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Magnesium in PDB 4jav: Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)

Enzymatic activity of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)

All present enzymatic activity of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V):
2.7.13.3;

Protein crystallography data

The structure of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V), PDB code: 4jav was solved by A.I.Podgornaia, P.Casino, A.Marina, M.T.Laub, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.55 / 3.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 119.319, 143.928, 138.969, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 25.3

Other elements in 4jav:

The structure of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) (pdb code 4jav). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V), PDB code: 4jav:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4jav

Go back to Magnesium Binding Sites List in 4jav
Magnesium binding site 1 out of 4 in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:40.4
occ:1.00
 OD1 A:ASN380 2.4 59.2 1.0
O1B A:ADP504 2.5 51.0 1.0
O1A A:ADP504 2.5 48.2 1.0
O3 A:SO4502 2.7 0.2 1.0
O A:HOH608 3.0 47.6 1.0
NZ A:LYS383 3.3 67.6 1.0
PB A:ADP504 3.3 52.4 1.0
CG A:ASN380 3.4 58.2 1.0
O3B A:ADP504 3.5 52.3 1.0
O3A A:ADP504 3.5 50.8 1.0
PA A:ADP504 3.6 48.8 1.0
ND2 A:ASN379 3.7 65.5 1.0
ND2 A:ASN380 3.8 58.7 1.0
CE A:LYS383 4.0 66.1 1.0
S A:SO4502 4.1 0.2 1.0
CA A:GLY445 4.4 52.5 1.0
O A:ASN376 4.5 56.2 1.0
O5' A:ADP504 4.5 50.7 1.0
O1 A:SO4502 4.6 0.1 1.0
N A:GLY445 4.7 52.6 1.0
O2 A:SO4502 4.7 0.9 1.0
O2B A:ADP504 4.8 49.7 1.0
O2A A:ADP504 4.8 49.4 1.0
CB A:ASN380 4.8 57.6 1.0
CG A:ASN379 4.9 65.9 1.0
CA A:ASN380 5.0 57.5 1.0

Magnesium binding site 2 out of 4 in 4jav

Go back to Magnesium Binding Sites List in 4jav
Magnesium binding site 2 out of 4 in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:60.8
occ:1.00
 O1A B:ADP505 2.5 70.6 1.0
OD1 B:ASN380 2.7 72.3 1.0
O3B B:ADP505 3.1 71.4 1.0
O1B B:ADP505 3.4 70.8 1.0
NZ B:LYS383 3.5 88.5 1.0
CG B:ASN380 3.7 72.6 1.0
ND2 B:ASN379 3.7 87.7 1.0
PB B:ADP505 3.7 70.1 1.0
O2 B:SO4503 3.8 0.4 1.0
PA B:ADP505 3.8 71.6 1.0
CA B:GLY445 3.9 66.5 1.0
ND2 B:ASN380 3.9 73.7 1.0
O B:ASN376 4.2 65.8 1.0
OD1 B:ASN376 4.3 74.1 1.0
O3A B:ADP505 4.3 70.5 1.0
O1 B:SO4503 4.6 0.9 1.0
N B:GLY445 4.6 67.7 1.0
O2A B:ADP505 4.6 71.0 1.0
S B:SO4503 4.7 0.7 1.0
CE B:LYS383 4.8 87.5 1.0
C B:GLY445 4.8 66.0 1.0
CG B:ASN379 4.9 85.5 1.0
O5' B:ADP505 5.0 72.3 1.0

Magnesium binding site 3 out of 4 in 4jav

Go back to Magnesium Binding Sites List in 4jav
Magnesium binding site 3 out of 4 in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:40.3
occ:1.00
 F1 C:BFD53 1.8 54.0 1.0
OD1 C:ASP10 2.2 55.7 1.0
O C:MET55 2.4 56.2 1.0
OD2 C:BFD53 2.4 48.7 1.0
O C:HOH304 3.0 50.3 1.0
BE C:BFD53 3.2 53.0 1.0
CG C:ASP10 3.2 54.1 1.0
CG C:BFD53 3.4 49.5 1.0
OD2 C:ASP10 3.4 55.3 1.0
C C:MET55 3.5 56.3 1.0
OD1 C:BFD53 3.7 49.6 1.0
OD1 C:ASP9 3.7 53.5 1.0
F2 C:BFD53 3.8 54.5 1.0
CB C:MET55 4.1 55.1 1.0
CA C:MET55 4.2 54.9 1.0
F3 C:BFD53 4.4 51.3 1.0
NZ C:LYS105 4.5 49.4 1.0
N C:MET55 4.5 54.4 1.0
CB C:ASP10 4.5 53.4 1.0
N C:ASP10 4.6 54.1 1.0
N C:MET56 4.6 56.6 1.0
CG C:MET56 4.6 54.2 1.0
CG C:ASP9 4.7 53.8 1.0
CB C:BFD53 4.8 48.4 1.0
N C:SER11 4.8 53.1 1.0
CA C:MET56 4.9 56.0 1.0

Magnesium binding site 4 out of 4 in 4jav

Go back to Magnesium Binding Sites List in 4jav
Magnesium binding site 4 out of 4 in the Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Basis of A Rationally Rewired Protein-Protein Interface (HK853WT and RR468MUTANT V13P, L14I, I17M and N21V) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:45.5
occ:1.00
 F1 D:BFD53 1.8 64.2 1.0
OD1 D:ASP10 2.2 57.9 1.0
O D:MET55 2.4 71.2 1.0
OD2 D:BFD53 2.4 55.8 1.0
BE D:BFD53 3.1 64.3 1.0
CG D:ASP10 3.1 56.1 1.0
OD2 D:ASP10 3.3 55.4 1.0
CG D:BFD53 3.5 57.2 1.0
C D:MET55 3.5 69.2 1.0
OD1 D:BFD53 3.8 56.9 1.0
F2 D:BFD53 3.9 65.5 1.0
OD1 D:ASP9 4.0 57.5 1.0
CB D:MET55 4.1 70.7 1.0
CA D:MET55 4.2 68.5 1.0
F3 D:BFD53 4.2 63.9 1.0
N D:MET55 4.4 66.4 1.0
CB D:ASP10 4.5 55.0 1.0
NZ D:LYS105 4.6 57.6 1.0
N D:MET56 4.6 67.3 1.0
N D:ASP10 4.6 55.3 1.0
CG D:MET56 4.7 60.8 1.0
CB D:BFD53 4.8 57.1 1.0
CG D:ASP9 4.9 58.8 1.0
CA D:MET56 4.9 66.6 1.0

Reference:

A.I.Podgornaia, P.Casino, A.Marina, M.T.Laub. Structural Basis of A Rationally Rewired Protein-Protein Interface Critical to Bacterial Signaling Structure V. 21 1636 2013.
ISSN: ISSN 0969-2126
PubMed: 23954504
DOI: 10.1016/J.STR.2013.07.005
Page generated: Mon Aug 11 14:41:07 2025

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