Magnesium in PDB 7k3z: P. Falciparum CPN60 D474A Mutant Bound to Atp

Protein crystallography data

The structure of P. Falciparum CPN60 D474A Mutant Bound to Atp, PDB code: 7k3z was solved by N.H.Tolia, D.Shi, B.Nguyen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.99 / 3.69
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 281.498, 281.498, 298.827, 90, 90, 120
R / Rfree (%) 22.7 / 27.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the P. Falciparum CPN60 D474A Mutant Bound to Atp (pdb code 7k3z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the P. Falciparum CPN60 D474A Mutant Bound to Atp, PDB code: 7k3z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7k3z

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Magnesium binding site 1 out of 7 in the P. Falciparum CPN60 D474A Mutant Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of P. Falciparum CPN60 D474A Mutant Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:97.6
occ:1.00
 O3G A:ATP702 2.3 168.7 1.0
O2A A:ATP702 2.8 158.7 1.0
OD1 A:ASP153 2.9 148.7 1.0
O1B A:ATP702 2.9 103.5 1.0
PG A:ATP702 3.7 185.1 1.0
O A:ALA217 3.8 118.7 1.0
N A:ASN219 3.9 116.9 1.0
CG A:ASP153 4.0 151.4 1.0
O A:ILE216 4.0 127.6 1.0
PB A:ATP702 4.0 111.1 1.0
PA A:ATP702 4.1 112.3 1.0
C A:ALA217 4.1 103.6 1.0
CA A:ASN219 4.2 106.7 1.0
O3A A:ATP702 4.2 93.2 1.0
O1G A:ATP702 4.3 168.1 1.0
O3B A:ATP702 4.3 165.4 1.0
CB A:ASN219 4.4 104.3 1.0
OD2 A:ASP153 4.4 165.8 1.0
OD1 A:ASN219 4.5 175.3 1.0
CA A:ALA217 4.5 106.0 1.0
CG A:ASN219 4.6 174.6 1.0
C5' A:ATP702 4.7 126.5 1.0
N A:SER218 4.8 104.6 1.0
O2G A:ATP702 4.8 197.6 1.0
C A:SER218 4.9 128.0 1.0
O5' A:ATP702 5.0 81.5 1.0

Magnesium binding site 2 out of 7 in 7k3z

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Magnesium binding site 2 out of 7 in the P. Falciparum CPN60 D474A Mutant Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of P. Falciparum CPN60 D474A Mutant Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:90.9
occ:1.00
 O2A B:ATP702 2.3 147.5 1.0
O3G B:ATP702 2.7 185.7 1.0
O1B B:ATP702 3.0 100.8 1.0
OD1 B:ASP153 3.3 133.4 1.0
N B:ASN219 3.5 127.5 1.0
CA B:ASN219 3.7 133.7 1.0
O B:ILE216 3.7 127.0 1.0
PA B:ATP702 3.7 145.1 1.0
OD1 B:ASN219 4.0 196.1 1.0
CB B:ASN219 4.0 170.9 1.0
PG B:ATP702 4.0 198.6 1.0
O B:ALA217 4.0 184.8 1.0
PB B:ATP702 4.1 110.9 1.0
O3A B:ATP702 4.1 130.7 1.0
CG B:ASN219 4.1 189.1 1.0
C B:ALA217 4.2 142.5 1.0
CG B:ASP153 4.4 158.8 1.0
C5' B:ATP702 4.4 104.6 1.0
O1G B:ATP702 4.4 182.7 1.0
O3B B:ATP702 4.5 161.9 1.0
CA B:ALA217 4.6 133.0 1.0
C B:SER218 4.6 135.6 1.0
O5' B:ATP702 4.6 94.5 1.0
N B:SER218 4.7 141.6 1.0
OD2 B:ASP153 4.7 137.6 1.0
C B:ILE216 4.8 143.7 1.0
O1A B:ATP702 4.8 138.0 1.0

Magnesium binding site 3 out of 7 in 7k3z

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Magnesium binding site 3 out of 7 in the P. Falciparum CPN60 D474A Mutant Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of P. Falciparum CPN60 D474A Mutant Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:124.1
occ:1.00
 O1B C:ATP702 2.2 129.7 1.0
O2A C:ATP702 2.6 169.8 1.0
O3G C:ATP702 2.7 191.4 1.0
OD1 C:ASP153 2.8 172.1 1.0
OD1 C:ASN219 3.2 167.4 1.0
O C:ILE216 3.5 118.1 1.0
PB C:ATP702 3.6 115.4 1.0
CG C:ASP153 3.7 179.4 1.0
PA C:ATP702 3.8 135.6 1.0
OD2 C:ASP153 3.9 163.0 1.0
C5' C:ATP702 4.0 140.2 1.0
PG C:ATP702 4.0 191.9 1.0
O3A C:ATP702 4.0 138.0 1.0
O3B C:ATP702 4.1 155.0 1.0
O C:ALA217 4.3 156.9 1.0
CA C:ALA217 4.3 119.7 1.0
C C:ALA217 4.3 120.2 1.0
CG C:ASN219 4.4 173.9 1.0
N C:ASN219 4.4 122.2 1.0
O5' C:ATP702 4.4 104.8 1.0
C C:ILE216 4.6 118.1 1.0
O1G C:ATP702 4.6 125.2 1.0
CA C:ASN219 4.7 126.9 1.0
O2B C:ATP702 4.8 90.4 1.0
N C:ALA217 4.9 119.2 1.0

Magnesium binding site 4 out of 7 in 7k3z

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Magnesium binding site 4 out of 7 in the P. Falciparum CPN60 D474A Mutant Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of P. Falciparum CPN60 D474A Mutant Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:122.7
occ:1.00
 O2A D:ATP702 2.2 169.1 1.0
O3G D:ATP702 2.5 168.1 1.0
O1B D:ATP702 2.7 114.6 1.0
OD1 D:ASP153 3.2 145.3 1.0
PA D:ATP702 3.6 129.1 1.0
OD1 D:ASN219 3.8 205.3 1.0
PB D:ATP702 3.8 112.3 1.0
PG D:ATP702 3.8 185.1 1.0
N D:ASN219 3.9 110.3 1.0
CA D:ASN219 3.9 114.6 1.0
O3A D:ATP702 3.9 105.6 1.0
O D:ILE216 4.0 143.3 1.0
CG D:ASN219 4.1 200.3 1.0
CB D:ASN219 4.1 170.9 1.0
O1G D:ATP702 4.2 161.6 1.0
CG D:ASP153 4.3 159.9 1.0
O3B D:ATP702 4.3 159.3 1.0
C5' D:ATP702 4.3 112.2 1.0
O5' D:ATP702 4.5 94.3 1.0
O D:ALA217 4.5 165.2 1.0
OD2 D:ASP153 4.6 178.1 1.0
O1A D:ATP702 4.7 129.2 1.0
C D:ALA217 4.7 151.7 1.0
ND2 D:ASN219 4.9 170.4 1.0
C D:SER218 5.0 132.6 1.0

Magnesium binding site 5 out of 7 in 7k3z

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Magnesium binding site 5 out of 7 in the P. Falciparum CPN60 D474A Mutant Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of P. Falciparum CPN60 D474A Mutant Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg701

b:149.4
occ:1.00
 OD1 E:ASP153 2.4 147.4 1.0
O1B E:ATP702 2.6 143.5 1.0
O3G E:ATP702 2.7 202.2 1.0
OD1 E:ASN219 2.8 192.5 1.0
O2A E:ATP702 2.9 139.4 1.0
CG E:ASP153 3.3 147.9 1.0
O E:ILE216 3.5 127.1 1.0
OD2 E:ASP153 3.6 122.8 1.0
O E:ALA217 3.6 186.6 1.0
C E:ALA217 3.8 144.5 1.0
PB E:ATP702 3.9 121.6 1.0
N E:ASN219 3.9 126.4 1.0
CA E:ALA217 4.0 128.8 1.0
CG E:ASN219 4.0 191.6 1.0
PG E:ATP702 4.1 204.2 1.0
PA E:ATP702 4.1 150.8 1.0
O3A E:ATP702 4.3 128.7 1.0
C5' E:ATP702 4.3 133.4 1.0
O3B E:ATP702 4.4 146.8 1.0
CA E:ASN219 4.4 131.0 1.0
C E:ILE216 4.5 127.4 1.0
N E:SER218 4.5 126.0 1.0
CB E:ASP153 4.7 149.3 1.0
O1G E:ATP702 4.8 210.3 1.0
N E:ALA217 4.8 126.3 1.0
O5' E:ATP702 4.8 105.0 1.0
CB E:ASN219 4.8 178.7 1.0
C E:SER218 4.9 120.8 1.0
ND2 E:ASN219 4.9 148.0 1.0

Magnesium binding site 6 out of 7 in 7k3z

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Magnesium binding site 6 out of 7 in the P. Falciparum CPN60 D474A Mutant Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of P. Falciparum CPN60 D474A Mutant Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg701

b:132.1
occ:1.00
 O3G F:ATP702 2.4 210.0 1.0
N F:ASN219 3.1 124.8 1.0
OD1 F:ASP153 3.2 174.1 1.0
CA F:ASN219 3.3 144.5 1.0
CB F:ASN219 3.4 163.5 1.0
O2A F:ATP702 3.4 187.6 1.0
O1B F:ATP702 3.6 101.3 1.0
CG F:ASN219 3.7 184.0 1.0
O F:ALA217 3.7 168.0 1.0
PG F:ATP702 3.8 181.5 1.0
OD1 F:ASN219 3.8 202.4 1.0
C F:SER218 4.0 123.4 1.0
C F:ALA217 4.1 125.5 1.0
O F:ILE216 4.3 131.5 1.0
O1G F:ATP702 4.4 160.2 1.0
CG F:ASP153 4.4 166.1 1.0
N F:SER218 4.5 120.0 1.0
ND2 F:ASN219 4.5 164.5 1.0
CA F:SER218 4.5 126.5 1.0
PB F:ATP702 4.6 116.2 1.0
O3B F:ATP702 4.7 146.2 1.0
PA F:ATP702 4.7 150.7 1.0
O2G F:ATP702 4.7 146.1 1.0
O3A F:ATP702 4.8 134.6 1.0
C F:ASN219 4.9 141.4 1.0
CA F:ALA217 4.9 125.7 1.0
O F:SER218 4.9 139.9 1.0

Magnesium binding site 7 out of 7 in 7k3z

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Magnesium binding site 7 out of 7 in the P. Falciparum CPN60 D474A Mutant Bound to Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of P. Falciparum CPN60 D474A Mutant Bound to Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg701

b:115.0
occ:1.00
 O2A G:ATP702 2.5 145.2 1.0
O3G G:ATP702 2.8 183.3 1.0
O1B G:ATP702 2.9 93.6 1.0
OD1 G:ASP153 3.1 134.0 1.0
N G:ASN219 3.6 102.1 1.0
O G:ILE216 3.6 105.9 1.0
CA G:ASN219 3.8 105.0 1.0
PA G:ATP702 3.9 88.5 1.0
O G:ALA217 4.0 131.8 1.0
C G:ALA217 4.1 97.1 1.0
CG G:ASP153 4.1 167.3 1.0
PB G:ATP702 4.1 111.9 1.0
PG G:ATP702 4.2 197.8 1.0
OD1 G:ASN219 4.2 195.5 1.0
CB G:ASN219 4.2 108.7 1.0
O3A G:ATP702 4.3 85.8 1.0
OD2 G:ASP153 4.4 187.7 1.0
CA G:ALA217 4.4 105.2 1.0
CG G:ASN219 4.4 193.6 1.0
C5' G:ATP702 4.4 143.2 1.0
N G:SER218 4.6 97.2 1.0
O3B G:ATP702 4.6 169.5 1.0
O1G G:ATP702 4.7 186.2 1.0
C G:SER218 4.7 101.8 1.0
C G:ILE216 4.7 109.0 1.0
O5' G:ATP702 4.7 77.4 1.0

Reference:

B.Nguyen, R.Ma, W.K.Tang, D.Shi, N.H.Tolia. Crystal Structure of P. Falciparum CPN60 Bound to Atp Reveals An Open Dynamic Conformation Before Substrate Binding. Sci Rep V. 11 5930 2021.
ISSN: ESSN 2045-2322
PubMed: 33723304
DOI: 10.1038/S41598-021-85197-3
Page generated: Wed Oct 2 22:08:23 2024

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