Zinc in PDB 6fnd: Crystal Structure of Toxoplasma Gondii Akmt

Protein crystallography data

The structure of Crystal Structure of Toxoplasma Gondii Akmt, PDB code: 6fnd was solved by Y.Pivovarova, G.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.07 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.935, 89.371, 91.720, 108.69, 101.31, 103.41
R / Rfree (%) 19.1 / 22.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Toxoplasma Gondii Akmt (pdb code 6fnd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Toxoplasma Gondii Akmt, PDB code: 6fnd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6fnd

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Zinc binding site 1 out of 8 in the Crystal Structure of Toxoplasma Gondii Akmt


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 Toxoplasma Gondii Akmt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:42.1
occ:0.60
 SG A:CYS510 2.2 42.7 1.0
SG A:CYS507 2.2 45.1 1.0
CB A:CYS510 2.3 41.1 1.0
SG A:CYS505 2.4 51.7 1.0
SG A:CYS449 2.4 44.1 1.0
CB A:CYS505 3.3 44.7 1.0
CB A:CYS507 3.5 48.6 1.0
CA A:CYS510 3.5 44.6 1.0
CB A:CYS449 3.5 42.2 1.0
N A:CYS510 3.6 46.9 1.0
N A:CYS507 3.8 49.1 1.0
CA A:CYS507 4.1 47.0 1.0
C A:CYS505 4.3 45.7 1.0
N A:CYS449 4.3 49.0 1.0
CA A:CYS505 4.4 46.3 1.0
NH2 A:ARG494 4.5 37.2 1.0
O A:CYS505 4.5 40.6 1.0
NE A:ARG494 4.5 37.4 1.0
CA A:CYS449 4.6 47.8 1.0
C A:CYS507 4.6 47.5 1.0
N A:GLN506 4.6 47.3 1.0
O A:CYS507 4.6 46.3 1.0
NE2 A:HIS447 4.7 50.8 1.0
C A:ARG509 4.7 47.9 1.0
C A:CYS510 4.7 48.1 1.0
C A:GLN506 4.9 48.1 1.0

Zinc binding site 2 out of 8 in 6fnd

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Zinc binding site 2 out of 8 in the Crystal Structure of Toxoplasma Gondii Akmt


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 Toxoplasma Gondii Akmt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:38.8
occ:0.79
 SG A:CYS547 2.3 35.6 1.0
SG A:CYS525 2.3 37.7 1.0
SG A:CYS522 2.4 33.6 1.0
SG A:CYS544 2.4 31.1 1.0
CB A:CYS522 3.1 33.2 1.0
CB A:CYS544 3.1 33.6 1.0
CB A:CYS525 3.2 36.8 1.0
CB A:CYS547 3.3 33.1 1.0
N A:CYS525 3.7 39.8 1.0
N A:CYS547 3.7 33.6 1.0
CA A:CYS547 4.0 31.8 1.0
CA A:CYS525 4.1 39.8 1.0
CA A:CYS522 4.6 35.0 1.0
CB A:LEU524 4.6 42.0 1.0
CA A:CYS544 4.6 34.4 1.0
C A:CYS547 4.6 32.0 1.0
N A:GLY528 4.7 30.9 1.0
O A:HOH944 4.7 53.4 1.0
N A:GLN548 4.8 30.6 1.0
C A:LEU524 4.8 39.2 1.0
CA A:GLY528 4.8 30.5 1.0
C A:ILE546 4.9 39.5 1.0
C A:CYS525 4.9 39.8 1.0
CB A:ILE546 5.0 41.5 1.0
N A:GLY526 5.0 37.6 1.0
C A:CYS522 5.0 39.2 1.0

Zinc binding site 3 out of 8 in 6fnd

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Zinc binding site 3 out of 8 in the Crystal Structure of Toxoplasma Gondii Akmt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Toxoplasma Gondii Akmt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:39.4
occ:0.76
 SG B:CYS505 2.2 40.8 1.0
SG B:CYS507 2.3 40.8 1.0
SG B:CYS510 2.4 38.6 1.0
SG B:CYS449 2.4 35.5 1.0
CB B:CYS449 3.2 33.3 1.0
CB B:CYS510 3.3 37.2 1.0
CB B:CYS505 3.4 43.6 1.0
CB B:CYS507 3.4 42.9 1.0
N B:CYS449 3.8 36.7 1.0
N B:CYS507 4.0 39.4 1.0
N B:CYS510 4.0 35.1 1.0
NE2 B:HIS447 4.1 42.0 1.0
CA B:CYS449 4.1 35.5 1.0
CA B:CYS507 4.3 42.1 1.0
CA B:CYS510 4.3 36.6 1.0
NE B:ARG494 4.5 37.5 1.0
CA B:CYS505 4.5 45.4 1.0
C B:CYS505 4.6 45.5 1.0
NH2 B:ARG494 4.6 34.8 1.0
CD2 B:HIS447 4.7 41.7 1.0
C B:CYS507 4.8 44.0 1.0
O B:CYS505 4.9 42.6 1.0
N B:GLN506 4.9 43.7 1.0
C B:SER448 4.9 36.6 1.0
O B:CYS507 5.0 47.7 1.0

Zinc binding site 4 out of 8 in 6fnd

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Zinc binding site 4 out of 8 in the Crystal Structure of Toxoplasma Gondii Akmt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Toxoplasma Gondii Akmt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:45.2
occ:0.75
 SG B:CYS525 2.1 76.5 1.0
SG B:CYS522 2.3 39.8 1.0
SG B:CYS547 2.3 42.0 1.0
SG B:CYS544 2.4 44.2 1.0
CB B:CYS522 3.0 37.1 1.0
CB B:CYS544 3.0 38.8 1.0
CB B:CYS525 3.0 65.8 1.0
CB B:CYS547 3.3 43.5 1.0
N B:CYS525 3.7 52.4 1.0
N B:CYS547 3.7 46.5 1.0
CA B:CYS525 4.0 57.9 1.0
CA B:CYS547 4.1 46.2 1.0
CA B:CYS522 4.5 40.3 1.0
CA B:CYS544 4.5 38.6 1.0
C B:CYS547 4.6 48.8 1.0
CB B:LEU524 4.7 54.7 1.0
N B:GLN548 4.7 52.3 1.0
N B:GLY528 4.7 48.4 1.0
CA B:GLY528 4.8 45.3 1.0
C B:LEU524 4.8 52.6 1.0
C B:ILE546 4.9 45.4 1.0
C B:CYS522 4.9 43.4 1.0
C B:CYS525 5.0 51.6 1.0

Zinc binding site 5 out of 8 in 6fnd

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Zinc binding site 5 out of 8 in the Crystal Structure of Toxoplasma Gondii Akmt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Toxoplasma Gondii Akmt within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:36.2
occ:0.75
 SG C:CYS505 2.3 31.8 1.0
SG C:CYS507 2.3 30.9 1.0
SG C:CYS510 2.4 32.1 1.0
SG C:CYS449 2.4 36.9 1.0
CB C:CYS449 3.2 34.6 1.0
CB C:CYS510 3.3 30.7 1.0
CB C:CYS505 3.3 30.7 1.0
CB C:CYS507 3.4 30.6 1.0
N C:CYS449 3.9 28.6 1.0
N C:CYS507 4.0 34.1 1.0
N C:CYS510 4.0 33.9 1.0
CA C:CYS449 4.2 31.1 1.0
CA C:CYS507 4.2 32.8 1.0
NE2 C:HIS447 4.2 31.5 1.0
CA C:CYS510 4.3 34.4 1.0
NE C:ARG494 4.5 33.6 1.0
CA C:CYS505 4.5 33.3 1.0
C C:CYS505 4.5 37.4 1.0
NH2 C:ARG494 4.6 28.2 1.0
CD2 C:HIS447 4.7 33.1 1.0
C C:CYS507 4.8 35.4 1.0
O C:CYS505 4.8 37.7 1.0
N C:GLN506 4.9 39.5 1.0
O C:CYS507 4.9 37.0 1.0
C C:SER448 5.0 30.4 1.0

Zinc binding site 6 out of 8 in 6fnd

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Zinc binding site 6 out of 8 in the Crystal Structure of Toxoplasma Gondii Akmt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Toxoplasma Gondii Akmt within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn802

b:38.0
occ:0.83
 SG C:CYS525 2.3 33.5 1.0
SG C:CYS544 2.3 32.8 1.0
SG C:CYS522 2.4 33.8 1.0
SG C:CYS547 2.4 31.3 1.0
CB C:CYS544 3.0 29.7 1.0
CB C:CYS522 3.0 33.1 1.0
CB C:CYS525 3.3 32.0 1.0
CB C:CYS547 3.4 31.8 1.0
N C:CYS547 3.7 36.0 1.0
N C:CYS525 3.8 31.0 1.0
CA C:CYS547 4.1 34.5 1.0
CA C:CYS525 4.1 34.3 1.0
CA C:CYS544 4.5 31.2 1.0
CA C:CYS522 4.5 33.5 1.0
N C:GLY528 4.6 31.3 1.0
CB C:LEU524 4.6 39.1 1.0
C C:CYS547 4.7 34.5 1.0
CA C:GLY528 4.7 32.8 1.0
N C:GLN548 4.8 35.0 0.5
N C:GLN548 4.8 35.0 0.5
C C:ILE546 4.8 33.2 1.0
CB C:ILE546 4.9 33.5 1.0
C C:LEU524 4.9 32.1 1.0
C C:CYS525 4.9 36.9 1.0
N C:ILE546 5.0 30.2 1.0
N C:GLY526 5.0 38.0 1.0

Zinc binding site 7 out of 8 in 6fnd

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Zinc binding site 7 out of 8 in the Crystal Structure of Toxoplasma Gondii Akmt


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Toxoplasma Gondii Akmt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:40.0
occ:1.00
 SG D:CYS507 2.3 33.2 1.0
SG D:CYS510 2.4 30.5 1.0
SG D:CYS505 2.4 34.8 1.0
SG D:CYS449 2.4 33.1 1.0
CB D:CYS449 3.1 30.6 1.0
CB D:CYS510 3.4 28.0 1.0
CB D:CYS505 3.4 35.6 1.0
CB D:CYS507 3.5 36.9 1.0
N D:CYS449 3.8 32.6 1.0
N D:CYS510 4.0 33.6 1.0
N D:CYS507 4.1 38.7 1.0
CA D:CYS449 4.1 32.8 1.0
NE2 D:HIS447 4.2 34.5 1.0
CA D:CYS510 4.3 32.2 1.0
CA D:CYS507 4.3 38.3 1.0
NE D:ARG494 4.4 34.2 1.0
CA D:CYS505 4.6 37.1 1.0
NH2 D:ARG494 4.6 33.4 1.0
C D:CYS505 4.6 39.4 1.0
CD2 D:HIS447 4.7 34.3 1.0
C D:CYS507 4.9 38.3 1.0
C D:SER448 4.9 31.1 1.0
N D:GLN506 4.9 40.5 1.0
O D:CYS505 5.0 36.0 1.0
CB D:ARG509 5.0 32.6 1.0

Zinc binding site 8 out of 8 in 6fnd

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Zinc binding site 8 out of 8 in the Crystal Structure of Toxoplasma Gondii Akmt


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Toxoplasma Gondii Akmt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:46.6
occ:1.00
 SG D:CYS547 2.3 33.5 1.0
SG D:CYS525 2.3 30.1 1.0
SG D:CYS522 2.3 33.0 1.0
SG D:CYS544 2.4 31.1 1.0
CB D:CYS522 3.1 35.4 1.0
CB D:CYS544 3.1 28.2 1.0
CB D:CYS525 3.2 31.2 1.0
CB D:CYS547 3.3 31.8 1.0
N D:CYS525 3.6 38.4 1.0
N D:CYS547 3.8 31.7 1.0
CA D:CYS525 4.0 37.3 1.0
CA D:CYS547 4.1 30.8 1.0
CA D:CYS522 4.5 38.4 1.0
CB D:LEU524 4.6 37.8 1.0
CA D:CYS544 4.6 30.3 1.0
N D:GLY528 4.7 34.1 1.0
C D:CYS547 4.7 31.3 1.0
C D:LEU524 4.8 43.2 1.0
CA D:GLY528 4.8 29.8 1.0
N D:GLN548 4.8 29.9 1.0
C D:CYS525 4.9 40.0 1.0
N D:GLY526 4.9 36.6 1.0
C D:ILE546 4.9 32.5 1.0
CB D:ILE546 4.9 32.7 1.0
C D:CYS522 5.0 36.6 1.0
O D:HOH929 5.0 35.8 1.0

Reference:

Y.Pivovarova, J.Liu, J.Lesigang, O.Koldyka, R.Rauschmeier, K.Hu, G.Dong. Structure of A Novel Dimeric Set Domain Methyltransferase That Regulates Cell Motility. J. Mol. Biol. V. 430 4209 2018.
ISSN: ESSN 1089-8638
PubMed: 30148980
DOI: 10.1016/J.JMB.2018.08.017
Page generated: Wed Dec 16 11:48:48 2020

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