHE323 5.0 36.4 1.0

Zinc binding site 8 out of 8 in 6mtw

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Zinc binding site 8 out of 8 in the Lysosomal Phospholipase A2 in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Lysosomal Phospholipase A2 in Complex with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn407

b:47.8
occ:1.00
 O B:HOH501 1.9 35.8 1.0
O B:HOH667 2.0 39.2 1.0
O B:HOH652 2.0 65.7 1.0
O B:HOH653 2.1 52.3 1.0
ZN B:ZN405 3.2 37.2 1.0
ZN B:ZN406 3.3 38.7 1.0
O B:HOH658 3.5 36.7 1.0
O B:HOH664 3.6 49.0 1.0
OG B:SER308 3.7 46.2 1.0
SG B:CYS322 4.2 37.5 1.0
NZ B:LYS247 4.3 41.4 1.0
CB B:SER308 4.6 41.9 1.0
OD1 B:ASP307 4.6 41.0 1.0
CB B:CYS322 4.9 37.1 1.0

Reference:

R.A.Bouley, V.Hinkovska-Galcheva, J.A.Shayman, J.J.G.Tesmer. Structural Basis of Lysosomal Phospholipase A2INHIBITION By ZN2. Biochemistry V. 58 1709 2019.
ISSN: ISSN 1520-4995
PubMed: 30830753
DOI: 10.1021/ACS.BIOCHEM.8B01124
Page generated: Wed Dec 16 12:20:32 2020

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