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Magnesium in PDB 1xfv: Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp

Enzymatic activity of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp

All present enzymatic activity of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp:
4.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp, PDB code: 1xfv was solved by Q.Shen, N.L.Zhukovskaya, Q.Guo, J.Florian, W.J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.57 / 3.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.599, 319.285, 142.054, 90.00, 90.22, 90.00
R / Rfree (%) 26.3 / 28.2

Other elements in 1xfv:

The structure of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp also contains other interesting chemical elements:

Calcium (Ca) 18 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp (pdb code 1xfv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp, PDB code: 1xfv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 1xfv

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Magnesium binding site 1 out of 12 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:5.2
occ:1.00
 NE2 A:HIS577 2.4 39.3 1.0
OD1 A:ASP491 2.4 49.2 1.0
OD2 A:ASP493 2.5 41.3 1.0
OD2 A:ASP491 2.6 52.1 1.0
CG A:ASP491 2.8 50.9 1.0
OD1 A:ASP493 3.0 40.1 1.0
CG A:ASP493 3.1 39.4 1.0
CE1 A:HIS577 3.3 41.8 1.0
CD2 A:HIS577 3.4 40.2 1.0
O A:LYS346 4.1 45.1 1.0
C3' A:3AT903 4.3 72.1 1.0
MG A:MG902 4.3 28.0 1.0
CB A:ASP491 4.4 48.8 1.0
ND1 A:HIS577 4.4 40.9 1.0
CG A:HIS577 4.5 39.5 1.0
CB A:ASP493 4.5 37.4 1.0
C2' A:3AT903 5.0 71.0 1.0
CA A:ASP493 5.0 38.2 1.0

Magnesium binding site 2 out of 12 in 1xfv

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Magnesium binding site 2 out of 12 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:28.0
occ:1.00
 O1A A:3AT903 2.1 85.8 1.0
O1G A:3AT903 2.4 87.4 1.0
O3B A:3AT903 2.8 91.6 1.0
PG A:3AT903 3.1 87.3 1.0
O3A A:3AT903 3.3 89.6 1.0
PA A:3AT903 3.3 85.6 1.0
PB A:3AT903 3.5 94.3 1.0
O2G A:3AT903 3.6 86.0 1.0
NZ A:LYS346 3.7 47.3 1.0
O1B A:3AT903 3.8 94.8 1.0
CE A:LYS346 4.0 50.3 1.0
O5' A:3AT903 4.3 81.2 1.0
MG A:MG901 4.3 5.2 1.0
C5' A:3AT903 4.4 75.0 1.0
O3G A:3AT903 4.4 86.9 1.0
C3' A:3AT903 4.4 72.1 1.0
O2A A:3AT903 4.4 85.7 1.0
OD1 A:ASP493 4.5 40.1 1.0
O2B A:3AT903 4.9 93.7 1.0
CD A:LYS346 4.9 49.0 1.0
C4' A:3AT903 4.9 74.5 1.0
NZ A:LYS353 4.9 69.9 1.0

Magnesium binding site 3 out of 12 in 1xfv

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Magnesium binding site 3 out of 12 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:17.1
occ:1.00
 OD2 B:ASP493 2.4 42.3 1.0
NE2 B:HIS577 2.4 40.3 1.0
OD1 B:ASP491 2.4 50.0 1.0
OD2 B:ASP491 2.5 53.4 1.0
CG B:ASP491 2.8 51.4 1.0
OD1 B:ASP493 3.0 39.5 1.0
CG B:ASP493 3.0 40.0 1.0
CE1 B:HIS577 3.3 42.3 1.0
CD2 B:HIS577 3.4 41.8 1.0
O B:LYS346 4.2 47.2 1.0
C3' B:3AT904 4.3 71.7 1.0
MG B:MG903 4.3 25.3 1.0
CB B:ASP491 4.4 49.6 1.0
ND1 B:HIS577 4.4 41.3 1.0
CB B:ASP493 4.4 38.5 1.0
CG B:HIS577 4.5 40.9 1.0
CA B:ASP493 4.9 38.9 1.0
C2' B:3AT904 5.0 70.8 1.0

Magnesium binding site 4 out of 12 in 1xfv

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Magnesium binding site 4 out of 12 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:25.3
occ:1.00
 O1A B:3AT904 2.1 85.7 1.0
O1G B:3AT904 2.4 88.8 1.0
O3B B:3AT904 2.8 92.7 1.0
PG B:3AT904 3.1 89.1 1.0
O3A B:3AT904 3.3 89.3 1.0
PA B:3AT904 3.3 85.4 1.0
PB B:3AT904 3.5 94.1 1.0
O2G B:3AT904 3.6 88.0 1.0
NZ B:LYS346 3.7 50.1 1.0
O1B B:3AT904 3.8 94.7 1.0
CE B:LYS346 4.0 51.7 1.0
O5' B:3AT904 4.3 81.3 1.0
MG B:MG902 4.3 17.1 1.0
C5' B:3AT904 4.3 74.9 1.0
C3' B:3AT904 4.4 71.7 1.0
O3G B:3AT904 4.4 88.3 1.0
O2A B:3AT904 4.4 86.3 1.0
OD1 B:ASP493 4.5 39.5 1.0
CD B:LYS346 4.9 50.0 1.0
C4' B:3AT904 4.9 73.8 1.0
O2B B:3AT904 4.9 93.3 1.0
NZ B:LYS353 4.9 68.7 1.0

Magnesium binding site 5 out of 12 in 1xfv

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Magnesium binding site 5 out of 12 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg903

b:9.0
occ:1.00
 OD1 C:ASP491 2.4 48.1 1.0
NE2 C:HIS577 2.4 40.4 1.0
OD2 C:ASP493 2.5 43.5 1.0
OD2 C:ASP491 2.5 51.6 1.0
CG C:ASP491 2.8 49.9 1.0
OD1 C:ASP493 3.1 39.4 1.0
CG C:ASP493 3.1 40.5 1.0
CE1 C:HIS577 3.3 42.9 1.0
CD2 C:HIS577 3.4 41.5 1.0
O C:LYS346 4.1 46.4 1.0
CB C:ASP491 4.3 48.9 1.0
MG C:MG904 4.3 27.0 1.0
C3' C:3AT905 4.4 72.6 1.0
ND1 C:HIS577 4.4 42.3 1.0
CG C:HIS577 4.5 41.3 1.0
CB C:ASP493 4.5 38.7 1.0
CA C:ASP493 5.0 38.8 1.0

Magnesium binding site 6 out of 12 in 1xfv

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Magnesium binding site 6 out of 12 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg904

b:27.0
occ:1.00
 O1A C:3AT905 2.1 86.4 1.0
O1G C:3AT905 2.5 88.5 1.0
O3B C:3AT905 2.8 92.9 1.0
PG C:3AT905 3.1 88.1 1.0
O3A C:3AT905 3.3 90.2 1.0
PA C:3AT905 3.3 86.0 1.0
PB C:3AT905 3.5 95.6 1.0
O2G C:3AT905 3.6 87.8 1.0
NZ C:LYS346 3.7 48.9 1.0
O1B C:3AT905 3.8 96.0 1.0
CE C:LYS346 4.0 51.6 1.0
O5' C:3AT905 4.3 82.2 1.0
C5' C:3AT905 4.3 76.2 1.0
MG C:MG903 4.3 9.0 1.0
C3' C:3AT905 4.4 72.6 1.0
O2A C:3AT905 4.5 86.1 1.0
OD1 C:ASP493 4.5 39.4 1.0
O3G C:3AT905 4.5 87.5 1.0
C4' C:3AT905 4.9 75.3 1.0
CD C:LYS346 4.9 49.4 1.0
O2B C:3AT905 4.9 94.3 1.0
NZ C:LYS353 4.9 69.5 1.0

Magnesium binding site 7 out of 12 in 1xfv

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Magnesium binding site 7 out of 12 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg904

b:8.3
occ:1.00
 OD1 D:ASP491 2.3 46.9 1.0
NE2 D:HIS577 2.4 41.3 1.0
OD2 D:ASP493 2.5 42.6 1.0
OD2 D:ASP491 2.5 51.6 1.0
CG D:ASP491 2.7 49.8 1.0
OD1 D:ASP493 3.1 39.4 1.0
CG D:ASP493 3.1 39.5 1.0
CE1 D:HIS577 3.3 43.3 1.0
CD2 D:HIS577 3.4 42.1 1.0
O D:LYS346 4.0 46.8 1.0
CB D:ASP491 4.3 48.5 1.0
MG D:MG905 4.4 43.7 1.0
C3' D:3AT906 4.4 72.6 1.0
ND1 D:HIS577 4.4 41.5 1.0
CG D:HIS577 4.5 40.7 1.0
CB D:ASP493 4.5 38.3 1.0
CA D:ASP493 5.0 38.8 1.0

Magnesium binding site 8 out of 12 in 1xfv

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Magnesium binding site 8 out of 12 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg905

b:43.7
occ:1.00
 O1A D:3AT906 2.1 84.7 1.0
O1G D:3AT906 2.5 89.5 1.0
O3B D:3AT906 2.8 93.3 1.0
PG D:3AT906 3.1 90.0 1.0
O3A D:3AT906 3.3 89.5 1.0
PA D:3AT906 3.3 84.6 1.0
PB D:3AT906 3.5 95.5 1.0
O2G D:3AT906 3.6 88.8 1.0
NZ D:LYS346 3.7 50.3 1.0
O1B D:3AT906 3.8 95.4 1.0
CE D:LYS346 4.0 52.7 1.0
O5' D:3AT906 4.2 80.8 1.0
C5' D:3AT906 4.3 75.2 1.0
MG D:MG904 4.4 8.3 1.0
C3' D:3AT906 4.4 72.6 1.0
O2A D:3AT906 4.4 85.6 1.0
O3G D:3AT906 4.5 88.7 1.0
OD1 D:ASP493 4.5 39.4 1.0
C4' D:3AT906 4.8 75.0 1.0
O2B D:3AT906 4.9 94.6 1.0
CD D:LYS346 4.9 50.8 1.0
NZ D:LYS353 4.9 71.1 1.0

Magnesium binding site 9 out of 12 in 1xfv

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Magnesium binding site 9 out of 12 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg905

b:20.1
occ:1.00
 OD1 E:ASP491 2.4 47.2 1.0
OD2 E:ASP491 2.5 51.0 1.0
NE2 E:HIS577 2.5 40.5 1.0
OD2 E:ASP493 2.5 44.0 1.0
CG E:ASP491 2.8 49.4 1.0
OD1 E:ASP493 3.1 40.1 1.0
CG E:ASP493 3.1 40.7 1.0
CE1 E:HIS577 3.4 43.2 1.0
CD2 E:HIS577 3.4 41.6 1.0
O E:LYS346 4.1 45.3 1.0
CB E:ASP491 4.3 48.5 1.0
MG E:MG906 4.3 26.2 1.0
C3' E:3AT907 4.4 72.2 1.0
ND1 E:HIS577 4.5 42.4 1.0
CB E:ASP493 4.5 38.9 1.0
CG E:HIS577 4.5 41.4 1.0
CA E:ASP493 5.0 39.0 1.0

Magnesium binding site 10 out of 12 in 1xfv

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Magnesium binding site 10 out of 12 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg906

b:26.2
occ:1.00
 O1A E:3AT907 2.1 86.2 1.0
O1G E:3AT907 2.4 91.0 1.0
O3B E:3AT907 2.8 94.7 1.0
PG E:3AT907 3.1 91.3 1.0
O3A E:3AT907 3.3 91.1 1.0
PA E:3AT907 3.3 86.9 1.0
PB E:3AT907 3.5 97.2 1.0
O2G E:3AT907 3.6 90.7 1.0
NZ E:LYS346 3.7 49.3 1.0
O1B E:3AT907 3.8 97.0 1.0
CE E:LYS346 4.0 51.6 1.0
O5' E:3AT907 4.3 82.7 1.0
MG E:MG905 4.3 20.1 1.0
C5' E:3AT907 4.4 76.2 1.0
O3G E:3AT907 4.4 90.3 1.0
C3' E:3AT907 4.4 72.2 1.0
O2A E:3AT907 4.4 87.5 1.0
OD1 E:ASP493 4.5 40.1 1.0
CD E:LYS346 4.9 49.6 1.0
O2B E:3AT907 4.9 96.3 1.0
C4' E:3AT907 4.9 75.1 1.0
NZ E:LYS353 4.9 71.0 1.0

Reference:

Q.Shen, N.L.Zhukovskaya, Q.Guo, J.Florian, W.J.Tang. Calcium-Independent Calmodulin Binding and Two-Metal-Ion Catalytic Mechanism of Anthrax Edema Factor. Embo J. V. 24 929 2005.
ISSN: ISSN 0261-4189
PubMed: 15719022
DOI: 10.1038/SJ.EMBOJ.7600574
Page generated: Tue Aug 13 17:34:50 2024

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