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Magnesium in PDB 4f24: Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb

Protein crystallography data

The structure of Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb, PDB code: 4f24 was solved by M.J.Yang, H.Xiang, J.W.Wang, B.Liu, Y.G.Chen, L.Liu, X.M.Deng, Y.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.23 / 2.51
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.423, 94.423, 86.717, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 28.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb (pdb code 4f24). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb, PDB code: 4f24:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4f24

Go back to Magnesium Binding Sites List in 4f24
Magnesium binding site 1 out of 5 in the Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:72.9
occ:1.00
 N A:GLY386 2.7 71.8 1.0
OD1 A:ASN388 2.7 70.1 1.0
CA A:GLY386 2.8 68.3 1.0
N A:ASN388 2.9 56.5 1.0
C A:GLY386 3.0 77.3 1.0
O A:ASP382 3.1 60.5 1.0
N A:GLN387 3.1 70.8 1.0
OH A:TYR493 3.3 64.9 1.0
OD1 A:ASP382 3.3 58.8 1.0
CA A:ASN388 3.6 60.5 1.0
C A:THR383 3.6 70.1 1.0
C A:ASP382 3.8 63.1 1.0
CG A:ASN388 3.8 64.4 1.0
CA A:THR383 3.8 61.4 1.0
O A:GLY386 3.8 83.5 1.0
O A:THR383 3.9 78.8 1.0
N A:ALA384 3.9 65.9 1.0
C A:SER385 3.9 79.3 1.0
C A:GLN387 3.9 60.5 1.0
CG A:ASP382 4.0 56.6 1.0
OG A:SER385 4.0 73.4 1.0
N A:THR383 4.0 60.2 1.0
CA A:GLN387 4.1 63.1 1.0
C A:ALA384 4.1 71.1 1.0
N A:SER385 4.2 71.0 1.0
CZ A:TYR493 4.2 68.7 1.0
CB A:ASN388 4.3 60.9 1.0
O A:ALA384 4.3 65.0 1.0
OD2 A:ASP382 4.5 61.9 1.0
CA A:SER385 4.5 73.7 1.0
CA A:ALA384 4.6 72.8 1.0
CB A:ASP382 4.7 53.3 1.0
CB A:SER385 4.8 72.6 1.0
ND2 A:ASN388 4.8 58.7 1.0
C A:ASN388 4.9 62.8 1.0
CE2 A:TYR493 4.9 66.2 1.0
CA A:ASP382 4.9 53.4 1.0
CB A:GLN387 4.9 65.2 1.0
O A:SER385 4.9 84.5 1.0

Magnesium binding site 2 out of 5 in 4f24

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Magnesium binding site 2 out of 5 in the Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:0.3
occ:1.00
 OD1 A:ASN508 2.6 88.3 1.0
O A:ASP516 2.7 94.7 1.0
O A:ASN370 2.9 71.6 1.0
O A:ASN508 3.0 61.1 1.0
C A:ASN508 3.3 71.2 1.0
CA A:ILE509 3.3 82.5 1.0
CG A:ASN508 3.4 81.5 1.0
N A:SER518 3.5 73.9 1.0
N A:ILE509 3.5 77.1 1.0
CB A:SER518 3.6 80.7 1.0
C A:ILE509 3.6 89.1 1.0
CG A:ASN370 3.6 0.2 1.0
ND2 A:ASN370 3.7 0.4 1.0
C A:ASP516 3.8 96.7 1.0
CB A:ASN370 3.9 0.6 1.0
OD1 A:ASN370 3.9 0.6 1.0
O A:ILE509 3.9 84.8 1.0
C A:TYR517 4.0 84.5 1.0
C A:ASN370 4.0 80.3 1.0
CA A:TYR517 4.0 87.2 1.0
ND2 A:ASN508 4.1 74.7 1.0
N A:ASP510 4.1 0.7 1.0
CA A:SER518 4.1 76.1 1.0
CB A:ASN508 4.3 75.7 1.0
CA A:ASN508 4.3 71.8 1.0
N A:TYR517 4.3 92.8 1.0
CE A:LYS368 4.3 91.3 1.0
CA A:ASN370 4.5 94.8 1.0
NZ A:LYS368 4.6 93.9 1.0
O A:LYS515 4.6 93.2 1.0
CB A:ILE509 4.7 90.8 1.0
O A:SER518 4.7 68.9 1.0
OG A:SER518 4.8 79.4 1.0
O A:TYR517 4.8 88.7 1.0
N A:ASN508 4.9 70.6 1.0
CB A:ASP516 4.9 89.1 1.0
C A:SER518 4.9 73.7 1.0
CA A:ASP516 5.0 93.3 1.0

Magnesium binding site 3 out of 5 in 4f24

Go back to Magnesium Binding Sites List in 4f24
Magnesium binding site 3 out of 5 in the Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:84.2
occ:1.00
 O A:TYR470 2.4 45.5 1.0
O A:TYR468 2.4 58.6 1.0
C A:TYR470 3.2 51.4 1.0
C A:TYR468 3.5 56.8 1.0
CA A:ASP471 3.7 57.4 1.0
N A:ASP471 3.8 50.7 1.0
CB A:TYR468 3.8 51.8 1.0
N A:ASN472 3.9 60.4 1.0
CA A:TYR468 4.1 49.8 1.0
N A:TYR470 4.1 74.5 1.0
CA A:TYR470 4.2 62.2 1.0
C A:ASP471 4.2 60.7 1.0
OD1 A:ASP471 4.3 88.8 1.0
C A:LYS469 4.3 83.4 1.0
O A:VAL424 4.4 54.3 1.0
O A:VAL473 4.5 65.2 1.0
O A:LYS469 4.5 88.5 1.0
N A:LYS469 4.5 67.8 1.0
N A:VAL473 4.8 64.2 1.0
CA A:LYS469 4.9 82.1 1.0
CG A:TYR468 4.9 55.0 1.0
CB A:ASP471 5.0 66.4 1.0

Magnesium binding site 4 out of 5 in 4f24

Go back to Magnesium Binding Sites List in 4f24
Magnesium binding site 4 out of 5 in the Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:0.0
occ:1.00
 O A:ALA347 2.8 73.2 1.0
O A:VAL219 2.9 79.1 1.0
O A:ASN216 3.2 91.7 1.0
C A:ALA347 3.9 77.7 1.0
C A:VAL219 4.0 89.2 1.0
CB A:ALA347 4.2 55.6 1.0
OE1 A:GLU349 4.2 0.1 1.0
C A:ASN216 4.2 92.0 1.0
OG1 A:THR220 4.4 98.8 1.0
CA A:THR220 4.4 84.6 1.0
N A:THR220 4.7 89.3 1.0
CB A:ASP348 4.7 0.5 1.0
CA A:ALA347 4.7 67.4 1.0
CA A:ASP217 4.8 94.6 1.0
C A:ASP348 4.8 80.0 1.0
CB A:GLU349 4.9 79.1 1.0
N A:ASP217 4.9 85.0 1.0
N A:ASP348 4.9 85.7 1.0
C A:ASP217 4.9 0.6 1.0
O A:ASP348 5.0 81.5 1.0
CB A:THR220 5.0 96.0 1.0

Magnesium binding site 5 out of 5 in 4f24

Go back to Magnesium Binding Sites List in 4f24
Magnesium binding site 5 out of 5 in the Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structures Reveal the Multi-Ligand Binding Mechanism of the Staphylococcus Aureus Clfb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:85.5
occ:1.00
 OD1 A:ASN477 2.6 76.5 1.0
OD1 A:ASN405 2.7 97.6 1.0
C A:ASN405 3.0 69.8 1.0
CA A:ASN405 3.1 69.3 1.0
O A:ASN405 3.2 70.2 1.0
NE1 A:TRP407 3.3 66.0 1.0
CG A:ASN405 3.3 89.7 1.0
CA A:GLY479 3.4 76.1 1.0
CG A:ASN477 3.4 74.7 1.0
O A:THR406 3.4 67.3 1.0
N A:GLY479 3.5 75.5 1.0
N A:THR406 3.5 67.2 1.0
CD1 A:TRP407 3.6 67.6 1.0
CE2 A:TRP407 3.7 62.0 1.0
CB A:ASN405 3.8 75.9 1.0
ND2 A:ASN477 3.8 76.0 1.0
C A:THR406 3.9 61.3 1.0
ND2 A:ASN405 4.2 90.1 1.0
CG A:TRP407 4.2 61.3 1.0
CZ2 A:TRP407 4.2 60.7 1.0
CD2 A:TRP407 4.3 58.5 1.0
CA A:THR406 4.3 65.1 1.0
N A:ASN405 4.3 70.4 1.0
C A:GLY479 4.6 76.6 1.0
CB A:ASN477 4.6 73.4 1.0
N A:TRP407 4.7 54.4 1.0
C A:PHE478 4.7 71.4 1.0
CA A:ASN477 4.7 70.4 1.0
N A:PHE478 4.7 68.4 1.0
C A:ASN477 4.9 67.7 1.0
O A:GLY479 5.0 74.8 1.0

Reference:

H.Xiang, Y.Feng, J.W.Wang, B.Liu, Y.G.Chen, L.Liu, X.M.Deng, M.J.Yang. Crystal Structures Reveal the Multi-Ligand Binding Mechanism of Staphylococcus Aureus Clfb Plos Pathog. V. 8 02751 2012.
ISSN: ISSN 1553-7366
PubMed: 22719251
DOI: 10.1371/JOURNAL.PPAT.1002751
Page generated: Mon Aug 11 12:34:25 2025

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